Genetics

Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population

1. Yiran Shen
2. Bhuwan Khatri
3. Santosh Rananaware
4. Danmeng Li
5. David A. Ostrov
6. Piyush K Jain
7. Christopher J. Lessard
8. Cuong Q. Nguyen

Reviewed by ScreenIT

Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

1. Alex N Nguyen Ba
2. Katherine R Lawrence
3. Artur Rego-Costa
4. Shreyas Gopalakrishnan
5. Daniel Temko
6. Franziska Michor
7. Michael M Desai

• Curated by eLife

  Evaluation Summary:

  Overall, this is an impressive and interesting piece of work that not only expands the identification of small-effect QTL, but also reveals epistatic interactions at an unprecedented scale. Their approach takes advantage of DNA barcodes to increase the scale of genetic mapping studies in yeast by an order of magnitude over previous studies, yielding a more complete and precise view of the QTL landscape and confirming widespread epistatic interactions between the different QTL.

  (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 #1 agreed to share their name with the authors.)

Reviewed by eLife

An auxin-inducible, GAL4-compatible, gene expression system for Drosophila

1. Colin D McClure
2. Amira Hassan
3. Gabriel N Aughey
4. Khushbakht Butt
5. Alicia Estacio-Gómez
6. Aneisha Duggal
7. Chee Ying Sia
8. Annika F Barber
9. Tony D Southall

• Curated by eLife

  Evaluation Summary:

  This work will be of interest to Drosophila geneticists in its development of a new tool for temporal control of gene induction by the widely-used bipartite Gal4/UAS system. By transferring protein modules from plants that mediate auxin-dependent protein degradation to control the stability of a Gal4-inhibitor (Gal80), the authors successfully demonstrate the ability to control Gal4 activity in flies through the provision of auxin in the food substrate and provide evidence for the sensitivity, specificity and non-toxicity of this tool.

  (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

NETMAGE: a humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS

1. Vivek Sriram
2. Manu Shivakumar
3. Sang-Hyuk Jung
4. Lisa Bang
5. Anurag Verma
6. Seunggeun Lee
7. Eun Kyung Choe
8. Dokyoon Kim

Reviewed by GigaScience

Interpretable network-guided epistasis detection

1. Diane Duroux
2. Héctor Climente-González
3. Chloé-Agathe Azencott
4. Kristel Van Steen

Reviewed by GigaScience

Gene-set Enrichment with Mathematical Biology (GEMB)

1. Amy L Cochran
2. Kenneth J Nieser
3. Daniel B Forger
4. Sebastian Zöllner
5. Melvin G McInnis

Reviewed by GigaScience

High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat

1. Xu Wang
2. Hong Xuan
3. Byron Evers
4. Sandesh Shrestha
5. Robert Pless
6. Jesse Poland

Reviewed by GigaScience

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

1. Tobias Moll
2. Valerie Odon
3. Calum Harvey
4. Mark O Collins
5. Andrew Peden
6. John Franklin
7. Emily Graves
8. Jack NG Marshall
9. Cleide dos Santos Souza
10. Sai Zhang
11. Lydia Castelli
12. Guillaume Hautbergue
13. Mimoun Azzouz
14. David Gordon
15. Nevan Krogan
16. Laura Ferraiuolo
17. Michael P Snyder
18. Pamela J Shaw
19. Jan Rehwinkel
20. Johnathan Cooper-Knock

Reviewed by ScreenIT

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

1. Qussai Abbas
2. Alexey Kusakin
3. Kinda Sharrouf
4. Susan Jyakhwo
5. Aleksey S Komissarov

Reviewed by ScreenIT

The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells

1. Dylane Detilleux
2. Peggy Raynaud
3. Berengere Pradet-Balade
4. Dominique Helmlinger

• Curated by eLife

  **Evaluation Summary:
  **
  This manuscript will be of interest to those studying gene transcription and its regulation by co-activator complexes in metazoans. The identification of the large TRAPP subunit shared between two conserved histone modification complexes as a negative regulator of the interferon type I pathway in colorectal cancer cell line provides novel insights into the functions of this TRAPP subunit, which was previously known only for this positive effects on gene transcription.

  (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 #1 agreed to share their name with the authors.)

Reviewed by eLife