- Feb 2022
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix103), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
Reviewer 1. Andrew Adey
In the manuscript by De Maere and Darling, the authors describe their computational simulator for HiC and 3C sequencing that models the 3D arrangement of chromatin and how that arrangement is conveyed via proximity ligation methods. Overall the manuscript is long and does not clearly describe the main goals of the simulator. The detail is appreciated, but not when it obfuscates the main goal of the manuscript. Also the figures could be condensed so that there are less figures with more panels. That being said, I do believe the simulator that the authors have developed is very sophisticated and appears to work well with a few exceptions. The major issue is the packaging of the method into more a concise and clear text. Below are some more specific comments:
My first thought is regarding where this simulator will be particularly useful? The authors mention it is primarily for software tool development and that the cost of generating HiC/3C data is very high and that many of the existing datasets are sparse. However, there are many existing datasets that are extremely rich and deep that would seem more appropriate. While I am not convinced on the utility for software development when abundant real data is publicly available, I do agree that having means to simulate sequence read data may have other valuable applications - primarily in exploring power in deconvolving metagenomic samples. For the eukaryotic simulated data there is a clear stretch of signal this is perpendicular to the diagonal as is typically observed for circular genomes, though this would not be expected for linear chromosomes (e.g. Figure 7). Does the simulator assume all chromosomes are circular? This is odd and needs to be addressed. Also on figure 7, the authors are highlighting that there is a greater inter chromosomal signal when compared to real data - is that a good thing? I can see that it may be desirable if the goal is to generate signal that would be generated under the assumption that there is no chromatin organization in the genome and thus be used as a background model. I can see this as a potential use, but it should be more clearly stated. The authors describe the ability to simulate TADs - however it is not clearly described how the TADs are decided upon - can users specify where TADs should be located (e.g. if they have a callset of TADs and want to create data simulating them that they can then alter - e.g. change one TAD and see how it effects signal nearby so they can know what to expect for an experiment where they may be altering TAD-forming loci). Or are they only created randomly (which seems the case given page 8 line 212). This could also be more clearly described by stating broadly what is done then going into the methods of how that is accomplished. Figure 2 is an extremely simple and small diagram – could it not just be added into figure 1? It seems a bit excessive to stand as its own figure. This goes for several other figures. Figure 8 - there is no description for c and d panels. I assume c is real and d is simulated. The strong perpendicular band midway through the chromosome is observed which is discouraging as I have commented on for Figure 7.
Re-review; The major issues I had with the manuscript previously were that it was too long and may have limited interest. The authors have addressed the first point. For the second, I believe that the interest is broad enough to warrant publication.
-
Background
Reviewer 2. Ming Hu
In this paper, the authors developed a software package Sim3C to simulate Hi-C data and other 3C-based data. This work addresses a very important research question, and has the potential to become a useful computational tool in genomics research. However, the authors need to provide more explanations and technical details to further improve the current manuscript.
Here are my specific comments: Major comments: 1. Figure 3. It is better to plot Figure 3 in log scale for both x-axis and y-axis. In log scale, the slope of contact probably has direct biophysical interpretation, as described by the first Hi-C paper (Lieberman-Aiden et al, Science, 2009). I am very curious to see how biophysics model contributes to the data generation mechanism. 2. In Rao et al, Cell, 2014 paper, they identified chromatin loops anchored by CTCF motifs. In Sim3C, the authors considered the 1D genomic distance effect and hierarchical TAD structures. It would be great if Sim3C can also take chromatin loops into consideration. 3. Hi-C data can help to detect allelic-specific chromatin interactions. Is Sim3C able to simulate allelic specific proximity ligation data? 4. It is very important to rigorously evaluate the data reproducibility. Using Sim3C, if users simulate Hi-C data multiple times with different random seeds, would the reproducibility between two simulated datasets be comparable to the reproducibility between two real biological replicates? 5. The authors showed simulated contact matrices of bacteria (Figure 6) and budding yeast (Figure 7). They also need to simulate both human and mouse genome-wide contact matrices, and compare the simulated contact matrices with real data.
Minor comments: 1.Please replace all 'HiC' by 'Hi-C'. 2. Page 6, line 116, "sciHiC" should be "scHi-C".
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaByte (see paper https://doi.org/10.46471/gigabyte.41), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
Reviewer 1. Mary Ann Tuli
Are all data available and do they match the descriptions in the paper? No. The paper states "The D. citri genome assembly (v3), OGS (v3) and transcriptomes are accessible on the Citrusgreening.org portal" I believe v2 is available, not v3 yet.
Additional Comments The paper states "The gene models will be part of an updated official gene set (OGS) for D. citri that will be submitted to NCBI." Until these models are available in NCBI their reuse is limited.
Recommendation: Minor Revision
-
Citrus greening disease
Reviewer 2. Xinyu Li
In the paper entitled “Annotation of glycolysis, gluconeogenesis, and trehaloneogenesis pathways provide insight into carbohydrate metabolism in the Asian citrus psyllid”, the authors conducted a high quality annotation of genes involved in glycolysis, gluconeogenesis, and trehaloneogenesis in Diaphorina citri genome, which provided the bases to develop gene-targeting therapeutics for this important pest species.
The MS is well-written, and the analyses are clear and proper. I found some minor concerns that should be addressed.
In the first paragraph of Page 10, the authors used cross symbol and the asterisk in the sentence “The number of genes identified in glycolysis….from NCBI, OrthoDB, and Flybase.”. However, the cross symbol and the asterisk are used without any explanation or citation. I suggest to cite the Appendix the authors referred to or add an explanation to make it clearer.
In Conclusion part, on Page 15, the authors stated “Expression analysis of the genes annotated in the carbohydrate metabolism pathways identified differences related to life stage, sex and tissue.”. But what are the differences are not mentioned here. I think it would be better to summarize the key/predominant differences about gene expression in the carbohydrate metabolism pathways.
In addition, it is interesting that the gene expression related with carbohydrate metabolism is sexually different in the Asian citrus psyllid. Is it common in insects or existed in some specific groups?
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
Reviewer 2. Bruno Fosso
The paper by Bremges et al. describe CAMITAX a workflow designed for the taxonomic classification of microbial genomes obtained from the application of NGS-based methodologies, such as single-cell sequencing and metagenomics. Even if the 4 implemented methodologies itself do not represent a real novelty in the field, their harmonization by using a classification algorithm is interesting. Moreover, the idea to deploy the workflow in a container greatly simplify both the installation and usage and ensure the analysis reproducibility.
The manuscript is well written and easy to read. All the proposed figures are appropriate and adequately support the data described in the main text. Figure 2 may be improved by using different colors allowing to easily discriminate the paths through the plot.
The CAMITAX GitHub repository clearly describe how to access and configure the container but very few information are available about the manual installation. The usage section needs an improvement.
I have some minor concerns about the paper: - the classification algorithm needs to be described more in deep. A figure may help the readers; - regarding the overall drop of CAMITAX recall in mid-range ranks, I was wondering if it may be due to the fact that CAMITAX seems to be more conservative than the Delmont classification (figure 2). Authors should discuss in how many cases CAMITAX results more conservative than the reference classification. - Moreover, the authors claim that "Notably, 95% of CAMITAX's predictions were consistent with Delmont et al., i.e. the two assignments were on the same taxonomic lineage and their LCA is either of the two." Does it mean the authors consider consistent a classification for which CAMITAX assigns to the kingdom rank while Dermont assigns to species? Please clarify
It would be useful to add some information about the technical requirements such as consumed RAM and required CPU time.
-
Now published in GigaScience doi: 10.1093/gigascience/giz154 Andreas Bremges 1Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany2German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andreas BremgesFor correspondence: andreas.bremges@helmholtz-hzi.de alice.mchardy@helmholtz-hzi.deAdrian Fritz 1Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlice C. Mchardy 1Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: andreas.bremges@helmholtz-hzi.de alice.mchardy@helmholtz-hzi.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz154 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102049
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the journal GigaByte under a CC-BY 4.0 license (see https://doi.org/10.46471/gigabyte.40)
Reviewer 1. Jianbo Jian
This submission described a reference genome for the Atlantic chub mackerel (Scomber colias) using the combination of PacBio HiFi long reads and Illumina short reads. The sequencing data process and genome assembling and related bioinformatics are comprehensive and adequate. The reported reference genome is the first genome and good continuity. It is a pity that the genome is not the chromosome level due to lack of the Hi-C data or genetic map data. However, the associated analysis and results make sense. In my opinion, as the first reference genome in the genus Scomber, this reference genome is a valuable genomic resource for population genetics, ecology and physiology and other future research. I have some concerns that should be addressed before publication in GigaByte.
1) In the project design, for genome assembly, two individuals were used for genomics DNA extraction. Why not used the same individual for avoiding the assembly error due to the genetic different between individuals? 2) Line 186-196, I have some confuse about the contamination process, is there some contamination in your sample? In general, most of the genome project will not contain contamination. This process is effective for the specific sample to avoid the contamination. 3) In Phylogenomics analysis, the divergence time was recommended, then the Figure should be updated make more sense. 4) Supp. Table 6 is blank. 5) All of the supplementary tables were not shown in manuscript. 6) The genome assemble for Illumina sequencing is useless compared with HiFi data. 7) In supplementary Table 5, N50 (Kb) should be N50 (bp).
Recommendation: Minor Revision
Reviewer 2. Rong Huang
Is there sufficient information for others to reuse this dataset or integrate it with other data? No. It is suggested that the author can make a simple table to show the assembly effects within the Order Scombriformes.
Additional Comments: Scomber colias is a valuable marine resource, with a high impact on the fisheries of several countries on the west coast of the Atlantic Ocean and/or the Mediterranean Sea. This study reports the first genome assembly of Atlantic chub mackerel. This genome is timely and the assembly process is clearly describedis, which contribute to the effective conservation, management, and sustainable exploitation of S. colias species in the Anthropocene. I still have the following questions.
The assembly effect of the genome does not seem to be particularly good. For example, the length of N50 length of scaffolds is not long enough. How many ploidy is this species? Do heterozygosity and repetition rate affect the assembly effect?
It is suggested that the author can make a simple table to show the assembly effects within the Order Scombriformes. It is helpful for relevant researchers to make use of the genomic resources.
Is "data validation" followed by the results section? And there is no subtitle in the result part. Is it required by this type of article?
Recommendation: Major Revision
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the journal GigaByte under a CC-BY 4.0 license (see paper), and is also part of the Asian citrus psyllid community annotation series of papers that can be viewed here: https://doi.org/10.46471/GIGABYTE_SERIES_0001
Reviewer 1. Alex Arp In “Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri” the authors did just that. The paper is well written, direct, and easy to follow. The reasoning of annotating these genes is clearly defined; that they are possible targets for RNAi based control for Diaphorina citri, an economically important pest of citrus. The annotation of the genes utilized genomic and transcriptomic databases and the gene expression profiles used existing datasets. Figures and Tables are clear and the phylogenetic trees give sufficient supporting evidence that the annotations are correct. Overall is a good manuscript and needs no major revision for publication.
Additional Comments: On Page 18 what is meant by "new protein" in "It is a relatively new protein critically associated with the assembly of a certain cell type V-ATPase and is still being studied"?
Reviewer 2. Mary Ann Tuli Are all data available and do they match the descriptions in the paper?
Yes. As with the other manuscripts, OGS v3 is mentioned, but this is not get available from the CGEN. The requesting data underlying table and figures has been uploaded.
Any Additional Overall Comments to the Author This manuscript is a comprehensive description of the manual curation of the V-ATPase genes, with clear aims and methodology.
Recommendation: Accept
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab063 Yilei Fu 1Department of Computer Science, Rice University, Houston, TX 77005, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yilei FuMedhat Mahmoud 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, United States of America3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States of AmericaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Medhat MahmoudViginesh Vaibhav Muraliraman 1Department of Computer Science, Rice University, Houston, TX 77005, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFritz J. Sedlazeck 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, United States of AmericaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fritz J. SedlazeckFor correspondence: Fritz.Sedlazeck@bcm.edu treangen@rice.eduTodd J. Treangen 1Department of Computer Science, Rice University, Houston, TX 77005, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Todd J. TreangenFor correspondence: Fritz.Sedlazeck@bcm.edu treangen@rice.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab063 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102841 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102842
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab062 Lukas M. Weber 1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lukas M. WeberAriel A. Hippen 2Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, PA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ariel A. HippenPeter F. Hickey 3Advanced Technology & Biology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter F. HickeyKristofer C. Berrett 4Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, UT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kristofer C. BerrettJason Gertz 4Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, UT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason GertzJennifer Anne Doherty 4Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, UT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephanie C. Hicks 1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephanie C. HicksFor correspondence: shicks19@jhu.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab062 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102826 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102827
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab064 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102834 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102835
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab056 Shufang Wu 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhencheng Fang 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJie Tan 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMo Li 3Peking University-Tsinghua University - National Institute of Biological Sciences (PTN) joint PhD program, School of Life Sciences, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChunhui Wang 3Peking University-Tsinghua University - National Institute of Biological Sciences (PTN) joint PhD program, School of Life Sciences, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQian Guo 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, China4Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Georgia 30332, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCongmin Xu 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, China4Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Georgia 30332, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaoqing Jiang 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuaiqiu Zhu 1State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China2Center for Quantitative Biology, Peking University, Beijing 100871, China4Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Georgia 30332, USA5Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Huaiqiu ZhuFor correspondence: hqzhu@pku.edu.cn
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab056 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102812 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102813
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab004 Fan Zhang 1Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fan ZhangFor correspondence: fanzhang@umich.eduHyun Min Kang 2Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab004 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102627 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102628
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz121 Yun-Ching Chen 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAbhilash Suresh 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChingiz Underbayev 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteClare Sun 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKomudi Singh 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFayaz Seifuddin 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdrian Wiestner 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMehdi Pirooznia 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: mehdi.pirooznia@nih.gov
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz121 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101927 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101928 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101929
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz118 Xiao Hu Find this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz118 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101954 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101955 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101956
-
-
www.biorxiv.org www.biorxiv.org
-
COVID-19 pandemic
Reviewer 3. Daniel Mietchen
This review includes supplemental files, videos and hypothes.is annotations of the preprint!: https://zenodo.org/record/4909923
The videos of the review process are also available on YouTube:
Part 1 (Screen Recording 2021-06-05 at 10.02.02.mov): https://youtu.be/_UnDdE3Oi-4 Part 2 (Screen Recording 2021-06-05 at 10.52.51.mov): https://youtu.be/z5xRK0lg3b4 Part 3 (Screen Recording 2021-06-05 at 11.27.01.mov): https://youtu.be/VnztlEqFW2A Part 4 (Screen Recording 2021-06-07 at 02.51.59.mov): https://youtu.be/IYtLfMcLTvA Part 5 (Screen Recording 2021-06-07 at 06.11.52.mov): https://youtu.be/Jv_AUHCASQw Part 6 (Screen Recording 2021-06-07 at 18.07.45.mov): https://youtu.be/6Y-yA9oahzM Part 7 (Screen Recording 2021-06-07 at 19.07.02.mov): https://youtu.be/LV5whFhfmEU
First round of review:
Summary The present manuscript provides an overview of how the English Wikipedia incorporated COVID-19-related information during the first months of the ongoing COVID-19 pandemic.
It focuses on information supported by academic sources and considers how specific properties of the sources (namely their status with respect to open access and preprints) correlate with their incorporation into Wikipedia, as well as the role of existing content and policies in mediating that incorporation.
No aspect of the manuscript would justify a rejection but there are literally lots of opportunities for improvements, so "Major revision" appears to be the most appropriate recommendation at this point.
General comments The main points that need to be addressed better: (1) documentation of the computational workflows; (2) adaptability of the Wikipedia approach to other contexts; (3) descriptions of or references to Wikipedia workflows; (4) linguistic presentation.
