Bioinformatics

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes

1. Craig Liddicoat
2. Robert A. Edwards
3. Michael Roach
4. Jake M. Robinson
5. Kiri Joy Wallace
6. Andrew D. Barnes
7. Joel Brame
8. Anna Heintz-Buschart
9. Timothy R. Cavagnaro
10. Elizabeth A. Dinsdale
11. Michael P. Doane
12. Nico Eisenhauer
13. Grace Mitchell
14. Bibishan Rai
15. Sunita A. Ramesh
16. Martin F. Breed

Reviewed by Arcadia Science

Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

1. Gilberto P. Pereira
2. Brian Jiménez-García
3. Riccardo Pellarin
4. Guillaume Launay
5. Sangwook Wu
6. Juliette Martin
7. Paulo C. T. Souza

Reviewed by Arcadia Science

Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants

1. Yunfan Fu
2. Justin Bedő
3. Anthony T Papenfuss
4. Alan F Rubin

Reviewed by GigaScience

A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution

1. Patrick Gemmell
2. Timothy B. Sackton
3. Scott V. Edwards
4. Jun S. Liu

Reviewed by Arcadia Science

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