- May 2024
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we can then shift to a better way of doing it and we knew what that was before genome sequencing
for - quote - better approach than gene sequence as universal panecea
quote - better approach than gene sequence as universal panecea - (see quote below)
- Look at the high-level organization of the system
- the living system
- Locate what is going wrong there and then work down to find what you might do
- at lower levels with a drug or any other kind of treatment for that matter to put it right
- That works much better than trying to go the other way because
- going the other way, the space for
- possible molecules and
- possible effects and
- even more possible combinations of effects
- because those complex diseases are going to require combinations of treatment
- There are too many
- You can't do clinical trials on all of those possibilities
- It's just far too expensive
- So I think we just take need to take a different
approach to medical research
- to try to benefit from the human genome sequencing
- in a way that's different from what they originally promised
- going the other way, the space for
- Look at the high-level organization of the system
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- Jan 2024
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6c CAACGCGARGAACCTTACC 966–984
967F primer
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URL
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- Oct 2023
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journals.plos.org journals.plos.org
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Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.
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- Jun 2023
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academic.oup.com academic.oup.com
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There has been an ongoing debate on whether rarefaction is a statistically defensible procedure.
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- Mar 2023
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www.frontiersin.org www.frontiersin.org
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Detailed descriptions, assumptions, limitations and test cases of many popular statistical methods for ecological research can be found in the GUSTAME server (Buttigieg and Ramette, 2014), and in the review by Paliy and Shankar (2016).
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- Nov 2022
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www.frontiersin.org www.frontiersin.org
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The advantages of using SSU rRNA for community fingerprinting are many: (i) This gene is found in all cellular life forms. (ii) It is a highly conserved gene, serving to a large degree as a reliable molecular chronometer. (iii) It is seldom transferred horizontally. (iv) It possesses both conserved and variable regions, so that the conserved regions can be targeted by polymerase chain reaction (PCR) primers and the variable ones be used as identifying markers. A handful of other genes, such as the large subunit (LSU) rRNA share these properties, but the length of ~1,500 bp of the bacterial SSU rRNA made it amenable to early molecular techniques, and the impressive body of knowledge that has since accumulated on the basis of this gene makes a switch to other markers very impractical, except in certain sub-fields such as mycology, where ITS and LSU are widely used.
very crisp summary
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- Oct 2022
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www.drive5.com www.drive5.comChimeras1
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the majority of chimeras are believed to arise from incomplete extension. During subsequent cycles of PCR, a partially extended strand can bind to a template derived from a different but similar sequence. This then acts as a primer that is extended to form a chimeric sequence
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- Aug 2022
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www.uml-diagrams.org www.uml-diagrams.org
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The interaction operator strict requires a strict sequencing (order) of the operands on the first level within the combined fragment
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The interaction operator seq means that the combined fragment represents a weak sequencing between the behaviors of the operands.
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Weak sequencing reduces to a parallel merge when the operands are on different sets of participants. Weak sequencing reduces to strict sequencing when the operands work on the same participant.
weak sequencing - reduces to: - or: - parallel (simultaneous) - strict sequencing
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Varmus, H. (2021, August 31). Covid has revealed the need for genomic sequencing around the world. Financial Times. https://www.ft.com/content/342fd3c3-5a22-49a0-9cef-135f2ccd8700
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twitter.com twitter.com
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ReconfigBehSci. (2021, November 26). RT @PeterHotez: …this info is more relevant than immune escape. For instance the B.1.351 from ZA last year never really took off. So transm… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464240155070447632
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- May 2022
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artic.network artic.network
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For background information on how tiling amplicon sequencing works, please prefer to the original “PrimalSeq” protocol paper as tested on Zika Quick et al. Nature Protocols and a follow-up paper Grubaugh, Gangavaparu et al. Genome Biology that focuses on in-host variation and Illumina sequencing.