Ad 1: while the code used for the analyses and for the visualizations seems to be shared rather comprehensively, it lacks sufficient documentation as to what was done in what order and what manual steps were involved. This makes it hard to replicate the findings presented here or to extend the analysis beyond the time frame considered by the authors. Ad 2: The authors allude to how pre-existing Wikipedia content and policies - which they nicely frame as Wikipedia's "scientific infrastructure" or "scientific backbone" - "may provide insight into how its unique model may be deployed in other contexts" but that potentially most transferrable part of the manuscript - which would presumably be of interest to many of its readers - is not very well developed, even though that backbone is well described for Wikipedia itself. Ad 3: there is a good number of cases where the Wikipedia workflows are misrepresented (sometimes ever so slightly), and while many of these do not affect the conclusions, some actually do, and overall comprehension is hampered. I highlighted some of these cases, and others have been pointed out in community discussions, notably at https://en.wikipedia.org/w/index.php?title=Wikipedia_talk:WikiProject_COVID- 19&oldid=1028476999#Review_of_Wikipedia's_coverage_of_COVID and http://bluerasberry.com/2021/06/review-of-paper-on-wikipedia-and-covid/ . Some resources particularly relevant to these parts of the manuscript have not been mentioned, be it scholarly ones like https://arxiv.org/abs/2006.08899 and https://doi.org/10.1371/journal.pone.0228786 or Wikimedia ones like https://en.wikipedia.org/wiki/Wikipedia_coverage_of_the_COVID-19_pandemic and https://commons.wikimedia.org/wiki/File:Wikimedia_Policy_Brief_-_COVID-19_- _How_Wikipedia_helps_us_through_uncertain_times.pdf . Likewise essentially missing - although this is a common feature in academic articles about Wikipedia - is a discussion of how valid the observations made for the English Wikipedia are in the context of other language versions (e.g. Hebrew). On that basis, it is understandable that no attempt is made to look beyond Wikipedia to see how coverage of the pandemic was handled in other parts of the Wikimedia ecosystem (e.g. Wikinews, Wikisource, Wikivoyage, Wikimedia Commons and Wikidata), but doing so might actually strengthen the above case for deployability of the Wikipedia approach in other contexts. Disclosure: I am closely involved with WikiProject COVID-19 on Wikidata too, e.g. as per https://doi.org/10.5281/zenodo.4028482 . Ad 4: The relatively high number of linguistic errors - e.g. typos, grammar, phrasing and also things like internal references or figure legends - needlessly distracts from the value of the paper. The inclusion of figures - both via the text body and via the supplement - into the narrative is also sometimes confusing and would benefit from streamlining. While GigaScience has technically asked me to review version 3 of the preprint (available via https://www.biorxiv.org/content/10.1101/2021.03.01.433379v3 and also via GigaScience's editorial system), that version was licensed incompatibly with publication in GigaScience, so I pinged the authors on this (via https://twitter.com/EvoMRI/status/1393114202349391872 ), which resulted (with some small additional changes) in the creation of version 4 (available via https://www.biorxiv.org/content/10.1101/2021.03.01.433379v4 ) that I concentrated on in my review.
Production of that version 4 - of which I eventually used both the PDF and the HTML, which became available to me at different times - took a while, during which I had a first full read of the manuscript in version 3.
In an effort to explore how to make the peer review process more transparent than simply sharing the correspondence, I recorded myself while reading the manuscript for the second time, commenting on it live. These recordings are available via https://doi.org/10.5281/zenodo.4909923 .
In terms of specific comments, I annotated version 4 directly using Hypothes.is, and these annotations are available via https://via.hypothes.is/https://www.biorxiv.org/content/10.1101/2021.03.01.433379v4.full .
Re-review: I welcome the changes the authors have made - both to the manuscript itself (of which I read the bioRxiv version 5) and to the WikiCitationHistoRy repo - in response to the reviewer comments. I also noticed comments they chose not to address, but as stated before, none of these would be ground for rejection. What I am irritated about is whether the proofreading has actually happened before the current version 5 was posted. For instance, reference 44 seems missing (some others are missing in the bioRxiv version, but I suspect that's not the authors' fault), while lots of linguistic issues in phrases like "to provide a comprehensive bibliometric analyses of english Wikipedia's COVID-19 articles" would still benefit from being addressed. At this point, I thus recommend that the authors (a) update the existing Zenodo repository such that there is some more structure in the way the files are shared (b) archive a release of WikiCitationHistoRy on Zenodo
-
Background
Reviewer 2. Dean Giustini This is a well-written manuscript. The methods are well-described. I've confined my comments to improving the reporting of your methods, some comments about the paper's structure, and a few about the readability of the figures and tables (which I think in general are too small, and difficult to read). Here are my main comments for your consideration as you work to improve your paper:
1) Title of manuscript - the title of your paper seems inadequate to me, and doesn't really convey its content. A more descriptive title that includes the idea of the "first wave" might be useful from my point of view as a reader who scans titles to see if I am interested. I'd recommend including words in the title that refer to your methods. What type of research is this - a quantitative analysis of citations? Title words say a lot about the robust nature of your methods. As you consider whether to keep your title as is, keep mind that title words will aid readers in understanding your research at a glance, and provide impetus to read your abstract (and one hopes the entire manuscript). These words will help researchers find the paper later as well via the Internet's many search engines (i.e., Google Scholar).
2) Abstract - The abstract is well-written. Could the aims of your research be more obvious? and clearly articulated? How about using a statement such as "This research aims to" or similar? I also don't understand the sentence that begins with "Using references as a readout". What is meant by a "readout" in this context? Do you mean to read a print-out of references later? Lower down, you introduce the concept of Wikipedia's references as a "scientific infrastructure", and place it in quotations. Why is it in quotations? I wondered what the concept was on first reading it. A recurring web of papers in Wikipedia constitutes a set of core references - but would I call them a scientific infrastructure? Not sure; they are a mere sliver of the scientific corpus. Not sure I have any suggestions to clarify the use of this phrase.
3) Introduction - This is an excellent introduction to your paper, and it provides a lot of useful context and background. You make a case for positioning Wikipedia as a trusted source of information based on the highly selective literature cited by the entries. However, I would only caution that some COVID-19 entries cite excellent research but the content is contested, and vice versa. One suggestion I had for this section was the possibility of tying citizen science (part of open science) to the rise of Wikipedia's medwiki volunteers. Wikipedia provides all kinds of ways for citizens to get involved in science. As an open science researcher, I appreciated all of the open aspects you mention. Clearly, open access to Wikipedia in all languages is a driving force in combatting misinformation generally, and the COVID "infodemic" specifically. I admit I struggled to understand the point of the section that begins, "Here, we asked what role does scientific literature, as opposed to general media, play in supporting the encyclopedia's coverage of the COVID-19 as the pandemic spread." The opening sentence articulates your a priori research question, always welcome for readers. Would some of the information that follows in this section around your methods be better placed in the following section under the "Material and Methods"? I found it jarring to read that "....after the pandemic broke out we observed a drop in the overall percentage of academic references in a given coronavirus article, used here as a metric for gauging scientificness in what we term an article's Scientific Score." These two ideas are introduced again later, but I had no idea on reading them here what they signified or whether they were related to research you were building on. You might consider adding a parenthetical statement that they will be described later, and that the idea of a score is your own.
4) Material and methods - Your methods section might benefit from writing a preamble to prepare your readers. As already mentioned, consider taking some of the previous section and recasting it as an introduction to your methods. Consider adding some information to orient readers, and elaborating in a sentence or two about why identifying COVID-19 citations / information sources is an important activity.
By the way, what is meant by this: "To delimit the corpus of Wikipedia articles containing DOIs"? Do you mean "identify" Wikipedia articles with DOIs in their references? As I mentioned (apologies in advance for the repetition), it strikes me as odd that you don't refer to this research as a form of citation analysis (isn't that what it is?). Instead you characterize it as "citation counting". If your use of words has been intentional, is there a distinction you are making that I simply do not understand? Also: bibliometricians and/or scientometricians might wonder why you avoid the phrase citation analysis. Further to your methods which are primarily quantitative and statistical - what are the qualitative methods used throughout the paper to analyze the data? How did you carry out this qualitative work? (On page 10, you state "we set out to examine in a temporal, qualitative and quantitative manner, the role of references in articles linked directly to the pandemic as it broke.") That part of your methods seems to be a bit under-developed, and may be worth reconsidering as you work to improve your reporting in the manuscript.
5) Table 1. I am not sure what this table adds to the methods given it leads off your visuals. Do you really need it? It doesn't reveal anything to me and could be in a supplemental file. I also have difficulties in properly seeing table 1; perhaps you could make it larger and more readable?
6) Figure 1. This is the most informative visual in the paper but it is hard to read and crowded. It deserves more space or the information it provides is not fully understood.
7) Figure 3. This is very bulky as a figure, although informative. Again, I'm not sure all of it needs inclusion. Perhaps select part of it, and include other parts in a supplement.
7) Limitations - The paper does not adequately address its limitations. A more fulsome evaluation of limitations would be beneficial to me as a reader, as it would place your work in a larger context. For example, consider asking whether the results are indicative of Wikipedia's other medical or scientific entries? Or are the results not generalizable at all? In other works, are they indicative of something very limited based on the timeframe that you examined? I found myself disagreeing with: "....the mainstream output of scientific work on the virus predated the pandemic's outbreak to a great extent". Is this still true? and what might its significance be now that we are in 2021? Would it be helpful to say that most of the foundational research re: the family of coronaviruses was published pre-2020, but entries about COVID-19 disease and treatment entries are now distinctly different in terms of papers cited, especially going forward. Wiki editors identify relevant papers over time but are not adept at identifying emerging evidence in my experience, or at incorporating important papers early; it's strange given that recency is one of its true calling cards. For me, the most confounding aspect of the infodemic is the constant shifts of evidence, and how to respond in a way that is prudent and evidence-based. As you point out, Wikipedia has a 8.7 year latency in citing highly relevant papers - and, it seem likely that many important COVID-19 papers were neglected in Wikipedia in the first wave especially about the disease. As you point out, this will form part of future research, which I hope you and your team will pursue.
8) Reference 31 lacks a source: Amit Arjun Verma and S. Iyengar. Tracing the factoids: the anatomy of information reorganization in wikipedia articles. 2021.
Good luck with the next stages in improving your manuscript for publication. I believe it adds to our understanding of Wikipedia's role in promoting sources of information.
-
Abstract
This paper has been published in GigaScience under a CC-BY 4.0 license (see: https://doi.org/10.1093/gigascience/giab095). As the journal carriers out open peer review these have also been published under the same license.
Reviewer 1. Dariusz Jemielniak This is a very solid article on a timely topic. I also commend you for the thorough and meticulous methodology.
One thing that I believe you could amplify on is what would your proposed solution to the "trade off between timeliness and scientificness"? After all, Wikipedia relies on the sources that are reliable, verifiable, but foremostly... available. At the time when there are no academic journal articles published (yet) the chosen modus operandi does not appear to be a trade-off, it is basically the only logical solution. A trade-off would occur if the less valuable sources were not replaced when more academic ones appear, and this is not the case. I believe you should mention the fact that Wikipedia has an agreement with Cochrane database, which likely affects the popularity of this source.
Additionally, I think that the literature review needs to be expanded. There are already some publications about Wikipedia and COVID-19, as well as about medical coverage on Wikipedia (some non-exhaustive references added below). Moreover, Wikipedia has been a topic covered in GigaScience and it would be reasonable to reflect on the previous conversations in the journal in your publication.
Chrzanowski, J., Sołek, J., & Jemielniak, D. (2021). Assessing Public Interest Based on Wikipedia's Most Visited Medical Articles During the SARS-CoV-2 Outbreak: Search Trends Analysis. Journal of medical Internet research, 23(4), e26331. Colavizza, G. (2020). COVID-19 research in Wikipedia. Quantitative Science Studies, 1-32. Jemielniak, D. (2019). Wikipedia: Why is the common knowledge resource still neglected by academics?. GigaScience, 8(12), giz139.
Jemielniak, D., Masukume, G., & Wilamowski, M. (2019). The most influential medical journals according to Wikipedia: quantitative analysis. Journal of medical Internet Research, 21(1), e11429.
Kagan, D., Moran-Gilad, J., & Fire, M. (2020). Scientometric trends for coronaviruses and other emerging viral infections. GigaScience, 9(8), giaa085.
-
- Jan 2022
-
www.biorxiv.org www.biorxiv.org
-
Abstract
Reviewer 2. Rhonda Bacher It is good to have alternative workflows for single-cell analysis, and I am glad to see the authors have submitted the package to Bioconductor. I hope the authors maintain the package and update with new methods as necessary such as if new normalizations or batch corrections are developed. I only have two comments that I hope the authors try to clarify further:
- The statement starting with "Optionally, after batch-to-batch normalisation, we also..." should not be in that location. It seems to suggest to readers that this is the recommended method, whereas later that is not the case. In these sentences the manuscript also claims that this normalization approach is more "robust" without providing any evidence or citation.
- It's still not completely clear to me how the authors extension of the sc-qPCR method is different from MAST. The same authors of the qPCR method extended it here: "MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data". MAST is also an LRT, but I am assuming that here you are not using the detection rate as a covariate? That's OK if true, it just needs to be clear to the reader. I imagine this could be a frequently asked question by users down the road, so even a sentence on how it is different from (or similar to) MAST would help. Suggestion only: I may have missed it, but it might be helpful to include a statement that says something like "Statistical methods for single-cell analysis are constantly evolving. Here we have implemented XX. The flexibility of ascend allows it to adapt as future methods are developed and prove useful".
-
Now published in GigaScience doi: 10.1093/gigascience/giz087 Anne Senabouth 1Institute for Molecular Bioscience, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSamuel W Lukowski 1Institute for Molecular Bioscience, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJose Alquicira Hernandez 1Institute for Molecular Bioscience, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStacey Andersen 1Institute for Molecular Bioscience, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXin Mei 2South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQuan H Nguyen 1Institute for Molecular Bioscience, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoseph E Powell 1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia3Queensland Brain Institute, University of Queensland, Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz087 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101872
-
-
www.biorxiv.org www.biorxiv.org
-
Background
Reviewer 2. Jianbo Jian In this manuscript, Xi et al reported a chromosome-level genome of the common vetch (Vicia sativa) with integration of Oxford Nanopore sequencing, Illumina sequencing, CHiCAGO and Hi-C. Then, the gene annotation and evolution were performed based on the reference genomes. These genomic resources are valuable for evolution research, genetic diversity and genomic breeding. I think this manuscript is suitable published in Gigabyte. Some minor comments and suggestions as following:
1) The Line Number is missed in this manuscript, which make the detailed comments is not inconvenient. 2) Page 6, “resequenced short-reads” should be “De novo sequencing” or “sequencing”. 3) For the 1.93 Gb assembled genome size, it is a little larger than that of estimated by the flow cytometry (1.77 Gb) and Genomescope (1.61 Gb). Maybe there are some duplicated sequences in this version of assembled genomes. Some redundancy removal software can deal with this question such as Haplotigs, Purge_dups and so on. 4) For the evaluation of genome, LTR Assembly Index (LAI) was suggested for the quality assessment. 5) In Table S2, the mapping rate is very well but the genome coverage is just 76% which looks a little low. What’s the reason? 6) In Table S4, the gene set was combined by August. However, in methods, the annotation software is BRAKER v2.1.6.
Recommendation Minor Revision
Re-review: The revised manuscript and response are satisfactory. The additional analyses that the authors have performed are correctly structured. The data presented is clear. In my opinion, I recommend accepting this manuscript.
-
Abstract
This paper has been published in GigaByte Journal under a CC-BY 4.0 Open Access license (see: https://doi.org/10.46471/gigabyte.38), and the open peer reviews have also been shared under this license. These reviews were as follows.
Reviewer 1. Jonathan Kreplak Is there sufficient detail in the methods and data-processing steps to allow reproduction?
No. For "Phylogenetic tree construction and divergence time estimation", 64 single copy orthologs are selected, they should be included in a supplementary table to be able to fully reproduce the analysis. Also, Supplementary table S9 should be related to fossil calibrations but show the length of chromosome.
