37 Matching Annotations
  1. Apr 2021
    1. This study describes the serendipitous discovery of Rickettsia amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mitochondrial DNA barcodes.

      Find out more in this GigaBlog posting on the project http://gigasciencejournal.com/blog/rickettsia-bacteria-to-rule-them-all/

  2. Apr 2020
    1. progression of respiratory diseases

      Including COVID-19, as it is estimated 50% of patients with COVID-19 who have died had secondary bacterial infections. Watch the COSMIC project looking at metagenomics of respiratory samples to identify the bacteria, fungi, and viral co-infections present in patients with COVID-19 https://www.covid-coinfections.org/t/cosmic-co-infections-and-secondary-microbial-infections-in-covid-19/17

    1. Supplemental File 1: Extended Chinese language (中文版) version on the editorial.

      See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

    2. A version of the editorial translated into Chinese is included as a Supplementary File

      See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html

    3. Here, we help clarify this and also provide a clear statement of our expectations around how authors are assigned to manuscripts submitted to GigaScience.

      A more detailed version of this clarification and background is available via our blog: http://gigasciencejournal.com/blog/appropriate-authorship/

    4. Laurie Goodman

      ‡ Senior author

  3. Mar 2020
    1. which is the basis of our planned second release (PLINK 2.0).

      See the homepage for updates taking it towards PLINO 2.0 alpha https://www.cog-genomics.org/plink/2.0/

      We also have phased and annotated data for use in plink2.0 worked examples in GigaDB http://dx.doi.org/10.5524/100516

    1. This must be achieved by sequencing and archiving huge numbers of microbial genomes, both from clinical cases and known environmental reservoirs, on a continual basis.

      Even without reference genomes, mining metagenomes for coronavirus sequences has become particularly topical in 2020. See the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660

    2. swine flu

      Jennifer Gardy discusses the groundbreaking H1N1 crowdsourcing efforts in her TEDx talk here (with lots of lessons for the coronavirus outbreak a decade later) https://www.youtube.com/watch?v=LmAugMSJ1-Y

    3. Escherichia coli O104: H4

      See more in GigaBlog about the novel "tweenome" method of datasharing for this project http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/

    1. MERS coronavirus

      Mining metagenomes for coronavirus sequences has become particularly topical in 2020 (see the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660)

    2. RNA viruses

      As this works with RNA viruses it has been made part of the "Free access to OUP resources on coronavirus and related topics" collection on the Oxford University Press website https://academic.oup.com/journals/pages/coronavirus

    1. direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date.

      This approach of using Oxford Nanopore direct-RNA sequencing for viruses has now been carried out on the SARSCov2/COVID19 causing coronavirus. See https://doi.org/10.1101/2020.03.05.976167

  4. Jan 2020
    1. This article argues that it is high time not only to acknowledge Wikipedia's quality but also to start actively promoting its use and development in academia.

      This argment is carried on in the Wikipedia Weekly facebook forum https://www.facebook.com/groups/wikipediaweekly/permalink/2538506099530539/

    2. Linus's Law: “given enough eyeballs, all bugs are shallow,”

      See The Cathedral and the Bazaar by Eric Steven Raymond which first named this in honour of Linux creator Linus Torvalds http://www.catb.org/~esr/writings/cathedral-bazaar/cathedral-bazaar/

    3. initiatives in computational biology

      See also the ISCB wikipedia competition that incentivizes (via a cash award) wikipedia entries on computational biology topics. See https://www.iscb.org/iscb-wikipedia-wikidata-competition and https://www.iscb.org/iscb-wikipedia-wikidata-competition

  5. Dec 2019
  6. Nov 2019
    1. nly 37 butterfly species in 6 families including 5 swallowtails (Papilionidae) have had their reference genomes dissected

      In July 2019 whole genome data for more than 160 representatives of skipper butterflies was published, although these were not de novo genome assemblies https://doi.org/10.3897/zookeys.861.34686

  7. Oct 2019