Genomics

  1. Evolution of Delta variant by non-Spike signature co-appearing mutations: trailblazer of COVID-19 disease outcome

    1. Anindita Banerjee
    2. Anup Mazumder
    3. Jayita Roy
    4. Agniva Majumdar
    5. Ananya Chatterjee
    6. Nidhan K Biswas
    7. Mamta Chawla Sarkar
    8. Arindam Maitra
    9. Shanta Dutta
    10. Saumitra Das

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  2. Characterization of sequence determinants of enhancer function using natural genetic variation

    1. Marty G Yang
    2. Emi Ling
    3. Christopher J Cowley
    4. Michael E Greenberg
    5. Thomas Vierbuchen

    • Curated by eLife

      Evaluation Summary:

      This manuscript describes a useful dataset for those interested in regulatory variation. The large scale of variants surveyed offers the potential to look for dependencies between nearby TF binding events at the same accessible site, and will likely be useful to those interested in dissecting sequence determinants of transcription-factor binding genome-wide.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  3. Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

    1. Yang Liu
    2. Marcello DiStasio
    3. Graham Su
    4. Hiromitsu Asashima
    5. Archibald Enninful
    6. Xiaoyu Qin
    7. Yanxiang Deng
    8. Pino Bordignon
    9. Marco Cassano
    10. Mary Tomayko
    11. Mina Xu
    12. Stephanie Halene
    13. Joseph E. Craft
    14. David Hafler
    15. Rong Fan

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  4. Genetic surveillance of SARS-CoV-2 M pro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

    1. Jonathan T. Lee
    2. Qingyi Yang
    3. Alexey Gribenko
    4. B. Scott Perrin
    5. Yuao Zhu
    6. Rhonda Cardin
    7. Paul A. Liberator
    8. Annaliesa S. Anderson
    9. Li Hao

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  5. Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

    1. Le Xiong
    2. Erik A Tolen
    3. Jinmi Choi
    4. Sergiy Velychko
    5. Livia Caizzi
    6. Taras Velychko
    7. Kenjiro Adachi
    8. Caitlin M MacCarthy
    9. Michael Lidschreiber
    10. Patrick Cramer
    11. Hans R Schöler

    • Curated by eLife

      Evaluation Summary:

      The manuscript by Xiong et al provides high resolution kinetic information on transcriptional events and enhancer activity after loss of Oct4. The authors conclude that Oct4 mainly acts as an activator whereas Sox2 maintains chromatin accessibility. These results are of interest for stem cell biologists and developmental biologists.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  6. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

    1. Derek M. Bickhart
    2. Lisa M. Koch
    3. Timothy P. L. Smith
    4. Heathcliffe Riday
    5. Michael L. Sullivan

    Reviewed by GigaByte

    2 evaluationsAppears in 1 listLatest version Latest activity

  7. A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

    1. André M. Machado
    2. André Gomes-dos-Santos
    3. Miguel M. Fonseca
    4. Rute R. da Fonseca
    5. Ana Veríssimo
    6. Mónica Felício
    7. Ricardo Capela
    8. Nélson Alves
    9. Miguel Santos
    10. Filipe Salvador-Caramelo
    11. Marcos Domingues
    12. Raquel Ruivo
    13. Elsa Froufe
    14. L. Filipe C. Castro

    Reviewed by GigaByte

    1 evaluationAppears in 1 listLatest version Latest activity

  8. Chromosome-level assembly of the common vetch (Vicia sativa) reference genome

    1. Hangwei Xi
    2. Vy Nguyen
    3. Christopher Ward
    4. Zhipeng Liu
    5. Iain R. Searle

    Reviewed by GigaByte

    2 evaluationsAppears in 1 listLatest version Latest activity

  9. A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

    1. Emma Peel
    2. Luke Silver
    3. Parice Brandies
    4. Carolyn J. Hogg
    5. Katherine Belov

    Reviewed by GigaByte

    1 evaluationAppears in 1 listLatest version Latest activity

  10. De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome

    1. Sydney Lamb
    2. Adam M. Taylor
    3. Tabitha A. Hughes
    4. Brock R. McMillan
    5. Randy T. Larsen
    6. Ruqayya Khan
    7. David Weisz
    8. Olga Dudchenko
    9. Erez Lieberman Aiden
    10. Nathaniel B. Edelman
    11. Paul B. Frandsen

    Reviewed by GigaByte

    2 evaluationsAppears in 1 listLatest version Latest activity
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