Recommendation: Minor revision
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa083 Andre Macedo Chronic Diseases Research Center (CEDOC), NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150-190, Lisbon, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andre MacedoFor correspondence: andre.macedo@nms.unl.pt alisson.gontijo@nms.unl.ptAlisson M. Gontijo Chronic Diseases Research Center (CEDOC), NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150-190, Lisbon, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alisson M. GontijoFor correspondence: andre.macedo@nms.unl.pt alisson.gontijo@nms.unl.pt
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa083 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102344 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102345
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz149 Michal Stolarczyk 1Center for Public Health Genomics, University of VirginiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVincent P. Reuter 1Center for Public Health Genomics, University of VirginiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNeal E. Magee 5Research Computing, University of VirginiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNathan C. Sheffield 1Center for Public Health Genomics, University of Virginia2Department of Public Health Sciences, University of Virginia3Department of Biomedical Engineering, University of Virginia4Department of Biochemistry and Molecular Genetics, University of VirginiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nathan C. SheffieldFor correspondence: nsheffield@virginia.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz149 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102075 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102076 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102077 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.102078
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz115 Bo Song 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYue Song 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China4BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYuan Fu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Balyejusa Kizito 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePamela Nahamya Kabod 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuan Liu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSandra Ndagire Kamenya 5Uganda Christian University, Bishop Tucker Road, Box 4, Mukono, UgandaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSamuel Muthemba 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRobert Kariba 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiuli Li 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSibo Wang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShifeng Cheng 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlice Muchugi 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRamni Jamnadass 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHoward-Yana Shapiro 6African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), Nairobi, Kenya7University of California, 1 Shields Ave, Davis, USA9Mars, Incorporated, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAllen Van Deynze 7University of California, 1 Shields Ave, Davis, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJian Wang 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDamaris Achieng Odeny 8ICRISAT-Nairobi, Nairobi, KenyaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: liuxin@genomics D.Odney@cigar.orgXin Liu 1BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China3State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: liuxin@genomics D.Odney@cigar.org
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz115 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101930 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101931 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101932
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz119 Sion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissFor correspondence: s.bayliss@bath.ac.ukHarry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeNicola M. Coyle 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicola M. CoyleSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Edward J. Feil
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz119 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101935 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101936 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101937
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz100 Elena Bushmanova 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDmitry Antipov 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlla Lapidus 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz100 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101881 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101882 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101883 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101884
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz105 Luca Alessandrì 2Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarco Beccuti 1Department of Computer Sciences, University of Torino, Corso Svizzera 185, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMaddalena Arigoni 2Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMartina Olivero 3Department of Oncology, University of Torino, SP142, 95, 10060 Candiolo TO, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGreta Romano 1Department of Computer Sciences, University of Torino, Corso Svizzera 185, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGennaro De Libero 4Department Biomedizin, University of Basel, Hebelstrasse 20, 4031 Basel, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuigia Pace 5IIGM, Via Nizza 52, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFrancesca Cordero 1Department of Computer Sciences, University of Torino, Corso Svizzera 185, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRaffaele A Calogero 2Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, Torino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz105 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101893 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101894
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz106 Yingxin Lin 1School of Mathematics and Statistics, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShila Ghazanfar 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia2Charles Perkins Centre, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDario Strbenac 1School of Mathematics and Statistics, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAndy Wang 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia3Sydney Medical School, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEllis Patrick 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia4Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDave Lin 5Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTerence Speed 6Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia7Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJean YH Yang 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia2Charles Perkins Centre, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jean YH YangPengyi Yang 1School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia2Charles Perkins Centre, University of Sydney, NSW 2006, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz106 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101910 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101911
-
-
-
Now published in GigaScience doi: 10.1093/gigascience/giz107 Thomas P. Quinn 1Bioinformatics Core Research Group, Deakin University, 3220, Geelong, Australia2Centre for Molecular and Medical Research, Deakin University, 3220, Geelong, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas P. QuinnIonas Erb 3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGreg Gloor 4Department of Biochemistry, University of Western Ontario, London, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCedric Notredame 3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMark F. Richardson 1Bioinformatics Core Research Group, Deakin University, 3220, Geelong, Australia5Genomics Centre, School of Life and Environmental Sciences, Deakin University, 3220, Geelong, Australia6Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, 3220, Geelong, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTamsyn M. Crowley 7Poultry Hub Australia, University of New England, 2351, Armidale, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz107 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101917 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101918
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz094 Marek Wiewiórka 1Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, PolandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marek WiewiórkaAgnieszka Szmurło 1Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, PolandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Agnieszka SzmurłoTomasz Gambin 1Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, PolandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tomasz Gambin
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz094 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101847 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101848 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101849
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa097
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa097 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102383
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz104
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz104 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101860 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101861 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101862
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz091
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz091 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101873 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101874 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101875
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix084 Jonathan A. Atkinson 1Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan A. AtkinsonGuillaume Lobet 2Agrosphere, IBG3, Forschungszentrum Jülich, Jülich, Germany3Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guillaume LobetManuel Noll 4InBios, Université de Liège, Liège, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatrick E. Meyer 4InBios, Université de Liège, Liège, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarcus Griffiths 1Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marcus GriffithsDarren M. Wells 1Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Darren M. Wells
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix084 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100810 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100811
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix100 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100867 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100868
-
-
www.biorxiv.org www.biorxiv.org
-
Leaf shape among
Reviewer 2. Tim Dickinson.
Review of GIGA-D-16-00069, "Morphometric analysis of Passiflora leaves I: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade" by D.H. Chitwood and W.C. Otoni.
This is a valuable contribution, both in terms of (a) the data collected (leaf outlines and landmarks from a large sample of Passiflora species exhibiting a wide range of leaf shapes), and (b) the well thought out analyses undertaken with care and, for the most part, attention to detail. The paper also showcases, at least for me, the range of tools now available for comparative biologists and others who seek to analyze patterns of morphological variation and ontogenetic change. Until relatively recently it appeared that there was no real replacement for MorphoSys (Meacham, 1993) and the ability of this MS-DOS based system for outline capture and measurement. In many ways there still isn't, leaving workers to pick through an assortment of programs with more limited scopes or (better), to learn to use the imageJ toolbox effectively (Schneider, Rasband, and Eliceiri, 2012). Or SHAPE (Iwata and Ukai, 2002), if only outline data are needed. And in the meantime, adepts from the morphometrics world have embraced R (R Core Team, 2016) as a data analysis and graphics environment, resulting in packages like shapes (Dryden, 2016) and Momocs (Bonhomme et al., 2014). Others (e.g. Jensen, Ciofani, and Miramontes, 2002), myself included, have compared results from different analytical methods based, variously, on landmark and outline data from a common sample of study objects.
The authors' correlation analysis (Fig. 7) is especially valuable (and as far as I know entirely original) for the way it enables the authors to infer connections between particular landmarks (their x or y coordinates) and particular elliptic Fourier coefficients (A, B, C, or D) for a given harmonic. Although they tend to contrast their landmark data as reflecting leaf vasculature features (because these provide the locations of several of their landmarks), as against overall shape features provided by their outline data, the authors also emphasize the complementarity of these two aspects of their study objects (p. 5). In their subsequent ms (GIGA-D-16-00070) the authors are more adroit in emphasizing this complementarity. Here, they occasionally sound as if they think these associations are somehow intrinsic in these data sources, as if the would obtain even in objects other than leaves (pp. 2, 3, 6). It may be that what's at issue here is just unnecessarily bringing forward interpretations of their results (as if they described the results) before those results have been fully presented. I have three concerns about this ms. First, the authors have been variously careless about details of spelling ("fratal," "heteroblatsy") and the agreement between verb and noun ("data" is a plural noun) and somewhat cavalier about explaining terms when first introduced ("eigenleaf"; "amplification factor," in the caption to Fig. 1).
Second, basic details of the authors' sampling are unclear, probably because they are so abundantly obvious to them. What is the actual sample size for their study? They refer (pp. 2, 4, 5, 10) to having analyzed more than 3,300 leaves, and (on p. 5) to making available a dataset comprising "...555 scans of leaves from 40 different species of Passiflora..." Presumably, the data released represent a subset of the total sample, but it would help to make this, and their overall sampling strategy, explicit by tabulating how many vines (with what numbers of leaves) were studied for each of the 40 species. These details are important in order to dispel any idea that their discriminant analyses are overfitted because of the large numbers of descriptors (30, 80, or 110) and binary-valued dummy variables for species and leaf position (39, 10); Gittins 'monograph on canonical analysis (Gittins, 1985) references simulation studies suggesting that upwards of 20 times as many study objects as descriptors (measured, plus those designating groups) are needed in order for an analysis to be anything other than a deterministic description of a particular dataset. One of the exciting aspects of this study is the refreshingly large sample size that appears to have been used.
The third, related, concern is that the way in which leaf position on individual vines was recorded is unclear, given that nothing seems to be said about whether the same number of leaves was produced on all vines of all species during the period during which the study material was grown. Numbering leaves from the youngest leaf at the tip of the shoot, to the base, suggests that the youngest leaf would be numbered 1, the next 2, and so on to N, the most basal leaf on the vine. If the total number of leaves varies from vine to vine then there won't be an exact homology between leaf positions. Figures 5 and 6 suggest that leaf position 1 (basal-most, left-most, respectively) is in fact the most basal leaf. Would this position in fact correspond to the cotyledons, or to the first post-cotyledonary leaf? Clarification would be helpful. I also wonder about the continued reference to "node position" and "heteroblastic node position" as well as, in one case, "shoot position." I suggest that a more transparent usage would be to refer throughout to leaf position (numbered from the most basal leaf), or to the position of a leaf on a shoot. Reference to "heteroblastic node position" seems completely unnecessary, since heteroblasty is an emergent property of some or all of the shoots studied, as seen from the way in which leaves vary over the course of shoot development in shape (or some other property) from the most basal to the most apical.
BONHOMME, V., S. PICQ, C. GAUCHEREL & J. CLAUDE. 2014. Momocs: Outline Analysis Using R. Journal of Statistical Software 56: 1-24. DRYDEN, I. L. 2016. shapes package, version 1.1-13. website: https://www.maths.nottingham.ac.uk/personal/ild/shapes/index.html. GITTINS, R. 1985. Canonical Analysis. Springer-Verlag, Berlin. IWATA, H. & Y. UKAI. 2002. SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93: 384-385. JENSEN, R. J., K. M. CIOFANI & L. C. MIRAMONTES. 2002. Lines, outlines, and landmarks: morphometric analyses of leaves of Acer rubrum, Acer saccharinum (Aceraceae) and their hybrid. Taxon 51: 475-492. MEACHAM, C. A. 1993. MorphoSys An interactive machine vision program for acquisition of morphometric data. In R. Fortuner [ed.], Advances in computer methods for systematic biology: Artificial intelligence, databases, computer vision, 393-402. R CORE TEAM. 2016. R: A language and environment for statistical computing. website: http://www.R-project.org. SCHNEIDER, C. A., W. S. RASBAND & K. W. ELICEIRI. 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9: 671-675.
Re-review; The authors have responded to my comments, and for the most part have satisfied my concerns. In this regard, the copy of the original ms marked up to show the changes the authors have made is extremely helpful. The material on github consists of the data files and R code used to produce the figures, and does not appear provide direct access to the original leaf spectra that would show the variation observed in outline and landmark position. For the publication, I trust that the journal will require that the raw data referenced as "44. Giga DB reference" will consist of a series of files, e.g. one for each species, comprising complete leaf spectra, with the leaves labeled acropetally, i.e. in the heteroblastic sequence from base to tip, for each plant referenced in Figure S1A. If these are provided as vector files (outlines plus landmarks) this data repository should not be excessively large. The vector format will also make it possible for the interested reader to zoom in and out without loss of resolution in order to examine the patterns of variation at different scales.
-
BACKGROUND
Reviewer 1. Christopher Jiggins. This paper assesses leaf shape variation in Passiflora using two different morphometric methods. I will say from the start that I am not an expert in these techniques and am not in a position to review the methods or statistics in this paper, so my comments are somewhat superficial and the paper should also be reviewed by a morphometrics/statistical expert.
Background: I'd like to see a bit more justification for the study- Is this aimed at developing automated methods for species identification, or quantifying ecological communities and their diversity of leaf shape? Or is it purely an assessment of the methods for shape quantification (Passiflora have such dramatic shape variation it should be an easy test case?) The analysis considers 'species' and developmental stage 'heteroblasty' separately and as independent factors. However I think this is the wrong approach because the plasticity of leaves is highly species dependent - so in analysing plasticity, species should be included in the model, such that the interaction of stage and species is considered. It is not really surprising that when considered independently, leaf position is not a very good predictor of leaf shape because the developmental process is different in each species. Or alternatively the leaf position analysis could be conducted on each species separately, if the data are sufficient.
It is interesting that more juvenile leaves show less species-specificity as detected in the dataset - anecdotally I have noticed the same thing.
Discussion: Are there any ecological implications of this work? Are the species sympatric, or where do they come from. I'd be interested to know about disparity in leaf shape among sympatric species, and whether this might be greater than expected by chance, as would perhaps be predicted by the Heliconius coevolution hypothesis. It would be interesting to think further about which ecological questions could be addressed with these methods
Page 3 Line 21 Refer to recent paper on shape learning Dell'aglio, D. D., Losada, M. E. & Jiggins, C. D. Butterfly Learning and the Diversification of Plant Leaf Shape. Front. Ecol. Evol. 4, 81 (2016).