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- Jan 2022
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www.theguardian.com www.theguardian.com
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Davis, N., & correspondent, N. D. S. (2022, January 21). Covid reinfection: How likely are you to catch virus multiple times? The Guardian. https://www.theguardian.com/world/2022/jan/21/covid-reinfection-how-likely-are-you-to-catch-virus-multiple-times
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- Dec 2021
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twitter.com twitter.com
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Eric Topol. (2021, November 27). View of key mutations of Omicron’s 50, with 30 in the spike protein, 15 in its receptor binding domain https://ft.com/content/42c5ff3d-e676-4076-9b9f-7243a00cba5e http://covariants.org @EllingUlrich @_b_meyer https://t.co/onMoNFVLFJ [Tweet]. @EricTopol. https://twitter.com/EricTopol/status/1464452102382448643
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Maxmen, A. (2021). Omicron blindspots: Why it’s hard to track coronavirus variants. Nature. https://doi.org/10.1038/d41586-021-03698-7
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- Nov 2021
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www.nature.com www.nature.com
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Cauchemez, S., & Bosetti, P. (2021). A reconstruction of early cryptic COVID spread. Nature. https://doi.org/10.1038/d41586-021-02989-3
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- Sep 2021
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www.businessinsider.com www.businessinsider.com
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COVID-19 Patients Not Allowed to Know Which Variant Infected Them. (n.d.). Retrieved September 7, 2021, from https://www.businessinsider.com/covid-patients-cant-know-which-variant-infected-them-delta-2021-8?r=US&IR=T
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- May 2021
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Mallapaty, S. (2021). India’s neighbours race to sequence genomes as COVID surges. Nature, 593(7860), 485–486. https://doi.org/10.1038/d41586-021-01287-2
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www.thelancet.com www.thelancet.com
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Morgan, O. W., Aguilera, X., Ammon, A., Amuasi, J., Fall, I. S., Frieden, T., Heymann, D., Ihekweazu, C., Jeong, E., Leung, G. M., Mahon, B., Nkengasong, J., Qamar, F. N., Schuchat, A., Wieler, L. H., & Dowell, S. F. (2021). Disease surveillance for the COVID-19 era: Time for bold changes. The Lancet, 0(0). https://doi.org/10.1016/S0140-6736(21)01096-5
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- Aug 2020
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Xu, G., Qi, F., Li, H., Yang, Q., Wang, H., Wang, X., Liu, X., Zhao, J., Liao, X., Liu, Y., Amit, I., Liu, L., Zhang, S., & Zhang, Z. (2020). The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. MedRxiv, 2020.08.15.20175638. https://doi.org/10.1101/2020.08.15.20175638
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www.biorxiv.org www.biorxiv.org
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Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510
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www.sciencedirect.com www.sciencedirect.com
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Xu, G., Qi, F., Li, H., Yang, Q., Wang, H., Wang, X., Liu, X., Zhao, J., Liao, X., Liu, Y., Amit, I., Liu, L., Zhang, S., & Zhang, Z. (2020). The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. MedRxiv, 2020.08.15.20175638. https://doi.org/10.1101/2020.08.15.20175638
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www.medrxiv.org www.medrxiv.org
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Addetia, A., Crawford, K. H., Dingens, A., Zhu, H., Roychoudhury, P., Huang, M., Jerome, K. R., Bloom, J. D., & Greninger, A. (2020). Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. MedRxiv, 2020.08.13.20173161. https://doi.org/10.1101/2020.08.13.20173161
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- Jul 2020
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www.nationalgeographic.com www.nationalgeographic.com
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How coronavirus mutations can track its spread—And disprove conspiracies. (2020, March 26). Science. https://www.nationalgeographic.com/science/2020/03/how-coronavirus-mutations-can-track-its-spread-and-disprove-conspiracies/
Tags
- lang:en
- sequencing
- genetics
- genome
- mutation
- research
- tracking
- COVID-19
- is:preprint
- conspiracy theory
- misinformation
- origin
- transmission
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www.thelancet.com www.thelancet.com
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Behrmann, Ole, and Martin Spiegel. ‘COVID-19: From Rapid Genome Sequencing to Fast Decisions’. The Lancet Infectious Diseases 0, no. 0 (14 July 2020). https://doi.org/10.1016/S1473-3099(20)30580-6.
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- Jun 2020
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www.nature.com www.nature.com
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Hiatt, J., Patwardhan, R., Turner, E. et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7, 119–122 (2010). https://doi.org/10.1038/nmeth.1416
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- May 2020
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www.theatlantic.com www.theatlantic.com
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Varmus, H. (2020, May 9). The World Doesn’t Yet Know Enough to Beat the Coronavirus. The Atlantic. https://www.theatlantic.com/ideas/archive/2020/05/lack-testing-holding-science-back/611422/
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Pinto, S. F., & Ferreira, R. S. (2020). Analyzing course programmes using complex networks. ArXiv:2005.00906 [Physics]. http://arxiv.org/abs/2005.00906
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- Jan 2020
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OCTOPUS, a light-weight, cost-effective, and robust method for full-plasmid sequence verification using next-generation sequencing
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- Mar 2018
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Improved Protocols for Illumina Sequencing
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www.nature.com www.nature.com
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Modified hybridization buffers.
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- Nov 2017
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images.nature.com images.nature.com
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Comparison of SNVs detected in the whole genome sequencing data with SNPs genotyped using arrays
inference of "%diploid coverage"
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