Bioinformatics

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

1. Ioannis Patramanis
2. Jazmín Ramos-Madrigal
3. Enrico Cappellini
4. Fernando Racimo

Reviewed by Peer Community in Paleontology

Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

1. Ben Vezina
2. Stephen C Watts
3. Jane Hawkey
4. Helena B Cooper
5. Louise M Judd
6. Adam WJ Jenney
7. Jonathan M Monk
8. Kathryn E Holt
9. Kelly L Wyres

• Curated by eLife

  eLife assessment

  This study presents Bactabolize, a valuable tool for the rapid genome-scale reconstruction of bacteria and the prediction of growth phenotypes. Using validated methodology, the tool relies on a reference pan-genome model to create strain-specific draft metabolic models, as demonstrated in this study using Klebsiella pneumoniae. While the evidence in this specific case is solid, validation across diverse bacterial species is yet to be confirmed.

Reviewed by eLife

Segment Anything for Microscopy

1. Anwai Archit
2. Luca Freckmann
3. Sushmita Nair
4. Nabeel Khalid
5. Paul Hilt
6. Vikas Rajashekar
7. Marei Freitag
8. Carolin Teuber
9. Melanie Spitzner
10. Constanza Tapia Contreras
11. Genevieve Buckley
12. Sebastian von Haaren
13. Sagnik Gupta
14. Marian Grade
15. Matthias Wirth
16. Günter Schneider
17. Andreas Dengel
18. Sheraz Ahmed
19. Constantin Pape

Reviewed by Arcadia Science

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

1. Mehdi Joodaki
2. Mina Shaigan
3. Victor Parra
4. Roman D Bülow
5. Christoph Kuppe
6. David L Hölscher
7. Mingbo Cheng
8. James S Nagai
9. Michaël Goedertier
10. Nassim Bouteldja
11. Vladimir Tesar
12. Jonathan Barratt
13. Ian SD Roberts
14. Rosanna Coppo
15. Rafael Kramann
16. Peter Boor
17. Ivan G Costa

Reviewed by Review Commons

GADMA2: more efficient and flexible demographic inference from genetic data

1. Ekaterina Noskova
2. Nikita Abramov
3. Stanislav Iliutkin
4. Anton Sidorin
5. Pavel Dobrynin
6. Vladimir I Ulyantsev

Reviewed by GigaScience

KGML-xDTD: a knowledge graph–based machine learning framework for drug treatment prediction and mechanism description

1. Chunyu Ma
2. Zhihan Zhou
3. Han Liu
4. David Koslicki

Reviewed by GigaScience

High-accuracy mapping of human and viral direct physical protein-protein interactions using the novel computational system AlphaFold-pairs

1. Christian Poitras
2. Felix Lamontagne
3. Nathalie Grandvaux
4. Hao Song
5. Maxime Pinard
6. Benoit Coulombe

Reviewed by Arcadia Science

AlphaFold2 predicts interactions amidst confounding structural compatibility

1. Juliette Martin

Reviewed by Arcadia Science

Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data

1. Rebekah A. Oomen
2. Halvor Knutsen
3. Esben M. Olsen
4. Sissel Jentoft
5. Nils Chr. Stenseth
6. Jeffrey A. Hutchings

Reviewed by Arcadia Science

Targeted decontamination of sequencing data with CLEAN

1. Marie Lataretu
2. Sebastian Krautwurst
3. Matthew R Huska
4. Mike Marquet
5. Adrian Viehweger
6. Sascha D Braun
7. Christian Brandt
8. Martin Hölzer

Reviewed by Arcadia Science