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper doi: 10.1093/gigascience/giw008), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
There is also a Q&A with the author here: http://gigasciencejournal.com/blog/a-passion-for-morphing-passiflora-leaves-author-qa-with-daniel-chitwood/
-
-
www.biorxiv.org www.biorxiv.org
-
ABSTRACT
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa147), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows: Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102559 and http://dx.doi.org/10.5524/REVIEW.102558 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102557
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab074 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102883 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102884 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102885
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab061 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102870 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102871
-
-
www.biorxiv.org www.biorxiv.org
-
https://doi.org/10.1101/2020.06.06.138248
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab066 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102862 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102863
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab052 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102790 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102791 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102792
-
-
www.biorxiv.org www.biorxiv.org
-
ABSTRACT
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab039 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102755 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102753
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab033 Colin Farrell 1Department of Human Genetics, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Colin FarrellMichael Thompson 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnela Tosevska 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdewale Oyetunde 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatteo Pellegrini 2Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: matteop@mcdb.ucla.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102730 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102731
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab029 Lucie A. Bergeron 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucie A. BergeronFor correspondence: guojie.zhang@bio.ku.dk lucie.a.bergeron@gmail.comSøren Besenbacher 2Department of Molecular Medicine, Aarhus University, Aarhus, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiao Zheng 4BGI-Shenzhen, Shenzhen 518083, Guangdong, China5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePanyi Li 4BGI-Shenzhen, Shenzhen 518083, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorge Pacheco 6Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMikkel-Holger S. Sinding 7Trinity College Dublin, Dublin, Ireland8Greenland Institute of Natural Resources, Nuuk, GreenlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMaria Kamilari 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM. Thomas P. Gilbert 6Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark9Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMikkel H. Schierup 10Bioinformatics Research Centre, Aarhus University, Aarhus, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuojie Zhang 1Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark4BGI-Shenzhen, Shenzhen 518083, Guangdong, China11State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China12Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guojie.zhang@bio.ku.dk lucie.a.bergeron@gmail.com
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab029 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102718 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102719
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab032 Guy M. Hagen 1UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guy M. HagenFor correspondence: ghagen@uccs.eduJustin Bendesky 1UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRosa Machado 1UCCS BioFrontiers Center, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTram-Anh Nguyen 2George Mason University, 4400 University Drive, Fairfax, Virginia, 22030Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTanmay Kumar 3Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, California, 93407Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJonathan Ventura 3Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, California, 93407Find this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab032 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102721 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102722
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab022 Mikhail G. Dozmorov 2Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA3Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mikhail G. DozmorovFor correspondence: Mikhail.Dozmorov@vcuhealth.org Joshua.Harrell@vcuhealth.orgKatarzyna M. Tyc 4VCU Massey Cancer Center, Richmond, VA, 23298, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Katarzyna M. TycNathan C. Sheffield 5Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nathan C. SheffieldDavid C. Boyd 3Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA6Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA, 23298, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David C. BoydAmy L. Olex 7C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Amy L. OlexJason Reed 4VCU Massey Cancer Center, Richmond, VA, 23298, USA8Department of Physics, Virginia Commonwealth University, Richmond, VA, 23220, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason ReedJ. Chuck Harrell 3Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for J. Chuck HarrellFor correspondence: Mikhail.Dozmorov@vcuhealth.org Joshua.Harrell@vcuhealth.org
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab022 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102709 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102710
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab023 Jeffrey B.S. Gaither Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGrant E. Lammi Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames L. Li Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid M. Gordon Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHarkness C. Kuck Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBenjamin J. Kelly Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames R. Fitch Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePeter White Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter WhiteFor correspondence: peter.white@nationwidechildrens.org
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab023 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102700 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102701
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab020 Carolina Peñaloza 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlejandro P. Gutierrez 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK2Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLel Eory 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShan Wang 3Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiming Guo 3Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlan L. Archibald 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTim P. Bean 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRoss D. Houston 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ross D. HoustonFor correspondence: ross.houston@roslin.ed.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab020 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102693 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102694
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab018 Ben Blamey 1Department of Information Technology, Uppsala University, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ben BlameyFor correspondence: ben.blamey@it.uu.seSalman Toor 1Department of Information Technology, Uppsala University, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMartin Dahlö 2Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Sweden3Science for Life Laboratory, Uppsala University, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHåkan Wieslander 1Department of Information Technology, Uppsala University, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePhilip J Harrison 2Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Sweden3Science for Life Laboratory, Uppsala University, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIda-Maria Sintorn 1Department of Information Technology, Uppsala University, Sweden3Science for Life Laboratory, Uppsala University, Stockholm, Sweden4Vironova AB, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlan Sabirsh 5Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarolina Wählby 1Department of Information Technology, Uppsala University, Sweden3Science for Life Laboratory, Uppsala University, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOla Spjuth 2Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Sweden3Science for Life Laboratory, Uppsala University, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ola SpjuthAndreas Hellander 1Department of Information Technology, Uppsala University, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab018 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102684 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102685 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102686
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab017 Anton Zamyatin 1Computer Technologies Laboratory, ITMO University, Saint Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anton ZamyatinPavel Avdeyev 2Department of Mathematics, The George Washington University, Washington, DC, USA3Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pavel AvdeyevJiangtao Liang 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jiangtao LiangAtashi Sharma 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Atashi SharmaChujia Chen 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVarvara Lukyanchikova 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA7Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences, Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Varvara LukyanchikovaNikita Alexeev 1Computer Technologies Laboratory, ITMO University, Saint Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nikita AlexeevZhijian Tu 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zhijian TuMax A. Alekseyev 2Department of Mathematics, The George Washington University, Washington, DC, USA3Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA8Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Max A. AlekseyevIgor V. Sharakhov 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Igor V. SharakhovFor correspondence: igor@vt.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab017 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102680 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102681
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab011 Holly C. Beale 1UC Santa Cruz Molecular, Cell and Developmental Biology; UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Holly C. BealeFor correspondence: hcbeale@ucsc.eduJacquelyn M. Roger 2UC Santa Cruz School of EngineeringFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatthew A. Cattle 2UC Santa Cruz School of EngineeringFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLiam T. McKay 2UC Santa Cruz School of EngineeringFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDrew K. A. Thomson 2UC Santa Cruz School of EngineeringFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKatrina Learned 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteA. Geoffrey Lyle 1UC Santa Cruz Molecular, Cell and Developmental Biology; UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEllen T. Kephart 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRob Currie 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDu Linh Lam 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLauren Sanders 1UC Santa Cruz Molecular, Cell and Developmental Biology; UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJacob Pfeil 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohn Vivian 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIsabel Bjork 3UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSofie R. Salama 4Dept. of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Howard Hughes Medical InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Haussler 4Dept. of Biomolecular Engineering, UC Santa Cruz Genomics Institute, Howard Hughes Medical InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlena M. Vaske 1UC Santa Cruz Molecular, Cell and Developmental Biology; UC Santa Cruz Genomics InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab011 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102677 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102678
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giab007 James K. Bonfield 1Wellcome Trust Sanger Institute Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for James K. BonfieldJohn Marshall 2University of Glasgow, Institute of Cancer SciencesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for John MarshallPetr Danecek 1Wellcome Trust Sanger Institute Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Petr DanecekHeng Li 3Dana-Farber Cancer Institute and Harvard UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Heng LiValeriu Ohan 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Valeriu OhanAndrew Whitwham 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrew WhitwhamFor correspondence: aw7@sanger.ac.ukThomas Keane 5EMBL-EBIFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas KeaneRobert M. Davies 4Wellcome Sanger InstituteFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert M. Davies
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab007 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102657 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102658
-
-
-
Now published in GigaScience doi: 10.1093/gigascience/giab005 Ruichen Rong 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShuang Jiang 2Department of Statistical Sciences, Southern Methodist University, Dallas, TX 75275, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLin Xu 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuanghua Xiao 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA3Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA4Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYang Xie 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA3Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA4Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDajiang J. Liu 5Institute for Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania, 17033, USA6Division of Biostatistics, Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania, 17033, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQiwei Li 7Department of Mathematical Sciences, The University of Texas at Dallas, Dallas, Texas, 75080, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaowei Zhan 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA8Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Xiaowei.Zhan@UTSouthwestern.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab005 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102648 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102649
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa162 Xinying Fang 1Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Xinying FangYu Liu 2Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhijie Ren 3Department of Electric Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYuheng Du 1Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQianhui Huang 1Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLana X. Garmire 2Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lana X. GarmireFor correspondence: lgarmire@med.umich.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa162 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102617 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102618
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa155 Nikhil Bhagwat 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nikhil153@gmail.com jean-baptiste.poline@mcgill.caAmadou Barry 2Lady Davis Institute for Medical Research, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteErin W. Dickie 3Kimel Family Translational Imaging-Genetics Research Lab, CAMH, Toronto, ON, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShawn T. Brown 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGabriel A. Devenyi 4Computational Brain Anatomy Laboratory, Douglas Mental Health Institute, Verdun, QC, Canada5Department of Psychiatry, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKoji Hatano 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth DuPre 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlain Dagher 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM. Mallar Chakravarty 4Computational Brain Anatomy Laboratory, Douglas Mental Health Institute, Verdun, QC, Canada5Department of Psychiatry, McGill University, Montreal, QC, Canada10Department of Biomedical Engineering, McGill UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCelia M. T. Greenwood 2Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada8Ludmer Centre for Neuroinformatics Mental Health, McGill University, Montreal, QC, Canada9Gerald Bronfman Department of Oncology; Department of Epidemiology, Biostatistics Occupational Health; Department of Human Genetics, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBratislav Misic 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid N. Kennedy 7Child and Adolescent Neurodevelopment Initiative, University of Massachusetts, Worcester, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJean-Baptiste Poline 1Montreal Neurological Institute Hospital, McGill University, Montreal, QC, Canada6Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada8Ludmer Centre for Neuroinformatics Mental Health, McGill University, Montreal, QC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nikhil153@gmail.com jean-baptiste.poline@mcgill.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa155 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102614 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102615
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper [insert DOI here]), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102603 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102604
-
-
www.biorxiv.org www.biorxiv.org131813401
-
Now published in GigaScience doi: 10.1093/gigascience/giaa154 Satria A. Kautsar 1Bioinformatics Group, Wageningen University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Satria A. KautsarJustin J. J. van der Hooft 1Bioinformatics Group, Wageningen University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Justin J. J. van der HooftDick de Ridder 1Bioinformatics Group, Wageningen University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Dick de RidderMarnix H. Medema 1Bioinformatics Group, Wageningen University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marnix H. MedemaFor correspondence: marnix.medema@wur.nl
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa154 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102605 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102606 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102607
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa159 Taras K. Oleksyk 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, Ukraine2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Taras K. OleksykFor correspondence: oleksyk@oakland.edu remills@umich.eduWalter W. Wolfsberger 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, Ukraine2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexandra Weber 4Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKhrystyna Shchubelka 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto Rico5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga T. Oleksyk 6A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga Levchuk 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlla Patrus 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNelya Lazar 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephanie O. Castro-Marquez 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatricia Boldyzhar 5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlina Urbanovych 8Lviv National Medical University, Lviv 79010, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKateryna Malyar 10I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSvitlana Chervyakova 11Chernihiv Regional Hospital, Chernihiv 14039, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlena Podoroha 12Sumy Diagnostic Center, Sumy 40000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNatalia Kovalchuk 13Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYaroslava Hasynets 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJuan L. Rodriguez-Flores 14Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSarah Medley 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFabia Battistuzzi 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRyan Liu 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYong Hou 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSiru Chen 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMeredith Yeager 16Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Dean 16Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael DeanRyan E. Mills 17Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: oleksyk@oakland.edu remills@umich.eduVolodymyr Smolanka 5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa159 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102600 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102601
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa152 Anup Kumar BioInformatics lab, Department of Computer Science, University of Freiburg, Freiburg, 79110, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBjörn Grüning BioInformatics lab, Department of Computer Science, University of Freiburg, Freiburg, 79110, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: gruening@informatik.uni-freiburg.deRolf Backofen BioInformatics lab, Department of Computer Science, University of Freiburg, Freiburg, 79110, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa152 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102581 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102582 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102583 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.102584
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa151 Matthew D Young 1Wellcome Trust Sanger Institute, University of CambridgeFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: my4@sanger.ac.ukSam Behjati 1Wellcome Trust Sanger Institute, University of Cambridge2Cambridge University Hospitals NHS Foundation Trust, University of Cambridge3Department of Paediatrics, University of CambridgeFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa151 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102569 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102570 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102571
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa137 Mathieu Rousseau-Gueutin 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mathieu Rousseau-GueutinFor correspondence: jmaury@genoscope.cns.frCaroline Belser 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Caroline BelserCorinne Da Silva 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Corinne Da SilvaGautier Richard 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gautier RichardBenjamin Istace 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Benjamin IstaceCorinne Cruaud 3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCyril Falentin 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Cyril FalentinFranz Boideau 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJulien Boutte 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRegine Delourme 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Regine DelourmeGwenaëlle Deniot 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStefan Engelen 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stefan EngelenJulie Ferreira de Carvalho 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Julie Ferreira de CarvalhoArnaud Lemainque 3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLoeiz Maillet 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Loeiz MailletJérôme Morice 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatrick Wincker 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Patrick WinckerFrance Denoeud 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for France DenoeudAnne-Marie Chèvre 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anne-Marie ChèvreJean-Marc Aury 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jean-Marc AuryFor correspondence: jmaury@genoscope.cns.fr
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa137 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102545 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102546 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102548
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa123 Dandan Lang 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Dandan LangShilai Zhang 2State Key laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, 650091, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePingping Ren 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFan Liang 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZongyi Sun 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuanliang Meng 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guanliang MengYuntao Tan 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiang Hu 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaokang Li Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteQihua Lai Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLingling Han 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDepeng Wang 1GrandOmics Biosciences, Beijing, 102200, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFengyi Hu 2State Key laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, 650091, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWen Wang 3State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, Yunnan, China4Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, 710072 Xi’an, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: liushanlin@grandomics.com wwang@mail.kiz.ac.cnShanlin Liu 1GrandOmics Biosciences, Beijing, 102200, China5Department of Entomology, College of Plant Protection, China Agricultural University, 100193 Beijing, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Shanlin LiuFor correspondence: liushanlin@grandomics.com wwang@mail.kiz.ac.cn
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa123 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102552 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102553 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102554
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa122 Lukas M. Simon 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lukas M. SimonFor correspondence: lukas.simon@uth.tmc.edu zhongming.zhao@uth.tmc.eduFangfang Yan 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhongming Zhao 1Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA2Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA3MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA4Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: lukas.simon@uth.tmc.edu zhongming.zhao@uth.tmc.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa122 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102528 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102529 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102530 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.102531
-
-
-
Now published in GigaScience doi: 10.1093/gigascience/giaa138 Aspyn Palatnick 1Cold Spring Harbor High School, Cold Spring Harbor, NY 117242Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 117243University of Pennsylvania, Philadelphia, PA 19104Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBin Zhou 4Department of Biology, New York University, New York, NY 10003Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteElodie Ghedin 4Department of Biology, New York University, New York, NY 100035Department of Epidemiology, School of Global Public Health, New York, NY 10003Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael C. Schatz 2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 117246Departments of Computer Science and Biology, Johns Hopkins University, Baltimore MD, 21211Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael C. SchatzFor correspondence: mschatz@cshl.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa138 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102518 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102519 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102520
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa134 Sanjit Singh Batra 1Computer Science Division, University of California, Berkeley, CA 94720Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichal Levy-Sakin 2Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJacqueline Robinson 3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoseph Guillory 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteffen Durinck 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 940805Bioinformatics and Computational Biology Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePui-Yan Kwok 2Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 941433Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLaura A. Cox 6Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 271017Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78245Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSomasekar Seshagiri 4Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteYun S. Song 1Computer Science Division, University of California, Berkeley, CA 947208Department of Statistics, University of California, Berkeley, CA 947209Chan Zuckerberg Biohub, San Francisco, CA 94158Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJeffrey D. Wall 3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: jeff.wall@ucsf.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa134 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102514 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102515 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102517
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa135 Christina Weiβbecker 1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christina WeiβbeckerBeatrix Schnabel 1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnna Heintz-Buschart 2German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Bioinformatics Unit1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anna Heintz-BuschartFor correspondence: anna.heintz-buschart@ufz.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa135 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102503 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102504
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa127 Miroslav Kratochvíl 1Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic2Department of Software Engineering, Faculty of Mathematics and Physics, Charles university, Prague, Czech RepublicFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Miroslav KratochvílFor correspondence: exa.exa@gmail.comOliver Hunewald 3Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLaurent Heirendt 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Laurent HeirendtVasco Verissimo 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiří Vondrášek 1Institute of Organic Chemistry and Biochemistry, Prague, Czech RepublicFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jiří VondrášekVenkata P. Satagopam 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, Luxembourg5ELIXIR Luxembourg, University of Luxembourg, Campus Belval, Belvaux, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Venkata P. SatagopamReinhard Schneider 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, Luxembourg5ELIXIR Luxembourg, University of Luxembourg, Campus Belval, Belvaux, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Reinhard SchneiderChristophe Trefois 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, Luxembourg5ELIXIR Luxembourg, University of Luxembourg, Campus Belval, Belvaux, LuxembourgFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christophe TrefoisMarkus Ollert 3Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg6Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, Odense University Hospital, University of Southern Denmark, Odense, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa127 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102479 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102480
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa117 Alexandra J. Lee 1Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA2Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexandra J. LeeYoSon Park 2Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for YoSon ParkGeorgia Doing 3Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, Hanover, NH, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Georgia DoingDeborah A. Hogan 3Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, Hanover, NH, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Deborah A. HoganCasey S. Greene 2Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA4Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, PA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Casey S. GreeneFor correspondence: greenescientist@gmail.com
