Genomics

A computational screen for alternative genetic codes in over 250,000 genomes

1. Yekaterina Shulgina
2. Sean R Eddy

• Curated by eLife

  Evaluation Summary:

  The Codetta method developed by Shulgina and Eddy is a powerful approach for inferring codon reassignment by comparative analysis of bacterial and archaeal genomes. Given the rapid advances of genomic and metagenomic sequencing, this will be an important tool for elucidating the genetic codes employed by prokaryotes.

  (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

High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein

1. Rohit Suratekar
2. Pritha Ghosh
3. Michiel J M Niesen
4. Gregory Donadio
5. Praveen Anand
6. Venky Soundararajan
7. A J Venkatakrishnan

Reviewed by ScreenIT

Analysis of long and short enhancers in melanoma cell states

1. David Mauduit
2. Ibrahim Ihsan Taskiran
3. Liesbeth Minnoye
4. Maxime de Waegeneer
5. Valerie Christiaens
6. Gert Hulselmans
7. Jonas Demeulemeester
8. Jasper Wouters
9. Stein Aerts

• Curated by eLife

  Evaluation Summary:

  This is a well-executed study describing multiple new findings related to the association between enhancer activity as measured by massively parallel reporter assay (MPRA), chromatin features, and underlying TF binding profiles in the context of different transcriptional states of cutaneous melanoma. There are several technical and conceptual advances including the refinement of MPRA assays and the understanding of regulatory mechanisms controlling cell state-specific enhancer activity that will be valuable for other investigators to adapt the experimental design and data analysis strategies. This work will be of broad interest to those seeking to understand cell type- or cell identify-specific gene regulation at the level of transcription and epigenetic control using these and related approaches.

  (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

Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

1. João H. C. Campos
2. Juliana T. Maricato
3. Carla T. Braconi
4. Fernando Antoneli
5. Luiz Mario R. Janini
6. Marcelo R. S. Briones

Reviewed by ScreenIT

Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients

1. Michael Tun Yin Lam
2. Sascha H. Duttke
3. Mazen F. Odish
4. Hiep D. Le
5. Emily A. Hansen
6. Celina T. Nguyen
7. Samantha Trescott
8. Roy Kim
9. Shaunak Deota
10. Max W. Chang
11. Arjun Patel
12. Mark Hepokoski
13. Mona Alotaibi
14. Mark Rolfsen
15. Katherine Perofsky
16. Anna S. Warden
17. Jennifer Foley
18. Sydney I. Ramirez
19. Jennifer M. Dan
20. Robert K. Abbott
21. Shane Crotty
22. Laura E. Crotty Alexander
23. Atul Malhotra
24. Satchidananda Panda
25. Christopher W. Benner
26. Nicole G. Coufal

Reviewed by ScreenIT

Gene Expression Risk Scores for COVID-19 Illness Severity

1. Derick R Peterson
2. Andrea M Baran
3. Soumyaroop Bhattacharya
4. Angela R Branche
5. Daniel P Croft
6. Anthony M Corbett
7. Edward E Walsh
8. Ann R Falsey
9. Thomas J Mariani

Reviewed by ScreenIT

Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection

1. Kei Iida
2. Masahiko Ajiro
3. Yukiko Muramoto
4. Toru Takenaga
5. Masatsugu Denawa
6. Ryo Kurosawa
7. Takeshi Noda
8. Masatoshi Hagiwara

Reviewed by ScreenIT

High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs

1. Dóra Tombácz
2. Ákos Dörmő
3. Gábor Gulyás
4. Zsolt Csabai
5. István Prazsák
6. Balázs Kakuk
7. Ákos Harangozó
8. István Jankovics
9. Béla Dénes
10. Zsolt Boldogkői

Reviewed by GigaScience, ScreenIT

A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

1. Weiwei Yang
2. Yu-Cheng Lin
3. William Johnson
4. Nan Dai
5. Romualdas Vaisvila
6. Peter Weigele
7. Yan-Jiun Lee
8. Ivan R Corrêa
9. Ira Schildkraut
10. Laurence Ettwiller

• Curated by eLife

  Evaluation Summary:

  This work will interest researchers who want to explore the functional potential in metagenomes. The authors present a new computational method, MetaGPA, for performing enrichment analysis on cohorts of metagenomes. They then use this approach to identify an enzyme that can modify cytosines in DNA from natural bacteriophage populations. Though successful, the approach needs to improve in clarity and methodology to be both reproducible and of broader impact, as claimed.

  (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

Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study

1. Sanjeet Kumar
2. Kanika Bansal

Reviewed by ScreenIT