Bioinformatics

The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation

1. Jagoda Jabłońska
2. Yao Chun-Chen
3. Liam M. Longo
4. Dan S. Tawfik
5. Ita Gruic-Sovulj

Reviewed by PREreview

Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2

1. Gabriel Monteiro da Silva
2. Jennifer Y Cui
3. David C Dalgarno
4. George P Lisi
5. Brenda M Rubenstein

Reviewed by PREreview

Spatial transformation of multi-omics data unlocks novel insights into cancer biology

1. Mateo Sokač
2. Asbjørn Kjær
3. Lars Dyrskjøt
4. Benjamin Haibe-Kains
5. Hugo JWL Aerts
6. Nicolai J Birkbak

• Curated by eLife

  eLife assessment

  This valuable manuscript presents a new approach to transform multi-omics datasets into images and to exploit Deep Learning methods for image analysis of the transformed datasets. As an example, the method is applied to multi-omics datasets on different cancers. While the evidence in this specific case is solid, whether the method is working as advertised in other settings is not yet known.

Reviewed by eLife

Surface-guided computing to quantify dynamic interactions between cell morphology and molecular signals in 3D

1. Felix Y. Zhou
2. Virangika K. Wimalasena
3. Qiongjing Zou
4. Andrew Weems
5. Gabriel M. Gihana
6. Edward Jenkins
7. Bingying Chen
8. Bo-Jui Chang
9. Meghan Driscoll
10. Andrew J. Ewald
11. Gaudenz Danuser

Reviewed by Arcadia Science

AlphaPulldown—a python package for protein–protein interaction screens using AlphaFold-Multimer

1. Dingquan Yu
2. Grzegorz Chojnowski
3. Maria Rosenthal
4. Jan Kosinski

Reviewed by Arcadia Science

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

1. Ulisses Nunes da Rocha
2. Jonas Coelho Kasmanas
3. René Kallies
4. Joao Pedro Saraiva
5. Rodolfo Brizola Toscan
6. Polonca Štefanič
7. Marcos Fleming Bicalho
8. Felipe Borim Correa
9. Merve Nida Baştürk
10. Efthymios Fousekis
11. Luiz Miguel Viana Barbosa
12. Julia Plewka
13. Alexander Probst
14. Petr Baldrian
15. Peter Stadler
16. CLUE-TERRA consortium

Reviewed by Arcadia Science

Biologically informed variational autoencoders allow predictive modeling of genetic and drug-induced perturbations

1. Daria Doncevic
2. Carl Herrmann

Reviewed by Arcadia Science

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

1. Hirotaka Suetake
2. Tsukasa Fukusato
3. Takeo Igarashi
4. Tazro Ohta

Reviewed by Arcadia Science, GigaScience

Sex-specificity of the C. elegans metabolome

1. Russell N. Burkhardt
2. Alexander B. Artyukhin
3. Erin Z. Aprison
4. Brian J. Curtis
5. Bennett W. Fox
6. Andreas H. Ludewig
7. Diana Fajardo Palomino
8. Jintao Luo
9. Amaresh Chaturbedi
10. Oishika Panda
11. Chester J. J. Wrobel
12. Victor Baumann
13. Douglas S. Portman
14. Siu Sylvia Lee
15. Ilya Ruvinsky
16. Frank C. Schroeder

Reviewed by Arcadia Science

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow

1. Zoé Pochon
2. Nora Bergfeldt
3. Emrah Kırdök
4. Mário Vicente
5. Thijessen Naidoo
6. Tom van der Valk
7. N. Ezgi Altınışık
8. Maja Krzewińska
9. Love Dalén
10. Anders Götherström
11. Claudio Mirabello
12. Per Unneberg
13. Nikolay Oskolkov

Reviewed by Arcadia Science