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa117 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102456 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102454
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa102 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102429 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102430
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa109 Francesca Pia Caruso 1Department of Science and Technologies, Università degli Studi del Sannio, 82100, Benevento, Italy2Bioinformatics Lab, BIOGEM, Ariano Irpino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuciano Garofano 1Department of Science and Technologies, Università degli Studi del Sannio, 82100, Benevento, Italy3Institute for Cancer Genetics, Columbia University, New York (NY), USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFulvio D’Angelo 2Bioinformatics Lab, BIOGEM, Ariano Irpino, Italy3Institute for Cancer Genetics, Columbia University, New York (NY), USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKai Yu 4Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFuchou Tang 4Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJinzhou Yuan 5Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA6Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJing Zhang 3Institute for Cancer Genetics, Columbia University, New York (NY), USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuigi Cerulo 1Department of Science and Technologies, Università degli Studi del Sannio, 82100, Benevento, Italy2Bioinformatics Lab, BIOGEM, Ariano Irpino, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavide Bedognetti 7Cancer Program, Sidra Medicine, Doha, QatarFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePeter A. Sims 5Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA6Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMario Suvà 8Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA9Broad Institute of Harvard and MIT, Cambridge, MA 02142, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiao-Dong Su 4Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnna Lasorella 3Institute for Cancer Genetics, Columbia University, New York (NY), USA10Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAntonio Iavarone 3Institute for Cancer Genetics, Columbia University, New York (NY), USA10Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA11Department of Neurology, Columbia University Medical Center, New York, NY, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichele Ceccarelli 2Bioinformatics Lab, BIOGEM, Ariano Irpino, Italy12Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: michele.ceccarelli@unina.it
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa109 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102411 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102412 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102413
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa091 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102408 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102409
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa099 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102384 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102385
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa088 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102358 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102359
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa085 Dima Kagan 1Department of Software and Information Systems Engineering, Ben-Gurion University of the NegevFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Dima KaganFor correspondence: kagandi@post.bgu.ac.ilJacob Moran-Gilad 2Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the NegevFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jacob Moran-GiladMichael Fire 1Department of Software and Information Systems Engineering, Ben-Gurion University of the NegevFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael Fire
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa085 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102352 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102353
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa076 Xiang Zhou 1School of Data and Computer Science, Sun Yat-sen University, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHua Chai 1School of Data and Computer Science, Sun Yat-sen University, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuiying Zhao 2Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChing-Hsing Luo 1School of Data and Computer Science, Sun Yat-sen University, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYuedong Yang 1School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China3Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-sen University), Ministry of Education, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yuedong YangFor correspondence: yangyd25@mail.sysu.edu.cn
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa076 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102310 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102311
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa072 Kirill Kryukov Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: kkryukov@gmail.comMahoko Takahashi Ueda Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSo Nakagawa Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTadashi Imanishi Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa072 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102308 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102307
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa070 Fu-Hao Lu 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNeil McKenzie 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMing-Cheng Luo 3Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony Hall 2Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael W Bevan 1Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: michael.bevan@jic.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa070 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102301 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102302
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa067 Lisa K. Johnson 1Department of Environmental Toxicology, University of California, Davis2Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lisa K. JohnsonRuta Sahasrabudhe 3DNA Technologies Core, Genome Center, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTony Gill 1Department of Environmental Toxicology, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJennifer Roach 1Department of Environmental Toxicology, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLutz Froenicke 3DNA Technologies Core, Genome Center, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteC. Titus Brown 2Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for C. Titus BrownAndrew Whitehead 1Department of Environmental Toxicology, University of California, DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: awhitehead@ucdavis.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa067 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102297 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102296 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102298
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa062 Victor A. Padilha 1Institute of Mathematics and Computer Sciences, University of São Paulo, Av. Trabalhador São Carlense 400, São Carlos, SP, 13564-002, BrazilFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOmer S. Alkhnbashi 2Chair of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 101, Freiburg, 79110, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShiraz A. Shah 3Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAndré C. P. L. F. de Carvalho 1Institute of Mathematics and Computer Sciences, University of São Paulo, Av. Trabalhador São Carlense 400, São Carlos, SP, 13564-002, BrazilFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRolf Backofen 2Chair of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 101, Freiburg, 79110, Germany4Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Georges-Köhler-Allee 101, Freiburg, 79110, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: backofen@informatik.uni-freiburg.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa062 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102294 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102295
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa051 Amanda Warr 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNabeel Affara 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBronwen Aken 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteH. Beiki 4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDerek M. Bickhart 5Dairy Forage Research Center, USDA-ARS, Madison, Wisconsin, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKonstantinos Billis 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteWilliam Chow 6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLel Eory 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHeather A. Finlayson 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Flicek 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarlos G. Girón 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDarren K. Griffin 7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard Hall 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGreg Hannum 9Denovium Inc., San Diego, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteThibaut Hourlier 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKerstin Howe 6Wellcome Sanger Institute, Cambridge, CB10 1SA, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid A. Hume 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteOsagie Izuogu 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKristi Kim 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey Koren 10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHaibou Liu 4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNancy Manchanda 11Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFergal J. Martin 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDan J. Nonneman 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRebecca E. O’Connor 7School of Biosciences, University of Kent, Canterbury CT2 7AF, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdam M. Phillippy 10Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGary A. Rohrer 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBenjamin D. Rosen 13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.AFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLaurie A. Rund 14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarole A. Sargent 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLawrence B. Schook 14Department of Animal Sciences, University of Illinois, Urbana, Illinois, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven G. Schroeder 13Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, U.S.AFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAriel S. Schwartz 9Denovium Inc., San Diego, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBen M. Skinner 2Department of Pathology, University of Cambridge, Cambridge CB2 1QP, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard Talbot 15Edinburgh Genomics, University of Edinburgh, Edinburgh EH9 3FL, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Tseng 8Pacific Biosciences, Menlo Park, California, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristopher K. Tuggle 4Department of Animal Science, Iowa State University, Ames, Iowa, U.S.A.11Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMick Watson 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.ukTimothy P. L. Smith 12USDA-ARS U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, U.S.A.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.ukAlan L. Archibald 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, U.K.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alan L. ArchibaldFor correspondence: alan.archibald@roslin.ed.ac.uk tim.smith@ARS.USDA.GOV mick.watson@roslin.ed.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa051 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102287 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102288
-
-
-
Now published in GigaScience doi: 10.1093/gigascience/giaa061 Saber Hafezqorani 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Saber HafezqoraniChen Yang 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKa Ming Nip 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ka Ming NipRené L Warren 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for René L WarrenInanc Birol 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada3Department of Medical Genetics, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Inanc BirolFor correspondence: ibirol@bcgsc.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa061 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102272 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102273
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa060 Wenxi Wang 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZihao Wang 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXintong Li 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhongfu Ni 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhaorong Hu 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMingming Xin 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuiru Peng 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYingyin Yao 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQixin Sun 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWeilong Guo 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guoweilong@cau.edu.cn
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa060 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102267 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102268
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa044 Benjamin B. Chu 1Department of Computational Medicine, UCLA, Los Angeles, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Benjamin B. ChuKevin L. Keys 2Department of Medicine, University of California, San Francisco, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kevin L. KeysChristopher A. German 3Department of Biostatistics, Fielding School of Public Health at UCLA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHua Zhou 3Department of Biostatistics, Fielding School of Public Health at UCLA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hua ZhouJin J. Zhou 4Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85724, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEric Sobel 1Department of Computational Medicine, UCLA, Los Angeles, USA5Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJanet S. Sinsheimer 1Department of Computational Medicine, UCLA, Los Angeles, USA5Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Janet S. SinsheimerFor correspondence: jsinshei@ucla.eduKenneth Lange 1Department of Computational Medicine, UCLA, Los Angeles, USA5Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kenneth LangeFor correspondence: klange@ucla.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa044 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102262 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102263
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa057 Junhua Li 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China3School of Bioscience & Bioengineering, South China University of Technology, Guangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Junhua LiHuanzi Zhong 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Huanzi ZhongYuliaxis Ramayo-Caldas 4INRA, Institut National de la Recherche Agronomique, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France5Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNicolas Terrapon 6CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France7INRA, USC 1408 AFMB, 13288 Marseille, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVincent Lombard 6CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France7INRA, USC 1408 AFMB, 13288 Marseille, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGabrielle Potocki-Veronese 8LISBP, Universite de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJordi Estellé 4INRA, Institut National de la Recherche Agronomique, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMilka Popova 9INRA, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, F-63122 Saint-Genès Champanelle, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZiyi Yang 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHui Zhang 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFang Li 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShanmei Tang 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWeineng Chen 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBing Chen 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJiyang Li 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJing Guo 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCécile Martin 9INRA, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, F-63122 Saint-Genès Champanelle, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmmanuelle Maguin 10INRA, Micalis Institute, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 1BGI-Shenzhen, Shenzhen 518083, China2China National GeneBank, BGI-Shenzhen, Shenzhen 518120, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 1BGI-Shenzhen, Shenzhen 518083, China11James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJian Wang 1BGI-Shenzhen, Shenzhen 518083, China11James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLise Madsen 1BGI-Shenzhen, Shenzhen 518083, China12Institute of Marine Research (IMR), Postboks 1870 Nordnes, 5817 Bergen, Norway13Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKarsten Kristiansen 1BGI-Shenzhen, Shenzhen 518083, China13Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: diego.morgavi@inra.fr stanislav.ehrlich@inra.fr kk@bio.ku.dkBernard Henrissat 6CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France7INRA, USC 1408 AFMB, 13288 Marseille, France14Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi ArabiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStanislav D. Ehrlich 15MGP MetaGenoPolis, INRA, Université Paris-Saclay, 78350 Jouy en Josas, France16Centre for Host Microbiome Interactions, Dental Institute, King’s College London, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: diego.morgavi@inra.fr stanislav.ehrlich@inra.fr kk@bio.ku.dkDiego P. Morgavi 9INRA, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, F-63122 Saint-Genès Champanelle, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Diego P. MorgaviFor correspondence: diego.morgavi@inra.fr stanislav.ehrlich@inra.fr kk@bio.ku.dk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa057 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102258 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102259
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa052 Alessandro Petrini 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: alessandro.petrini@unimi.itMarco Mesiti 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMax Schubach 2Berlin Institute of Health (BIH), Berlin, Germany3Charité – Universitätsmedizin Berlin, Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarco Frasca 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDaniel Danis 4The Jackson Laboratory for Genomic Medicine, Farmington CT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatteo Re 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGiuliano Grossi 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuca Cappelletti 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTiziana Castrignanò 5CINECA, SCAI SuperComputing Applications and Innovation Department, Roma, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePeter N. Robinson 4The Jackson Laboratory for Genomic Medicine, Farmington CT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter N. RobinsonGiorgio Valentini 1AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa052 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102239 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102240
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa050 Annarita Marrano 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: amarrano@ucdavis.eduMonica Britton 2Bioinformatics Core Facility, Genome Center, University of California Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaulo A. Zaini 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAleksey V. Zimin 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRachael E. Workman 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDaniela Puiu 4Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuca Bianco 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca BiancoErica Adele Di Pierro 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBrian J. Allen 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSandeep Chakraborty 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichela Troggio 5Research and Innovation Center, Department of Genomics and Biology of Fruit Crops, Fondazione E Mach, San Michele all’ Adige (TN) 38010, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCharles A. Leslie 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWinston Timp 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Winston TimpAbhaya Dandekar 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven L. Salzberg 3Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA4Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA6Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid B. Neale 1Department of Plant Sciences, University of California, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa050 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102235 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102236
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa048 Morteza Hosseini 1IEETA/DETI, University of Aveiro, 3810-193 Aveiro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: seyedmorteza@ua.ptDiogo Pratas 1IEETA/DETI, University of Aveiro, 3810-193 Aveiro, Portugal2Department of Virology, University of Helsinki, 00100 Helsinki, FinlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBurkhard Morgenstern 3Department of Bioinformatics, University of Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany4Göttingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteArmando J. Pinho 1IEETA/DETI, University of Aveiro, 3810-193 Aveiro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa048 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102233 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102234
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa049 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102230 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102231 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102232
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa045 Graham J Etherington The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Graham J EtheringtonFor correspondence: graham.etherington@earlham.ac.uk Federica.dipalma@earlham.ac.ukDarren Heavens The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Darren HeavensDavid Baker The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAshleigh Lister The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ashleigh ListerRose McNelly The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGonzalo Garcia The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gonzalo GarciaBernardo Clavijo The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Bernardo ClavijoIain Macaulay The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Iain MacaulayWilfried Haerty The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Wilfried HaertyFederica Di Palma The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Federica Di PalmaFor correspondence: graham.etherington@earlham.ac.uk Federica.dipalma@earlham.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa045 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102226 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102227
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa041 Alejandra N. Gonzalez-Beltran 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK2Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra N. Gonzalez-BeltranPaola Masuzzo 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, Belgium5Institute for Globally Distributed Open Research and Education (IGDORE), Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paola MasuzzoChristophe Ampe 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christophe AmpeGert-Jan Bakker 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gert-Jan BakkerSébastien Besson 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sébastien BessonRobert H. Eibl 8German Cancer Research Center, DKFZ Alumni Association, Heidelberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert H. EiblPeter Friedl 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands9David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, Houston, TX, USA10Cancer Genomics Center, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter FriedlMatthias Gunzer 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthias GunzerMark Kittisopikul 12Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA13Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark KittisopikulSylvia E. Le Dévédec 14Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sylvia E. Le DévédecSimone Leo 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK15Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Simone LeoJosh Moore 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Josh MooreYael Paran 16IDEA Bio-Medical Ltd, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yael ParanJaime Prilusky 17Life Science Core Facilities, Weizmann Institute of Science, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jaime PriluskyPhilippe Rocca-Serra 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPhilippe Roudot 18Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe RoudotMarc Schuster 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marc SchusterGwendolien Sergeant 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gwendolien SergeantStaffan Strömblad 19Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Staffan StrömbladJason R. Swedlow 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason R. SwedlowMerijn van Erp 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merijn van ErpMarleen Van Troys 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marleen Van TroysAssaf Zaritsky 20Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Assaf ZaritskySusanna-Assunta Sansone 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.beLennart Martens 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lennart MartensFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.be
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa041 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102224 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102225
-
Now published in GigaScience doi: 10.1093/gigascience/giaa041 Alejandra N. Gonzalez-Beltran 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK2Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra N. Gonzalez-BeltranPaola Masuzzo 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, Belgium5Institute for Globally Distributed Open Research and Education (IGDORE), Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paola MasuzzoChristophe Ampe 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christophe AmpeGert-Jan Bakker 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gert-Jan BakkerSébastien Besson 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sébastien BessonRobert H. Eibl 8German Cancer Research Center, DKFZ Alumni Association, Heidelberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert H. EiblPeter Friedl 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands9David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, Houston, TX, USA10Cancer Genomics Center, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter FriedlMatthias Gunzer 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthias GunzerMark Kittisopikul 12Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA13Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark KittisopikulSylvia E. Le Dévédec 14Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sylvia E. Le DévédecJosh Moore 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Josh MooreYael Paran 16IDEA Bio-Medical Ltd, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yael ParanJaime Prilusky 17Life Science Core Facilities, Weizmann Institute of Science, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jaime PriluskyPhilippe Rocca-Serra 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPhilippe Roudot 18Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe RoudotMarc Schuster 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marc SchusterGwendolien Sergeant 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gwendolien SergeantStaffan Strömblad 19Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Staffan StrömbladJason R. Swedlow 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason R. SwedlowMerijn van Erp 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merijn van ErpMarleen Van Troys 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marleen Van TroysAssaf Zaritsky 20Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Assaf ZaritskySusanna-Assunta Sansone 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.beLennart Martens 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lennart MartensFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.be
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa041 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102224 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102225
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa046 Rafael R. C. Cuadrat 1Molecular Epidemiology Department, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfEFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Rafael R. C. CuadratMaria Sorokina 2Friedrich-Schiller University, Lessingstrasse 8, 07743 Jena, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Maria SorokinaBruno G. Andrade 3Embrapa Southeast Livestock - EMBRAPAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTobias Goris 4Department of Molecular Toxicology, Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfEFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlberto M. R. Dávila 5Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ. Av Brasil 4365, Rio de Janeiro, RJ, Brasil. 21040-900Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alberto M. R. DávilaFor correspondence: alberto.davila@fiocruz.br
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa046 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102215 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102216 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102217
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa037 Nathan J Kenny 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UK2Oxford Brookes University, Headington Rd, Oxford OX3 0BP, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nathan J KennyShane A McCarthy 3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga Dudchenko 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA5The Center for Theoretical Biological Physics, Rice University, Houston, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKatherine James 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UK6Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmma Betteridge 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCraig Corton 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJale Dolucan 7Wellcome Sanger Institute, Cambridge CB10 1SA, UK8Freeline Therapeutics Limited, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2FX, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDan Mead 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKaren Oliver 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteArina D Omer 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSarah Pelan 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYan Ryan 9School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK10Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, L3 5RFFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYing Sims 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJason Skelton 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichelle Smith 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames Torrance 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Weisz 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnil Wipat 9School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteErez L Aiden 4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA5The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA11Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China12School of Agriculture and Environment, University of Western Australia, Perth, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKerstin Howe 7Wellcome Sanger Institute, Cambridge CB10 1SA, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSuzanne T Williams 1Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Suzanne T WilliamsFor correspondence: s.williams@nhm.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa037 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102199 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102200 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102201
