Bioinformatics

Contamination detection and microbiome exploration with GRIMER

1. Vitor C Piro
2. Bernhard Y Renard

Reviewed by GigaScience

ViReMa : a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids

1. Stephanea Sotcheff
2. Yiyang Zhou
3. Jason Yeung
4. Yan Sun
5. John E Johnson
6. Bruce E Torbett
7. Andrew L Routh

Reviewed by GigaScience

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

1. Chen Yang
2. Theodora Lo
3. Ka Ming Nip
4. Saber Hafezqorani
5. René L Warren
6. Inanc Birol

Reviewed by GigaScience

FAIR data station for lightweight metadata management and validation of omics studies

1. Bart Nijsse
2. Peter J Schaap
3. Jasper J Koehorst

Reviewed by GigaScience

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

1. Mihaly Varadi
2. Sreenath Nair
3. Ian Sillitoe
4. Gerardo Tauriello
5. Stephen Anyango
6. Stefan Bienert
7. Clemente Borges
8. Mandar Deshpande
9. Tim Green
10. Demis Hassabis
11. Andras Hatos
12. Tamas Hegedus
13. Maarten L Hekkelman
14. Robbie Joosten
15. John Jumper
16. Agata Laydon
17. Dmitry Molodenskiy
18. Damiano Piovesan
19. Edoardo Salladini
20. Steven L. Salzberg
21. Markus J Sommer
22. Martin Steinegger
23. Erzsebet Suhajda
24. Dmitri Svergun
25. Luiggi Tenorio-Ku
26. Silvio Tosatto
27. Kathryn Tunyasuvunakool
28. Andrew Mark Waterhouse
29. Augustin Žídek
30. Torsten Schwede
31. Christine Orengo
32. Sameer Velankar

Reviewed by GigaScience

Making Common Fund data more findable: catalyzing a data ecosystem

1. Amanda L Charbonneau
2. Arthur Brady
3. Karl Czajkowski
4. Jain Aluvathingal
5. Saranya Canchi
6. Robert Carter
7. Kyle Chard
8. Daniel J B Clarke
9. Jonathan Crabtree
10. Heather H Creasy
11. Mike D'Arcy
12. Victor Felix
13. Michelle Giglio
14. Alicia Gingrich
15. Rayna M Harris
16. Theresa K Hodges
17. Olukemi Ifeonu
18. Minji Jeon
19. Eryk Kropiwnicki
20. Marisa C W Lim
21. R Lee Liming
22. Jessica Lumian
23. Anup A Mahurkar
24. Meisha Mandal
25. James B Munro
26. Suvarna Nadendla
27. Rudyard Richter
28. Cia Romano
29. Philippe Rocca-Serra
30. Michael Schor
31. Robert E Schuler
32. Hongsuda Tangmunarunkit
33. Alex Waldrop
34. Cris Williams
35. Karen Word
36. Susanna-Assunta Sansone
37. Avi Ma'ayan
38. Rick Wagner
39. Ian Foster
40. Carl Kesselman
41. C Titus Brown
42. Owen White

Reviewed by GigaScience

Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals

1. Yunchi Zhu
2. Xin Liao
3. Tingyu Han
4. J.-Y. Chen
5. Chunpeng He
6. Zuhong Lu

Reviewed by GigaScience

What the Phage: A scalable workflow for the identification and analysis of phage sequences

1. Mike Marquet
2. Martin Hölzer
3. Mathias W. Pletz
4. Adrian Viehweger
5. Oliwia Makarewicz
6. Ralf Ehricht
7. Christian Brandt

Reviewed by GigaScience

Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

1. Matthew Roberts
2. Julia Ogden
3. AS Mukarram Hossain
4. Anshuman Chaturvedi
5. Alastair RW Kerr
6. Caroline Dive
7. Jennifer Ellen Beane
8. Carlos Lopez-Garcia

• Curated by eLife

  eLife assessment

  The authors have developed a useful and user-friendly software to analyse gene expression data from four datasets representing premalignant lung lesions. This software would be of interest to those working in lung cancer and specifically the pre-malignant space. The major strength is the ease of use while the major limitation is the inability for the user to integrate other datasets.

Reviewed by eLife

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

1. Varuni Sarwal
2. Jaqueline Brito
3. Serghei Mangul
4. David Koslicki

Reviewed by GigaScience