Genomics

The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS-CoV-2 coronavirus

1. José L. Oliver
2. Pedro Bernaola-Galván
3. Francisco Perfectti
4. Cristina Gómez Martín
5. Silvia Castiglione
6. Pasquale Raia
7. Miguel Verdú
8. Andrés Moya

Reviewed by ScreenIT

SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution

1. Urvashi B. Singh
2. Sushanta Deb
3. Rama Chaudhry
4. Kiran Bala
5. Lata Rani
6. Ritu Gupta
7. Lata Kumari
8. Jawed Ahmed
9. Sudesh Gaurav
10. Sowjanya Perumalla
11. Md. Nizam
12. Anwita Mishra
13. J. Stephenraj
14. Jyoti Shukla
15. Deepika Bhardwaj
16. Jamshed Nayer
17. Praveen Aggarwal
18. Madhulika Kabra
19. Vineet Ahuja
20. Subrata Sinha
21. Randeep Guleria

Reviewed by ScreenIT

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

1. Stefano G Giulieri
2. Romain Guérillot
3. Sebastian Duchene
4. Abderrahman Hachani
5. Diane Daniel
6. Torsten Seemann
7. Joshua S Davis
8. Steven YC Tong
9. Bernadette C Young
10. Daniel J Wilson
11. Timothy P Stinear
12. Benjamin P Howden

• Curated by eLife

  Evaluation Summary:

  This study offers a comprehensive examination of Staphylococcus aureus evolution during infection. This manuscript will be of broad interest to readers in the field of microbiology and infectious disease. It provides a useful analysis of a comprehensive set of genetic signatures of bacterial adaptation. A combination of multiple layers of genome annotation and point mutation variant detection compellingly supports the correlation of infection outcomes with adaptation signatures in S. aureus.

  (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 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

1. John T Lovell
2. Avinash Sreedasyam
3. M Eric Schranz
4. Melissa Wilson
5. Joseph W Carlson
6. Alex Harkess
7. David Emms
8. David M Goodstein
9. Jeremy Schmutz

• Curated by eLife

  Evaluation Summary:

  This manuscript describing GENESPACE was found to be of high interest for the genomics community across many different fields. GENESPACE is a new and straightforward computational tool to include synteny information in the calculation of genome-wide sets of orthologs. This is very timely as more and more chromosome-scale assembled genomes are becoming available.

  (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

Activated interstitial macrophages are a predominant target of viral takeover and focus of inflammation in COVID-19 initiation in human lung

1. Timothy Ting-Hsuan Wu
2. Kyle J. Travaglini
3. Arjun Rustagi
4. Duo Xu
5. Yue Zhang
6. Leonid Andronov
7. SoRi Jang
8. Astrid Gillich
9. Roozbeh Dehghannasiri
10. Giovanny Martínez-Colón
11. Aimee Beck
12. Daniel Dan Liu
13. Aaron J. Wilk
14. Maurizio Morri
15. Winston L. Trope
16. Rob Bierman
17. Irving L. Weissman
18. Joseph B. Shrager
19. Stephen R. Quake
20. Christin S. Kuo
21. Julia Salzman
22. W. E. Moerner
23. Peter S. Kim
24. Catherine A. Blish
25. Mark A. Krasnow

Reviewed by ScreenIT

Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection

1. Martin Jankowiak
2. Fritz H. Obermeyer
3. Jacob E. Lemieux

Reviewed by ScreenIT

Transcriptome-wide association study and eQTL colocalization identify potentially causal genes responsible for human bone mineral density GWAS associations

1. Basel Maher Al-Barghouthi
2. Will T Rosenow
3. Kang-Ping Du
4. Jinho Heo
5. Robert Maynard
6. Larry Mesner
7. Gina Calabrese
8. Aaron Nakasone
9. Bhavya Senwar
10. Louis Gerstenfeld
11. James Larner
12. Virginia Ferguson
13. Cheryl Ackert-Bicknell
14. Elise Morgan
15. David Brautigan
16. Charles R Farber

• Curated by eLife

  Evaluation Summary:

  This manuscript is of broad interest to geneticists and bone biologists because it describes a method to filter candidate genes, identified from GWAS, and pinpoint the gene that affects bone biology. This method identified a gene with a previously unknown role in bone biology and the authors showed that its loss reduces bone mineral density, supporting the key claims in the paper.

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

Reviewed by eLife

Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration

1. Julian Wolf
2. Anja Schlecht
3. Dennis-Dominik Rosmus
4. Stefaniya Boneva
5. Hansjürgen Agostini
6. Günther Schlunck
7. Peter Wieghofer
8. Clemens Lange

• Curated by eLife

  Evaluation Summary:

  The authors present here an analysis of the gene expression patterns of lesions as found in patients wet age-related macular degeneration, known as choroidal neovascularization. This gene expression analysis is compared to an experimental mouse model. Using this analysis, the authors have identified a candidate target, FN14, as a potential target for the treatment of choroidal neovascularization. Identifying an alternative treatment modality is important for the treatment of these lesions beyond the current standard of care.

  (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 #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

1. Brandon D. Pickett
2. Sheena Talma
3. Jessica R. Glass
4. Daniel Ence
5. Timothy P. Johnson
6. Paul D. Cowley
7. Perry G. Ridge
8. John S. K. Kauwe

Reviewed by GigaByte

COVID-19 infection and transmission includes complex sequence diversity

1. Ernest R. Chan
2. Lucas D. Jones
3. Marlin Linger
4. Jeffrey D. Kovach
5. Maria M. Torres-Teran
6. Audric Wertz
7. Curtis J. Donskey
8. Peter A. Zimmerman

Reviewed by ScreenIT