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa030 Mitchell J. Feldmann 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitchell J. FeldmannFor correspondence: mjfeldmann@ucdavis.eduMichael A. Hardigan 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRandi A. Famula 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Randi A. FamulaCindy M. López 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAmy Tabb 2USDA-ARS-AFRS, 2217 Wiltshire Rd, Kearneysville, WV 25430, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Amy TabbGlenn S. Cole 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven J. Knapp 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Steven J. Knapp
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa030 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102204 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102205 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102208
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa035 Karl Johnson 1UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuy M. Hagen 1UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guy M. HagenFor correspondence: ghagen@uccs.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa035 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102185 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102186 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102187
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa033 Marco Antonio Tangaro 1Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marco Antonio TangaroGiacinto Donvito 2National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126 Bari, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Giacinto DonvitoMarica Antonacci 2National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126 Bari, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marica AntonacciMatteo Chiara 3Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matteo ChiaraPietro Mandreoli 3Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGraziano Pesole 1Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy4Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Graziano PesoleFederico Zambelli 1Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy3Department of Biosciences, University of Milan, via Celoria 26, 20133 Milano, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Federico Zambelli
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102183 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102184
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa026 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102179 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102180 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102182
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa028 Olexiy Kyrgyzov 1CEA Genoscope, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVincent Prost 1CEA Genoscope, Evry, France2CEA LIST, Gif-sur-Yvette, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStéphane Gazut 2CEA LIST, Gif-sur-Yvette, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBruno Farcy 3Bull Technologies, Les Clayes-sous-Bois, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas Brüls 1CEA Genoscope, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: bruls@genoscope.cns.fr
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa028 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102154 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102155
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa025 Thomas McGowan 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames E. Johnson 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePraveen Kumar 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 554553Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRay Sajulga 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSubina Mehta 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePratik D. Jagtap 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTimothy J. Griffin 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: tgriffin@umn.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa025 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102152 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102153
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa010 Edi Prifti 1Institute of Cardiometabolism and Nutrition, Integromics, ICAN, Paris, France2Sorbonne University, IRD, UMMISCO, UMI 209, Paris, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Edi PriftiYann Chevaleyre 3Paris-Dauphine University, PSL Research University, CNRS, UMR 7243, LAMSADE, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yann ChevaleyreBlaise Hanczar 4IBISC, University Paris-Saclay, University Evry, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Blaise HanczarEugeni Belda 1Institute of Cardiometabolism and Nutrition, Integromics, ICAN, Paris, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Eugeni BeldaAntoine Danchin 5Institute of Cardiometabolism and Nutrition, ICAN, Paris, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Antoine DanchinKarine Clément 6Sorbonne University, INSERM, Nutriomics team, Paris, France7Assistance Publique-Hôpitaux de Paris, Nutrition department, CRNH Ile de France, Paris, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Karine ClémentJean-Daniel Zucker 1Institute of Cardiometabolism and Nutrition, Integromics, ICAN, Paris, France2Sorbonne University, IRD, UMMISCO, UMI 209, Paris, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jean-Daniel Zucker
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa010 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102131 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102132
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa005 Ekaterina Noskova 1ITMO University, St. Petersburg, Russia2JetBrains Research, St. Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: ekaterina.e.noskova@gmail.comVladimir Ulyantsev 1ITMO University, St. Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKlaus-Peter Koepfli 3Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia5National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephen J. O’Brien 3Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia4Oceanographic Center, Nova Southeastern University Ft Lauderdale, Ft Lauderdale, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePavel Dobrynin 3Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia5National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa005 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102116 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102117
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa004 Zheng Li Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zheng LiMichael S Barker Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael S Barker
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa004 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102092 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102093
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa003 Jerven Bolleman 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jerven BollemanFor correspondence: jerven.bolleman@sib.swissEduoard de Castro 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Eduoard de CastroDelphine Baratin 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Delphine BaratinSebastien Gehant 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sebastien GehantBeatrice A. Cuche 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Beatrice A. CucheAndrea H. Auchincloss 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrea H. AuchinclossElisabeth Coudert 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Elisabeth CoudertChantal Hulo 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Chantal HuloPatrick Masson 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Patrick MassonIvo Pedruzzi 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ivo PedruzziCatherine Rivoire 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Catherine RivoireIoannis Xenarios 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland2CHUV/LICR, Agora Centre, CH-1005 Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ioannis XenariosNicole Redaschi 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicole RedaschiAlan Bridge 1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alan Bridge
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa003 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102090 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102091
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz165 George Alter 1University of MichiganFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for George AlterAlejandra Gonzalez-Beltran 2University of OxfordFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra Gonzalez-BeltranLucila Ohno-Machado 3University of California at San DiegoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucila Ohno-MachadoPhilippe Rocca-Serra 4University of OxfordFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-Serra
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz165 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102087 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102088 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102089
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa007 Stephen J. Bush 1Nuffield Department of Medicine, University of Oxford, Oxford, UK2National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephen J. BushFor correspondence: stephen.bush@roslin.ed.ac.ukDona Foster 1Nuffield Department of Medicine, University of Oxford, Oxford, UK3National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid W. Eyre 1Nuffield Department of Medicine, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David W. EyreEmily L. Clark 4The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Emily L. ClarkNicola De Maio 1Nuffield Department of Medicine, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLiam P. Shaw 1Nuffield Department of Medicine, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Liam P. ShawNicole Stoesser 1Nuffield Department of Medicine, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicole StoesserTim E. A. Peto 1Nuffield Department of Medicine, University of Oxford, Oxford, UK2National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK3National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDerrick W. Crook 1Nuffield Department of Medicine, University of Oxford, Oxford, UK2National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK3National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteA. Sarah Walker 1Nuffield Department of Medicine, University of Oxford, Oxford, UK2National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK3National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa007 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102084 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102085
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giaa002 Miranda E. Pitt 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Miranda E. PittFor correspondence: miranda.pitt@imb.uq.edu.au l.coin@imb.uq.edu.auSon H. Nguyen 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Son H. NguyenTânia P.S. Duarte 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tânia P.S. DuarteMark A.T. Blaskovich 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark A.T. BlaskovichLachlan J.M. Coin 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lachlan J.M. CoinFor correspondence: miranda.pitt@imb.uq.edu.au l.coin@imb.uq.edu.au
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa002 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102080 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102081 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102082
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz158 Mitsutaka Kadota 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitsutaka KadotaHisashi Miura 2Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hisashi MiuraKaori Tanaka 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIchiro Hiratani 2Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ichiro Hiratani
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz158 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102051 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102052 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102053
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz160 Weiwen Wang 1Research School of Biology, the Australian National University, Canberra, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Weiwen WangFor correspondence: wei.wang@anu.edu.au rob.lanfear@anu.edu.auAshutosh Das 1Research School of Biology, the Australian National University, Canberra, Australia2Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University, Chittagong, BangladeshFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ashutosh DasDavid Kainer 1Research School of Biology, the Australian National University, Canberra, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David KainerMiriam Schalamun 1Research School of Biology, the Australian National University, Canberra, Australia3Institute of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, AustriaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Miriam SchalamunAlejandro Morales-Suarez 4Department of Biological Sciences, Macquarie University, Sydney, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandro Morales-SuarezBenjamin Schwessinger 1Research School of Biology, the Australian National University, Canberra, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Benjamin Schwessinger
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz160 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102038 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102039
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz141 Lu Zhang 1Department of Computer Science, Hong Kong Baptist University2Department of Pathology, Stanford University3Department of Computer Science, Stanford UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXin Zhou 3Department of Computer Science, Stanford UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZiming Weng 2Department of Pathology, Stanford UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteArend Sidow 2Department of Pathology, Stanford University4Department of Genetics, Stanford UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: arend@stanford.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz141 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101987 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101988
-
-
www.biorxiv.org www.biorxiv.org
-
ABSTRACT
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz120 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101977 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101978
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz132 Ekaterina Osipova 1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany2Max Planck Institute for the Physics of Complex Systems, Dresden, Germany3Center for Systems Biology Dresden, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNikolai Hecker 1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany2Max Planck Institute for the Physics of Complex Systems, Dresden, Germany3Center for Systems Biology Dresden, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Hiller 1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany2Max Planck Institute for the Physics of Complex Systems, Dresden, Germany3Center for Systems Biology Dresden, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: hiller@mpi-cbg.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz132 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101980 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101981
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz136 Joeri S. Strijk 1State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China2Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China3Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, LaosFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Joeri S. StrijkFor correspondence: jsstrijk@hotmail.comDamien D. Hinsinger 2Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China3Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, LaosFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Damien D. HinsingerFeng-Ping Zhang 4Evolutionary Ecology of Plant Reproductive Systems Group, Kunming Institute of Botany, Kunming, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKunFang Cao 1State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz136 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101974 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101975
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz123 Robail Yasrab 1School of Computer Science, University of Nottingham, NG8 1BB, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robail YasrabJonathan A Atkinson 2School of Biosciences, University of Nottingham, LE12 5RD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan A AtkinsonDarren M Wells 2School of Biosciences, University of Nottingham, LE12 5RD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Darren M WellsAndrew P French 1School of Computer Science, University of Nottingham, NG8 1BB, UK2School of Biosciences, University of Nottingham, LE12 5RD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrew P FrenchTony P Pridmore 1School of Computer Science, University of Nottingham, NG8 1BB, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tony P PridmoreMichael P Pound 1School of Computer Science, University of Nottingham, NG8 1BB, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael P PoundFor correspondence: michael.pound@nottingham.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz123 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101967 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101968 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101969
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz110 Varuna Chander 1Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard A. Gibbs 1Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFritz J. Sedlazeck 1Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fritz J. SedlazeckFor correspondence: fritz.sedlazeck@bcm.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz110 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101890 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101891
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz074 Timothy H. Webster 1School of Life Sciences, Arizona State UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Timothy H. WebsterMadeline Couse 2Child and Family Research Institute, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBruno M. Grande 3Department of Molecular Biology and Biochemistry, Simon Fraser UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Bruno M. GrandeEric Karlins 4Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of HealthFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTanya N. Phung 5Interdepartmental Program in Bioinformatics, UCLAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tanya N. PhungPhillip A. Richmond 6Centre for Molecular Medicine and Therapeutics, University of British Columbia7BC Children’s HospitalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Phillip A. RichmondWhitney Whitford 8School of Biological Sciences, The University of AucklandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Whitney WhitfordMelissa A. Wilson Sayres 1School of Life Sciences, Arizona State University9Center for Evolution and Medicine, Arizona State UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Melissa A. Wilson Sayres
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz074 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101812 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101813
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz084 Michael Kotliar 1Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OHFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael KotliarAndrey V. Kartashov 1Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OHFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrey V. KartashovArtem Barski 1Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH2Division of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OHFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Artem BarskiFor correspondence: Artem.Barski@cchmc.org
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz084 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101838 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101839
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz063 Jay Ghurye 1Department of Computer Science, University of Maryland, College Park, MD2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSergey Koren 2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteScott T. Small 3Department of Biological Sciences, University of Notre Dame, South Bend, INFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSeth Redmond 4Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA5Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, MAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Howell 6Centers for Disease Control, Atlanta, GAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdam M. Phillippy 2Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNora J. Besansky 3Department of Biological Sciences, University of Notre Dame, South Bend, INFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz063 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101744 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101745
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz037 Mathieu Bourgey 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guil.bourque@mcgill.ca mathieu.bourgey@mcgill.caRola Dali 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRobert Eveleigh 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKuang Chung Chen 3McGill HPC Centre, McGill University, Montréal, QC, Canada.4Calcul Québec, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLouis Letourneau 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoel Fillon 5Department of Human Genetics, McGill University, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarc Michaud 2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMaxime Caron 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.5Department of Human Genetics, McGill University, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohanna Sandoval 6Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFrancois Lefebvre 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGary Leveque 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteEloi Mercier 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Bujold 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePascale Marquis 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatrick Tran Van 7Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Morais 8Centre de calcul scientifique (ccs) - Université de Sherbrooke, Sherbrooke, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJulien Tremblay 9Energy, Mining and Environment, National Research Council Canada, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaojian Shao 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteEdouard Henrion 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmmanuel Gonzalez 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre-Olivier Quirion 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBryan Caron 3McGill HPC Centre, McGill University, Montréal, QC, Canada.4Calcul Québec, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuillaume Bourque 1Canadian Centre for Computational Genomics, Montréal, QC, Canada.2McGill University and Genome Québec Innovation Center, Montréal, QC, Canada.5Department of Human Genetics, McGill University, Montréal, QC, Canada.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guil.bourque@mcgill.ca mathieu.bourgey@mcgill.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz037 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101755 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101756 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101759
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz064 Amartya Singh 1Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA2Center for Systems and Computational Biology, Rutgers Cancer Institute, Rutgers University, New Brunswick, NJ, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGyan Bhanot 1Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA2Center for Systems and Computational Biology, Rutgers Cancer Institute, Rutgers University, New Brunswick, NJ, USA3Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHossein Khiabanian 1Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA2Center for Systems and Computational Biology, Rutgers Cancer Institute, Rutgers University, New Brunswick, NJ, USA3Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USA4Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hossein Khiabanian
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz064 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101761 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101762 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101763
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz077 Lu Gan Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lu GanFor correspondence: lu@anaphase.orgCai Tong Ng Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Cai Tong NgChen Chen Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteShujun Cai Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Shujun Cai
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz077 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101801 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101802
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz047 Yi Zhao 1BGI-Shenzhen, Shenzhen 518083, China3School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiao Li 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJingwan Wang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZiyun Wan 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKai Gao 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGang Yi 4Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXie Wang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJinghua Wu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBingbing Fan 2Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWei Zhang 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFang Chen 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 1BGI-Shenzhen, Shenzhen 518083, China5James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJian Wang 1BGI-Shenzhen, Shenzhen 518083, China5James D. Watson Institute of Genome Sciences, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBin Li 1BGI-Shenzhen, Shenzhen 518083, China4Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShiping Liu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWeihua Zhao 2Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYong Flou 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiao Liu 1BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz047 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101675 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101676 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101677
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz055 Angela Tam 1Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, CA2Douglas Hospital Research Centre, McGill University, Montréal, CA3McGill University, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Angela TamFor correspondence: angela.tam@mail.mcgill.ca pierre.bellec@criugm.qc.caChristian Dansereau 1Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, CA4Département d’Informatique et de recherche opérationnelle, Université de Montréal, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYasser Itturia-Medina 3McGill University, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSebastian Urchs 3McGill University, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre Orban 1Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, CA5Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, Montréal, CA6Département de Psychiatrie, Université de Montréal, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHanad Sharmarke 1Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohn Breitner 2Douglas Hospital Research Centre, McGill University, Montréal, CA3McGill University, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre Bellec 1Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, CA4Département d’Informatique et de recherche opérationnelle, Université de Montréal, Montréal, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: angela.tam@mail.mcgill.ca pierre.bellec@criugm.qc.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz055 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101681 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101682 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101683
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz043 Samuel M. Nicholls 1Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel M. NichollsJoshua C. Quick 1Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Joshua C. QuickShuiquan Tang 2Zymo Research Corporation, Irvine, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNicholas J. Loman 1Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicholas J. Loman
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz043 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101702 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101703
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz028 Venice Juanillas 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexis Dereeper 2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alexis DereeperNicolas Beaume 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicolas BeaumeGaetan Droc 3CIRAD, UMR AGAP, F-34398 Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gaetan DrocJoshua Dizon 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohn Robert Mendoza 8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJon Peter Perdon 8Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLocedie Mansueto 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLindsay Triplett 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lindsay TriplettJillian Lang 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jillian LangGabriel Zhou 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKunalan Ratharanjan 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kunalan RatharanjanBeth Plale 4Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Beth PlaleJason Haga 5National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 1,1-1-1 Umezono, Tsukuba, Ibaraki 305-8560 JAPANFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason HagaJan E. Leach 7Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jan E. LeachManuel Ruiz 3CIRAD, UMR AGAP, F-34398 Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Thomson 1International Rice Research Institute, Manila, Philippines6Department of Soil and Crop Sciences, Texas A&M University, Houston, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNickolai Alexandrov 1International Rice Research Institute, Manila, Philippines10Inari Agriculture Inc., 200 Sidney St, Cambridge, Massachusetts, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre Larmande 2Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pierre LarmandeTobias Kretzschmar 1International Rice Research Institute, Manila, Philippines9Southern Cross Plant Science, Southern Cross University, Lismore, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRamil P. Mauleon 1International Rice Research Institute, Manila, PhilippinesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ramil P. Mauleon
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz028 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101705 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101706
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz059 Bruno Louro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGianluca De Moro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarlos Garcia 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCymon J. Cox 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAna Veríssimo 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephen J. Sabatino 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAntónio M. Santos 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdelino V. M. Canário 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Adelino V. M. CanárioFor correspondence: acanario@ualg.pt
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz059 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101710 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101711
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz061 Martijn R. Molenaar §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Martijn R. MolenaarAike Jeucken §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTsjerk A. Wassenaar ‡Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChris H. A. van de Lest §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJos F. Brouwers §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJ. Bernd Helms §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: J.B.Helms@uu.nl
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz061 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101733 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101734 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101735
