Genomics

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

Elucidating host cell response pathways and repurposing therapeutics for SARS-CoV-2 and other coronaviruses using gene expression profiles of chemical and genetic perturbations

1. Zhewei Shen
2. Anna Halberg
3. Jia Yi Fong
4. Jingyu Guo
5. Gavin Song
6. Brent Louie
7. Gregory R. Luedtke
8. Viwat Visuthikraisee
9. Andy Protter
10. Xiaoying Koh
11. Taegon Baik
12. Pek Yee Lum

Reviewed by ScreenIT

Tracking the circulating SARS-CoV-2 variants in Turkey: Complete genome sequencing and molecular characterization of 1000 SARS-CoV-2 samples

1. Faruk Berat Akçeşme
2. Tuğba Kul Köprülü
3. Burçin Erkal
4. Şeyma İş
5. Birsen Cevher Keskin
6. Betül Akçeşme
7. Kürşad Nuri Baydili
8. Bahar Gezer
9. Jülide Balkan
10. Bihter Uçar
11. Osman Gürsoy
12. Mehmet Taha Yıldız
13. Halil Kurt
14. Nevzat Ünal
15. Mustafa Altındiş
16. Celalettin Korkmaz
17. Hasan Türkez
18. Özlem Bayraktar
19. Barış Demirkol
20. Yasemin Çağ
21. Melih Akay Arslan
22. Hilal Abakay
23. Şükran Köse
24. Abdülkadir Özel
25. Neslihan Mutluay
26. Şaban Tekin

Reviewed by ScreenIT

Genomic surveillance unfolds the dynamics of SARS-CoV-2 transmission and divergence in Bangladesh over the past two years

1. Tushar Ahmed Shishir
2. Taslimun Jannat
3. Iftekhar Bin Naser

Reviewed by ScreenIT