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  1. Last 7 days
  2. 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. 3.Li Z, Barker MS. Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: Access to gene family phylogenies and age distributions. bioRxiv. 2019:735076. https://www.biorxiv.org/content/10.1101/735076v1.

      A peer reviewed and updated version of this has now been published in GigaScience https://doi.org/10.1093/gigascience/giaa004

    2. chlorophyte green algae

      Some of the authors have recorded a podcast discussing the implications for algae research from this data https://podcasts.apple.com/us/podcast/gane-ka-shu-wong-michael-melkonian-on-if-algae-can/id1420197433?i=1000458893924

    1. hypothes.is (use the hashtag/tag #chromosomenomenclature)

      Please add comments directly on the key parts of the commentary you would like to raise any issues with.

    1. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.

      Using hypothes.is this information can also be updated via annotations here. e.g. adding mention of Twist biosciences, whose Oligo pools are utilized in many CRISPR applications including generation of CRISPR guide RNA (sgRNA) libraries. See https://www.twistbioscience.com/products/oligopools

    2. Table S1. Online tools for TALEN and CRISPR/Cas9. Collected online tools for TALEN and CRISPR/Cas9 are presented in this table. Updates can be accessed in GitHub [107]. Table S2. Commercial service for TALEN and CRISPR/Cas9. Collected commercial service for TALEN and CRISPR/Cas9 are presented in this table. Updates could can accessed in GitHub [107]. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.

      Given that new methods, kits, and services continue to be rapidly developed and updated, an editable version we set up on Github wiki, and readers encourage to update it. See https://github.com/gigascience/paper-chen2014/wiki

    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

  3. Feb 2020
  4. Oct 2019
    1. African eggplant

      Also know as the scarlet eggplant or bitter tomato.

    2. “orphan crop”

      The African eggplant is a good example of the work of the Africa Orphan Crop consortium and many of the authors are consortium members. You can read more on the first genomes released in GigaBlog here: http://gigasciencejournal.com/blog/democratising-data-aocc/