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz030 Matthew A. Conte 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRajesh Joshi 2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEmily C. Moore 3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSri Pratima Nandamuri 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWilliam J. Gammerdinger 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteReade B. Roberts 3Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKaren L. Carleton 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSigbjørn Lien 2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NorwayFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas D. Kocher 1Department of Biology, University of Maryland, College Park, MD 20742, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz030 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101604 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101605
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz026 Justin Jiang 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Justin JiangAndrea M. Quattrini 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrea M. QuattriniWarren R. Francis 2University of Southern Denmark, Dept. of Biology, Campusvej 55, Odense M 5230, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Warren R. FrancisJoseph F. Ryan 3Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd. St. Augustine, FL 32080, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEstefanía Rodríguez 4Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Estefanía RodríguezCatherine S. McFadden 1Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Catherine S. McFadden
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz026 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101602 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101603
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz033 Wenbo Chen 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Wenbo ChenSara Shakir 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 148533Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liège, Gembloux, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sara ShakirMahdiyeh Bigham 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mahdiyeh BighamZhangjun Fei 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 148532US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zhangjun FeiGeorg Jander 1Boyce Thompson Institute, 533 Tower Road, Ithaca NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Georg JanderFor correspondence: gj32@cornell.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101619 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101620 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101621
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz024 Ermin Hodzic 1Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, BC, Canada2School of Computing Science, Simon Fraser University, Burnaby, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRaunak Shrestha 1Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, BC, Canada3Department of Urologic Sciences, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Raunak ShresthaKaiyuan Zhu 4Department of Computer Science, Indiana University, Bloomington, IN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKuoyuan Cheng 5Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteColin C. Collins 1Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, BC, Canada3Department of Urologic Sciences, University of British Columbia, Vancouver, BC, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteS. Cenk Sahinalp 1Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, Vancouver, BC, Canada4Department of Computer Science, Indiana University, Bloomington, IN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for S. Cenk SahinalpFor correspondence: cenksahi@indiana.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz024 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101626 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101627
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz040 Brent S. Pedersen 1Department of Human Genetics, University of Utah. Salt Lake City, UT3USTAR Center for Genetic Discovery, University of Utah. Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brent S. PedersenAaron R. Quinlan 1Department of Human Genetics, University of Utah. Salt Lake City, UT2Department of Biomedical Informatics, University of Utah. Salt Lake City, UT3USTAR Center for Genetic Discovery, University of Utah. Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Aaron R. Quinlan
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz040 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101641 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101642
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz052 Tazro Ohta 1Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tazro OhtaTomoya Tanjo 2National Institute of Informatics, Research Organization of Information and Systems, Tokyo 101–8430, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tomoya TanjoOsamu Ogasawara 3DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Osamu Ogasawara
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz052 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101638 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101639 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101640
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz045 Ren-Hua Chung 1Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, TaiwanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: rchung@nhri.org.twChen-Yu Kang 1Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, TaiwanFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz045 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101652 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101653
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz044 Samuel Lampa 1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden2Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel LampaMartin Dahlö 1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Martin DahlöJonathan Alvarsson 1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan AlvarssonOla Spjuth 1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ola Spjuth
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz044 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101656 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101657 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101659
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy163 Pirita Paajanen 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorge Kettleborough 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for George KettleboroughElena López-Girona 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Giolai 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDarren Heavens 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Baker 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAshleigh Lister 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ashleigh ListerGail Wilde 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteIngo Hein 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteIain Macaulay 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Iain MacaulayGlenn J. Bryan 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatthew D. Clark 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthew D. ClarkFor correspondence: matt.clark@earlham.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy163 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101497 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101498
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz003 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101502 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101503 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101504
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giz018 Laura-jayne Gardiner 1Earlham Institute, Norwich, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas Brabbs 1Earlham Institute, Norwich, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlina Akhunova 2Kansas State University, Department of Plant Pathology, Manhattan, KS, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHikmet Budak 3Montana State University, Department of Plant Sciences and Plant Pathology, Bozeman, MT, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTodd Richmond 4Roche Sequencing Solutions, Seattle, WA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSukwinder Singh 5CIMMYT, Obregon, MexicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLeah Catchpole 1Earlham Institute, Norwich, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEduard Akhunov 2Kansas State University, Department of Plant Pathology, Manhattan, KS, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony Hall 1Earlham Institute, Norwich, UK6School of Biological Sciences, University of East Anglia, Norwich, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz018 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101535 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101536
-
-
www.biorxiv.org www.biorxiv.org
-
ABSTRACT
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz010 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101551 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101552
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz009 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101555
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy121
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy121 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101388 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101389
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy123 Ricardo Wurmus 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBora Uyar 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBrendan Osberg 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVedran Franke 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexander Gosdschan 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKatarzyna Wreczycka 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJonathan Ronen 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAltuna Akalin 1The Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Altuna AkalinFor correspondence: altuna.akalin@mdc-berlin.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy123 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101393 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101392
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy124 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101485 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101486 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101487
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy128 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101408 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101409
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy133 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101411 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101412
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy127 Xiaofeng Dong 1Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom2Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China3School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China4Institute of Infection & Global Health, University of Liverpool, L3 5RF, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKittipong Chaisiri 4Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom5Faculty of Tropical Medicine, Mahidol University, Ratchathewi Bangkok 10400, ThailandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDong Xia 4Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom6The Royal Veterinary College, London NW1 0TU, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Dong XiaStuart D. Armstrong 4Institute of Infection & Global Health, University of Liverpool, L3 5RF, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYongxiang Fang 1Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yongxiang FangMartin J. Donnelly 7Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Martin J. DonnellyTatsuhiko Kadowaki 2Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tatsuhiko KadowakiJohn W. McGarry 8Institute of Veterinary Science, University of Liverpool, Liverpool L3 5RP, United Kingdom.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlistair C. Darby 1Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alistair C. DarbyBenjamin L. Makepeace 4Institute of Infection & Global Health, University of Liverpool, L3 5RF, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Benjamin L. MakepeaceFor correspondence: blm1@liv.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy127 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101420 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101421
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy140 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101432 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101429 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101431
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy142 Giulio Formenti 1Department of Environmental Science and Policy, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Giulio FormentiFor correspondence: giulio.formenti@unimi.itMatteo Chiara 2Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matteo ChiaraFor correspondence: matteo.chiara@unimi.itLucy Poveda 3Functional Genomics Center of Zurich, University of Zurich, (Zurich, Switzerland) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucy PovedaFor correspondence: lucy.poveda@fgcz.uzh.chKees-Jan Francoijs 4Bionano Genomics (San Diego, CA, USA) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kees-Jan FrancoijsFor correspondence: kfrancoijs@bionanogenomics.comAndrea Bonisoli-Alquati 5Department of Biological Sciences, California State Polytechnic University, Pomona (Pomona, CA, USA) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrea Bonisoli-AlquatiFor correspondence: kfrancoijs@bionanogenomics.comLuca Canova 6Department of Biochemistry, University of Pavia (Pavia, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca CanovaFor correspondence: canova@unipv.itLuca Gianfranceschi 7Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca GianfranceschiFor correspondence: luca.gianfranceschi@unimi.itDavid Stephen Horner 8Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David Stephen HornerFor correspondence: david.horner@unimi.itNicola Saino 9Department of Environmental Science and Policy, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicola SainoFor correspondence: nicola.saino@unimi.it
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy142 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101444 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101445
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy137 Y. A. Tsepilov 1Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteS. Zh. Sharapov 1Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia2Novosibirsk State University, 630090 Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteO. O. Zaytseva 1Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia2Novosibirsk State University, 630090 Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJ. Krumsek 3Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteC. Prehn 4Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJ. Adamski 4Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.5Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany6German Center for Diabetes Research, 85764 Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteG. Kastenmüller 7Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteR. Wang-Sattler 6German Center for Diabetes Research, 85764 Neuherberg, Germany8Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany9Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteK. Strauch 10Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany11Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 80539, Munich, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteC. Gieger 6German Center for Diabetes Research, 85764 Neuherberg, Germany8Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany9Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteY. S. Aulchenko 1Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia2Novosibirsk State University, 630090 Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: yurii@bionet.nsc.ru
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy137 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101442 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101443
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy147 Angelica da Silva Lantyer Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNiccolò Calcini Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAte Bijlsma Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKoen Kole Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMelanie Emmelkamp Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteManon Peeters Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWim J. J. Scheenen Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFleur Zeldenrust Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTansu Celikel Department of Neurophysiology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen - the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy147 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101446 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101447 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101448
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy148 Chris-Andre Leimeister 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJendrik Schellhorn 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSvenja Schöbel 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Gerth 2Institute for Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB Liverpool, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristoph Bleidorn 3University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle 2, 37073 Göttingen, Germany4Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), 28006 Madrid, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBurkhard Morgenstern 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, Germany5Göttingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 GöttingenFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy148 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101560 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101561 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101562 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101563 Reviewer 5: http://dx.doi.org/10.5524/REVIEW.101564
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy149 Kristian Peters 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kristian PetersJames Bradbury 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSven Bergmann 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarco Capuccini 5Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarta Cascante 7Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marta CascantePedro de Atauri 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pedro de AtauriTimothy M D Ebbels 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarles Foguet 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Carles FoguetRobert Glen 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom10Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlejandra Gonzalez-Beltran 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra Gonzalez-BeltranUlrich Guenther 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEvangelos Handakas 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas Hankemeier 12Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands13Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for DrugFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas HankemeierKenneth Haug 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kenneth HaugStephanie Herman 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephanie HermanPetr Holub 29BBMRI-ERIC, Graz, AustriaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Petr HolubMassimiliano Izzo 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Massimiliano IzzoDaniel Jacob 16INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d’Ornon, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Johnson 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David JohnsonFabien Jourdan 17INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNamrata Kale 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Namrata KaleIbrahim Karaman 18Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary’s Campus, Norfolk Place, W2 1PG, London, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ibrahim KaramanBita Khalili 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePayam Emami Khonsari 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Payam Emami KhonsariKim Kultima 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kim KultimaSamuel Lampa 6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel LampaAnders Larsson 19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anders LarssonChristian Ludwig 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePablo Moreno 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pablo MorenoSteffen Neumann 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany20German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Steffen NeumannJon Ander Novella 19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteClaire O’Donovan 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Claire O’DonovanJake TM Pearce 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jake TM PearceAlina Peluso 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alina PelusoLuca Pireddu 21Distributed Computing Group, CRS4, Pula, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca PiredduMichelle AC Reed 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michelle AC ReedPhilippe Rocca-Serra 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPierrick Roger 23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAntonio Rosato 24Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Antonio RosatoRico Rueedi 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Rico RueediChristoph Ruttkies 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christoph RuttkiesNoureddin Sadawi 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Noureddin SadawiReza M Salek 25European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, U.KFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Reza M SalekSusanna-Assunta Sansone 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneVitaly Selivanov 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Vitaly SelivanovOla Spjuth 6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ola SpjuthDaniel Schober 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Daniel SchoberEtienne A. Thévenot 23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Etienne A. ThévenotMattia Tomasoni 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMerlijn van Rijswijk 26ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands27Netherlands Metabolomics Center, Leiden, 2333 CC, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merlijn van RijswijkMichael van Vliet 28Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael van VlietMark R Viant 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark R ViantRalf J. M. Weber 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGianluigi Zanetti 21Distributed Computing Group, CRS4, Pula, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gianluigi ZanettiChristoph Steinbeck 30Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christoph Steinbeck
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy149 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101467 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101468
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy136 Fadhl M. Al-Akwaa 2Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Fadhl M. Al-AkwaaSijia Huang 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLana X. Garmire 1University of Hawaii Cancer Center, Department of Epidemiology, 701 Ilalo Street, Honolulu, HI USA 968132Molecular Biology and Bioengineering Graduate Program, University of Hawaii at Monoa, Honolulu, HI, USA 96822Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Lgarmire@cc.hawaii.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy136 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101473 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101474 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101475
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy154 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101574 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101575 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101576 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101579 Reviewer 5: http://dx.doi.org/10.5524/REVIEW.101580
-
-
www.biorxiv.org www.biorxiv.org
-
ABSTRACT
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy131 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101417 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101418
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy158 Lisa K. Johnson 1Department of Population Health & Reproduction, School of Veterinary Medicine, University of California Davis2Molecular, Cellular, and Integrative Physiology Graduate Group, University of California DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lisa K. JohnsonHarriet Alexander 1Department of Population Health & Reproduction, School of Veterinary Medicine, University of California DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harriet AlexanderC. Titus Brown 1Department of Population Health & Reproduction, School of Veterinary Medicine, University of California Davis2Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis3Genome Center, University of California DavisFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for C. Titus Brown
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy158 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101581 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101582 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101583 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101584
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy112 Simon P Sadedin 1Bioinformatics, Murdoch Childrens Research Institute, Royal Children's Hospital Flemington Road, Parkville, Victoria 3052 AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJustine A Ellis 2Genes Environment & Complex Disease, Murdoch Childrens Research Institute, Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052 Australia3Department of Paediatrics, University of Melbourne, Victoria 3010 Australia4Centre for Social and Early Emotional Development, Faculty of Health, Deakin University, Burwood, Victoria 3125 AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Justine A EllisSeth L Masters 5Inflamation Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlicia Oshlack 1Bioinformatics, Murdoch Childrens Research Institute, Royal Children's Hospital Flemington Road, Parkville, Victoria 3052 Australia6Department of BioScience, University of Melbourne, Parkville 3050, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy112 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101340 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101341 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101342 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101343 Reviewer 5: http://dx.doi.org/10.5524/REVIEW.101345
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy117 Zhouchun Shang 1Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, China4Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDongsheng Chen 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQuanlei Wang 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, China4Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen, China5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShengpeng Wang 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQiuting Deng 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLiang Wu 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, China5BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China6Shenzhen Key Laboratory of Neurogenomics, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiangning Ding 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShiyou Wang 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJixing Zhong 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDoudou Zhang 7Department of Neurosurgery, Shenzhen Second People’s Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaodong Cai 7Department of Neurosurgery, Shenzhen Second People’s Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen, Guangdong, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShida Zhu 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, China4Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 2BGI-Shenzhen, Shenzhen, China8James D. Watson Institute of Genome Sciences, Hangzhou, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLongqi Liu 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJ. Lynn Fink 2BGI-Shenzhen, Shenzhen, China9The University of Queensland, Diamantina Institute (UQDI), Brisbane, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFang Chen 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, China10Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaoqing Liu 1Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhengliang Gao 1Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: xuxun@genomics.cnXun Xu 2BGI-Shenzhen, Shenzhen, China3China National GeneBank, BGI-Shenzhen, Shenzhen, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: xuxun@genomics.cn
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy117 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101371 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101372
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy103 Matthew Jacobson 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdriana Estela Sedeño-Cortés 3Graduate Program in Bioinformatics, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul Pavlidis 1Michael Smith Laboratories, University of British Columbia2Department of Psychiatry, University of British ColumbiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paul PavlidisFor correspondence: paul@msl.ubc.ca
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy103 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101302 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101303
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy126 Jakub Pospíšil 1Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 16627 Prague 6, Czech RepublicFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTomáš Lukeš 1Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 16627 Prague 6, Czech Republic2Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJustin Bendesky 3UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKarel Fliegel 1Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 16627 Prague 6, Czech RepublicFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKathrin Spendier 3UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USA4Department of Physics and Energy Science, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGuy M. Hagen 3UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guy M. Hagen
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy126 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101401 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101402
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy090 Jie Zheng 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: jie.zheng@bristol.ac.uk tom.gaunt@bristol.ac.ukTom G. Richardson 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLouise A. C. Millard 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;2Intelligent Systems Laboratory, University of Bristol, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGibran Hemani 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristopher Raistrick Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBjarni Vilhjalmsson 3Århus Center for Bioinformatics BIRC, Aarhus UniversityFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePhilip Haycock 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTom R Gaunt 1MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: jie.zheng@bristol.ac.uk tom.gaunt@bristol.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy090 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101321 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101322
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy096 Sung-Huan Yu 1Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sung-Huan YuJörg Vogel 1Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jörg VogelKonrad U. Förstner 1Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany2Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Konrad U. FörstnerFor correspondence: konrad.foerstner@uni-wuerzburg.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy096 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101337 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101338 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101339
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy079 Breon M Schmidt 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNadia M Davidson 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnthony DK Hawkins 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRay Bartolo 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIan J Majewski 2Walter and Eliza Hall Institute of Medical Research, Royal Parade, Vic 3050, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePaul G Ekert 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlicia Oshlack 1Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Vic, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia Oshlack
