Genomics

Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy

1. Marco A. Albuquerque
2. Bruno M. Grande
3. Elie J. Ritch
4. Selin Jessa
5. Martin Krzywinski
6. Jasleen K. Grewal
7. Sohrab P. Shah
8. Paul C. Boutros
9. Ryan D. Morin

Reviewed by GigaScience

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

1. Judith Risse
2. Marian Thomson
3. Garry Blakely
4. Georgios Koutsovoulos
5. Mark Blaxter
6. Mick Watson

Reviewed by GigaScience

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

1. Vikas Gupta
2. April D. Estrada
3. Ivory Blakley
4. Rob Reid
5. Ketan Patel
6. Mason D. Meyer
7. Stig Uggerhøj Andersen
8. Allan F. Brown
9. Mary Ann Lila
10. Ann E. Loraine

Reviewed by GigaScience

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

1. Joshua Quick
2. Aaron Quinlan
3. Nicholas J Loman

Reviewed by GigaScience

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

1. Ralf C Mueller
2. Patrik Ellström
3. Kerstin Howe
4. Marcela Uliano-Silva
5. Richard I Kuo
6. Katarzyna Miedzinska
7. Amanda Warr
8. Olivier Fedrigo
9. Bettina Haase
10. Jacquelyn Mountcastle
11. William Chow
12. James Torrance
13. Jonathan M D Wood
14. Josef D Järhult
15. Mahmoud M Naguib
16. Björn Olsen
17. Erich D Jarvis
18. Jacqueline Smith
19. Lél Eöry
20. Robert H S Kraus

Reviewed by GigaScience

Comparison of long read methods for sequencing and assembly of a plant genome

1. Valentine Murigneux
2. Subash Kumar Rai
3. Agnelo Furtado
4. Timothy J.C. Bruxner
5. Wei Tian
6. Qianyu Ye
7. Hanmin Wei
8. Bicheng Yang
9. Ivon Harliwong
10. Ellis Anderson
11. Qing Mao
12. Radoje Drmanac
13. Ou Wang
14. Brock A. Peters
15. Mengyang Xu
16. Pei Wu
17. Bruce Topp
18. Lachlan J.M. Coin
19. Robert J. Henry

Reviewed by GigaScience

Biodiversity genomics of small metazoans: high quality de novo genomes from single specimens of field-collected and ethanol-preserved springtails

1. Clément Schneider
2. Christian Woehle
3. Carola Greve
4. Cyrille A. D’Haese
5. Magnus Wolf
6. Axel Janke
7. Miklós Bálint
8. Bruno Hüttel

Reviewed by GigaScience

Omicron variant of SARS-COV-2 gains new mutations in New Zealand and Hong Kong

1. Xiang-Jiao Yang

Reviewed by ScreenIT

Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections

1. Hailey Sounart
2. Enikő Lázár
3. Yuvarani Masarapu
4. Jian Wu
5. Tibor Várkonyi
6. Tibor Glasz
7. András Kiss
8. Erik Borgström
9. Andrew Hill
10. Sefanit Rezene
11. Soham Gupta
12. Aleksandra Jurek
13. Anezka Niesnerová
14. Henrik Druid
15. Olaf Bergmann
16. Stefania Giacomello

Reviewed by ScreenIT

The human FLT1 regulatory element directs vascular expression and modulates angiogenesis pathways in vitro and in vivo

1. Julian Stolper
2. Holly K. Voges
3. Michael See
4. Neda Rahmani Mehdiabadi
5. Gulrez Chahal
6. Mark Drvodelic
7. Michael Eichenlaub
8. Tanya Labonne
9. Benjamin G. Schultz
10. Alejandro Hidalgo
11. Lazaro Centanin
12. Jochen Wittbrodt
13. Enzo R. Porrello
14. David A. Elliott
15. Mirana Ramialison

• Curated by eLife

  Evaluation Summary:

  This paper aims to identify enhancers controlling human cardiovascular development. The authors identified a set of highly conserved regulatory elements bioinformatically and tested one of these in vivo, in medaka, and in vitro, in hESC differentiated into endothelial cells. They find deletion of this enhancer had no significant effect on the expression of FLT1 mRNA in the human cell line or on the formation of tube formation. However, deletion of the orthologous enhancer in medaka showed phenotypic effects in blood clot formation. Together, the data provide insights into the function of an enhancer controlling FLT1. This manuscript will be of interest to scientists interested in gene regulation, vascular biology and developmental biology.

  (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