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy079 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101243 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101244 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101245
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy081 Li Charlie Xia 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 943052Department of Statistics, the Wharton School, University of Pennsylvania, Philadelphia, PA 18014Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Li Charlie XiaDongmei Ai 3School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083 P. R. ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHojoon Lee 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNoemi Andor 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteChao Li 3School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083 P. R. ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNancy R. Zhang 2Department of Statistics, the Wharton School, University of Pennsylvania, Philadelphia, PA 18014Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHanlee P. Ji 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 943054Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: genomics_ji@stanford.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy081 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101246 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101247 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101248
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy083 Luke Zappia 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luke ZappiaAlicia Oshlack 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia Oshlack
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy083 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101258 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101259 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101260
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy086 Jang-il Sohn 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea2Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKyoungwoo Nam 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHyosun Hong 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJun-Mo Kim 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDajeong Lim 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKyung-Tai Lee 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYoon Jung Do 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChang Yeon Cho 4Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon 55717, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNamshin Kim 5Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHan-Ha Chae 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJin-Wu Nam 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea2Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy086 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101252 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101253
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy093 Luca Venturini 1Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca VenturiniShabhonam Caim 1Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, United Kingdom2Institute of Food Research, Norwich Research Park, NR4 7UA Norwich, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Shabhonam CaimGemy G Kaithakottil 1Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gemy G KaithakottilDaniel L Mapleson 1Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Daniel L MaplesonDavid Swarbreck 1Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David SwarbreckFor correspondence: david.swarbreck@earlham.ac.uk
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy093 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101278 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101279
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy092 Pai Zhang Institute of Technology, University of Washington, Tacoma, Washington 98402, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLing-Hong Hung Institute of Technology, University of Washington, Tacoma, Washington 98402, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWes Lloyd Institute of Technology, University of Washington, Tacoma, Washington 98402, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKa Yee Yeung Institute of Technology, University of Washington, Tacoma, Washington 98402, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy092 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101280 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101281 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101282
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy069 Fernando Meyer 1Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany2Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePeter Hofmann 1Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany2Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePeter Belmann 1Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany2Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany3Faculty of Technology, Bielefeld University, Bielefeld, Germany4Center for Biotechnology, Bielefeld University, Bielefeld, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRuben Garrido-Oter 5Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany6Cluster of Excellence on Plant Sciences (CEPLAS)Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdrian Fritz 1Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany2Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexander Sczyrba 3Faculty of Technology, Bielefeld University, Bielefeld, Germany4Center for Biotechnology, Bielefeld University, Bielefeld, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlice C. McHardy 1Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany2Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Alice.McHardy@helmholtz-hzi.de
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy069 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101202 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101203
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy070 LM Simon 1Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for LM SimonAJ Westermann 2Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany3Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM Engel 1Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany4Helmholtz Zentrum München, German Research Center for Environmental Health, Scientific Computing Research Unit, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAHA Elbehery 5Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteB Hense 1Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM Heinig 1Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for M HeinigL Deng 5Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFJ Theis 1Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany6Department of Mathematics, Technische Universität München, Munich, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for FJ Theis
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy070 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101204 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101205
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy072 Alessia Visconti 1Department of Twin Research and Genetic Epidemiology, King’s College LondonFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alessia ViscontiFor correspondence: alessia.visconti@kcl.ac.ukTiphaine C. Martin 1Department of Twin Research and Genetic Epidemiology, King’s College LondonFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMario Falchi 1Department of Twin Research and Genetic Epidemiology, King’s College LondonFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy072 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101208 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101209
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy073 Carlos A. Manacorda 1Instituto de Biotecnología, CICVyA, INTA, ArgentinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSebastian Asurmendi 1Instituto de Biotecnología, CICVyA, INTA, Argentina2CONICET, ArgentinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy073 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101211 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101212 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101213
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy077 Yang-Min Kim 1Institut Pasteur, Human Genetics and Cognitive Functions Unit, Paris, France,2CNRS UMR 3571 Genes, Synapses and Cognition, Institut Pasteur, Paris, France,3University Paris Diderot, Sorbonne Paris Cité, Paris, France,4Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur and CNRS), Paris, France,Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yang-Min KimJean-Baptiste Poline 5Henry H. Wheeler Jr. Brain Imaging Center, Helen Wills Neuroscience Institute, University of California, Berkeley, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jean-Baptiste PolineGuillaume Dumas 1Institut Pasteur, Human Genetics and Cognitive Functions Unit, Paris, France,2CNRS UMR 3571 Genes, Synapses and Cognition, Institut Pasteur, Paris, France,3University Paris Diderot, Sorbonne Paris Cité, Paris, France,4Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur and CNRS), Paris, France,Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Guillaume Dumas
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy077 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101237 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101238
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy045 Nadia M Davidson 1Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia2School of Bio-Sciences, University of Melbourne, Victoria, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: nadia.davidson@mcri.edu.au alicia.oshlack@mcri.edu.auAlicia Oshlack 1Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia2School of Bio-Sciences, University of Melbourne, Victoria, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia OshlackFor correspondence: nadia.davidson@mcri.edu.au alicia.oshlack@mcri.edu.au
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy045 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101125
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy048 Alex Di Genova 1Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Iba´n˜ez, Santiago, Chile.2Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.3Inria Grenoble Rhonˆe-Alpes, 655, Avenue de l’Europe, 38334 Montbonnot, France.4CNRS, UMR5558, Universite´ Claude Bernard Lyon 1, 43, Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France.5Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGonzalo A. Ruz 1Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Iba´n˜ez, Santiago, Chile.6Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarie-France Sagot 3Inria Grenoble Rhonˆe-Alpes, 655, Avenue de l’Europe, 38334 Montbonnot, France.4CNRS, UMR5558, Universite´ Claude Bernard Lyon 1, 43, Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: marie-france.sagot@inria.fr amaass@dim.uchile.clAlejandro Maass 2Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.5Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.7Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: marie-france.sagot@inria.fr amaass@dim.uchile.cl
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy048 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101129 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101130
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy053 Fu-Hao Lu 1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteNeil McKenzie 1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorge Kettleborough 2The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDarren Heavens 2The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatthew D. Clark 2The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael W. Bevan 1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael W. Bevan
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy053 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101147 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101148
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy057 Bérénice Batut 1Bioinformatics Group, Department of Computer Science, University of Freiburg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Bérénice BatutFor correspondence: berenice.batut@gmail.com pierre.peyret@uca.frKévin Gravouil 2Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France3Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France4Université Clermont Auvergne, CNRS, LIMOS, F-63000 Clermont-Ferrand, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kévin GravouilClémence Defois 2Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSaskia Hiltemann 5Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3015 CE, NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Saskia HiltemannJean-François Brugère 2Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEric Peyretaillade 2Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePierre Peyret 2Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: berenice.batut@gmail.com pierre.peyret@uca.fr
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy057 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101163 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101164 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101165
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy061 Kingshuk Mukherjee 1Department of Computer and Information Science and Engineering, University of Florida, GainesvilleFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: kingdgp@ufl.eduDarshan Washimkar 2Department of Computer Science, Colorado State University, Fort CollinsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMartin D. Muggli 2Department of Computer Science, Colorado State University, Fort CollinsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLeena Salmela 3Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of HelsinkiFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristina Boucher 1Department of Computer and Information Science and Engineering, University of Florida, GainesvilleFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy061 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101178 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101179 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101180
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy059 Swati Parekh 1Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Martinsried, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Swati ParekhChristoph Ziegenhain 1Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Martinsried, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christoph ZiegenhainBeate Vieth 1Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Martinsried, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Beate ViethWolfgang Enard 1Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Martinsried, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteInes Hellmann 1Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Martinsried, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ines Hellmann
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy059 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101183 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101184
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy064 Jonathan R. Belyeu 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan R. BelyeuThomas J. Nicholas 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas J. NicholasBrent S. Pedersen 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brent S. PedersenThomas A. Sasani 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas A. SasaniJames M. Havrilla 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephanie N. Kravitz 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephanie N. KravitzMegan E. Conway 1Department of Human Genetics, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBrian K. Lohman 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brian K. LohmanAaron R. Quinlan 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT3Department of Biomedical Informatics, University of Utah, Salt Lake City, UT+To whom correspondence should be addressedFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Aaron R. QuinlanRyan M. Layer 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT+To whom correspondence should be addressedFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ryan M. Layer
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy064 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101187 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101188
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy034 Florence McLean 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Florence McLeanDuncan Berger 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Duncan BergerDominik R. Laetsch 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Dominik R. LaetschHillel T. Schwartz 2Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hillel T. SchwartzMark Blaxter 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark Blaxter
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy034 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101075 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101076
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy033 Aaron Pomerantz 1Department of Integrative Biology, University of California, Berkeley, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Pomerantz_aaron@berkeley.edu stprost@stanford.eduNicolás Peñafiel 2Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLucas Bustamante 3Tropical Herping, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFrank Pichardo 3Tropical Herping, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuis A. Coloma 4Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Otonga, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCésar L. Barrio-Amorós 5Doc Frog Expeditions, Uvita, Costa RicaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Salazar-Valenzuela 2Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStefan Prost 1Department of Integrative Biology, University of California, Berkeley, CA, USA6Program for Conservation Genomics, Department of Biology, Stanford University, Stanford, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Pomerantz_aaron@berkeley.edu stprost@stanford.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101071 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101072
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy037 Haotian Teng 1Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: haotian.teng@uq.net.au l.coin@imb.uq.edu.auMinh Duc Cao 1Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Minh Duc CaoMichael B. Hall 1Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael B. HallTania Duarte 1Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Tania DuarteSheng Wang 2Department of Human Genetics, University of Chicago, IL 60637, United States Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLachlan J.M. Coin 1Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lachlan J.M. CoinFor correspondence: haotian.teng@uq.net.au l.coin@imb.uq.edu.au
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy037 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101102 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101103 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101104
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy015 Harry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeSion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Edward J. Feil
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy015 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101033 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101034
-
-
www.biorxiv.org www.biorxiv.org
-
Abstract
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy025 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101059 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101060
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy004 C Foulon aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.cCentre de Neuroimagerie de Recherche CENIR, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for C FoulonFor correspondence: hd.chrisfoulon@gmail.com michel.thiebaut@gmail.comL Cerliani aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.cCentre de Neuroimagerie de Recherche CENIR, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteS Kinkingnéhun aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteR Levy bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteC Rosso cCentre de Neuroimagerie de Recherche CENIR, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.dAbnormal Movements and Basal Ganglia team, Inserm U 1127, CNRS UMR 7225, Sorbonne Universities, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épinière, ICM, Paris, FranceeAPHP, Urgences Cérébro-Vasculaires, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteM Urbanski aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.fMedicine and Rehabilitation Department, Hôpitaux de Saint-Maurice, Saint-Maurice, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteE Volle aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.cCentre de Neuroimagerie de Recherche CENIR, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteM Thiebaut de Schotten aBrain Connectivity and Behaviour Group, Sorbonne Universities, Paris France.bFrontlab, Institut du Cerveau et de la Moelle épinière (ICM), UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France.cCentre de Neuroimagerie de Recherche CENIR, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: hd.chrisfoulon@gmail.com michel.thiebaut@gmail.com
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy004 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101000 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101001
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/giy009 Rachael E. Workman 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexander M. Myrka 2Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Tseng 4Pacific Biosciences, Menlo Park, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteG. William Wong 3Department of Physiology and Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKenneth C. Welch Jr.2Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kenneth C. Welch Jr.Winston Timp 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Winston Timp
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy009 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101011 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101012
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix136 Quan H. Nguyen 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, Australia2Divisions of Genomics of Development and Disease, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Quan H. NguyenRoss L. Tellam 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ross L. TellamMarina Naval-Sanchez 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marina Naval-SanchezLaercio R. Porto-Neto 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Laercio R. Porto-NetoWilliam Barendse 3School of Veterinary Science, University of Queensland, Gatton, 4343, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for William BarendseAntonio Reverter 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBenjamin Hayes 4The Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames Kijas 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for James KijasBrian P. Dalrymple 1CSIRO Agriculture, 306 Carmody Road, St. Lucia, 4067, QLD, Australia5Institute of Agriculture, The University of Western Australia, Perth, Western Australia, 6009, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brian P. DalrympleFor correspondence: brian.dalrymple@uwa.edu.au
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix136 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101018 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101019
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix135 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100980 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100979
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy002 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100989 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100988
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix107 Joshua Lynch 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKaren Tang 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSambhawa Priya 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJoanna Sands 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMargaret Sands 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEvan Tang 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDan Knights 4Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA5Biotechnology Institute, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: blekhman@umn.edu dknights@umn.eduRan Blekhman 1Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA2Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: blekhman@umn.edu dknights@umn.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix107 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100893
-
-
www.biorxiv.org www.biorxiv.org
-
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix102 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100883 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100884
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix117 Zhikai Liang 1Center for Plant Science Innovation, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zhikai LiangPiyush Pandey 2Department of Biological System Engineering, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVincent Stoerger 3Plant Phenotyping Facilities Manager, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYuhang Xu 4Department of Statistics, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYumou Qiu 4Department of Statistics, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYufeng Ge 2Department of Biological System Engineering, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames C. Schnable 1Center for Plant Science Innovation, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68503, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for James C. Schnable
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix117 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100930
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix134 Robert Bukowski 1Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteXiaosen Guo 2BGI-Shenzhen, Shenzhen 518083, China3Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, DenmarkFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYanli Lu 4Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCheng Zou 5Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facilities for Crop Gene Resource and Genetic Improvement, Beijing 100081, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBing He 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhengqin Rong 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBo Wang 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDawen Xu 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBicheng Yang 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChuanxiao Xie 5Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facilities for Crop Gene Resource and Genetic Improvement, Beijing 100081, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLongjiang Fan 6Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou 310058, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteShibin Gao 4Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXun Xu 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGengyun Zhang 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYingrui Li 2BGI-Shenzhen, Shenzhen 518083, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYinping Jiao 7Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJohn Doebley 8Department of Genetics, University of Wisconsin, Madison, Wisconsin, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJeffrey Ross-Ibarra 9Department of Plant Sciences, University of California, Davis, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVince Buffalo 9Department of Plant Sciences, University of California, Davis, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteM. Cinta Romay 10Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteEdward S. Buckler 10Institute for Genomic Diversity, Cornell University, Ithaca, NY 1485311US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteYunbi Xu 5Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facilities for Crop Gene Resource and Genetic Improvement, Beijing 100081, China12International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, MexicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDoreen Ware 7Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQi Sun 1Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853Find this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix134 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100974 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100975
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix096 Valerie De Anda 1Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510 México D.F.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Valerie De AndaFor correspondence: valdeanda@ciencias.unam.mx bcontreras@eead.csic.es souza@unam.mxIcoquih Zapata-Peñasco 2Dirección de Investigación en Transformación de Hidrocarburos. Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas, Norte 152, Col. San Bartolo Atepehuacan, 07730, MéxicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAugusto Cesar Poot-Hernandez 3Departamento de Ingeniería de Sistemas Computacionales y Automatización. Sección de Ingeniería de Sistemas Computacionales. Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuis E. Eguiarte 1Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510 México D.F.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteBruno Contreras-Moreira 4Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana, 1005, Zaragoza 50059, Spain5Fundación ARAID, calle María de Luna 11, 50018 Zaragoza, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: valdeanda@ciencias.unam.mx bcontreras@eead.csic.es souza@unam.mxValeria Souza 1Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 70-275, Coyoacán 04510 México D.F.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: valdeanda@ciencias.unam.mx bcontreras@eead.csic.es souza@unam.mx
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix096 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100872 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100873
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix097 Aleksey V. Zimin 1Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD2Institute for Physical Sciences and Technology, University of Maryland, College Park, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDaniela Puiu 1Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRichard Hall 3Pacific Biosciences, Menlo Park, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSarah Kingan 3Pacific Biosciences, Menlo Park, CAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven L. Salzberg 1Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD5Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MDFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Steven L. SalzbergFor correspondence: salzberg@jhu.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix097 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100877 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100879 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.100878 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.100880
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix090 Brent S. Pedersen 1Department of Human Genetics, University of Utah, Salt Lake City, UT3USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRyan L. Collins 4Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA6Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA7Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael E. Talkowski 4Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA5Department of Neurology, Harvard Medical School, Boston, MA6Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA7Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAaron R. Quinlan 1Department of Human Genetics, University of Utah, Salt Lake City, UT2Department of Biomedical Informatics, University of Utah, Salt Lake City, UT3USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this site
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix090 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100844 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100845
-
-
www.biorxiv.org www.biorxiv.org
-
Now published in GigaScience doi: 10.1093/gigascience/gix056 Gregory D. Marquart , Bethesda, MD 20892Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteKathryn M. Tabor , Bethesda, MD 20892Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMary Brown , Bethesda, MD 20892Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteHarold A. Burgess , Bethesda, MD 20892Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harold A. Burgess
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/gix056 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100800
-