Bioinformatics

Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing

1. Jessie J -Y Chang
2. Xuan Yang
3. Haotian Teng
4. Jianshu Zhang
5. Benjamin Reames
6. Shuxin Zhang
7. Vincent Corbin
8. Lachlan J M Coin

Reviewed by GigaScience

Nanopore- and AI-empowered microbial viability inference

1. Harika Ürel
2. Sabrina Benassou
3. Hanna Marti
4. Tim Reska
5. Ela Sauerborn
6. Yuri Pinheiro Alves De Souza
7. Albert Perlas
8. Enrique Rayo
9. Michael Biggel
10. Stefan Kesselheim
11. Nicole Borel
12. Edward J Martin
13. Constanza B Venegas
14. Michael Schloter
15. Kathrin Schröder
16. Jana Mittelstrass
17. Simone Prospero
18. James M Ferguson
19. Lara Urban

Reviewed by GigaScience

WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning

1. Hoang-Hai Nguyen
2. Josip Rudar
3. Nathaniel Lesperance
4. Oksana Vernygora
5. Graham W. Taylor
6. Chad Laing
7. David Lapen
8. Carson K. Leung
9. Oliver Lung

Reviewed by GigaScience

SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis

1. Xiao Li
2. Ximo Pechuan-Jorge
3. Tyler Risom
4. Conrad Foo
5. Alexander Prilipko
6. Artem Zubkov
7. Caleb Chan
8. Patrick Chang
9. Frank Peale
10. James Ziai
11. Sandra Rost
12. Derrek Hibar
13. Lisa McGinnis
14. Evgeniy Tabatsky
15. Xin Ye
16. Hector Corrada Bravo
17. Zhen Shi
18. Malgorzata Nowicka
19. Jon Scherdin
20. James Cowan
21. Jennifer Giltnane
22. Darya Orlova
23. Rajiv Jesudason

Reviewed by GigaScience

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

1. Chengzhong Ye
2. Gonzalo Benegas
3. Carlos Albors
4. Jianan Canal Li
5. Sebastian Prillo
6. Peter D. Fields
7. Brian Clarke
8. Yun S. Song

Reviewed by Arcadia Science

Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

1. Eric Greene
2. Richard Muniz
3. Hiroki Yamamura
4. Samuel E Hoff
5. Priyanka Bajaj
6. D John Lee
7. Erin M Thompson
8. Angelika Arada
9. Gyun Min Lee
10. Massimiliano Bonomi
11. Justin M Kollman
12. James S Fraser

• Curated by eLife

  eLife Assessment

  This manuscript employs cryo-EM, mutational analysis, and biochemical assays to explore the molecular basis by which glutamine promotes filamentation and regulates the activity of human glutamine synthetase (hGS) by stabilizing interactions between hGS decamers. The studies supporting this mechanism are solid, but could be improved by providing more clarity and by addressing methodological issues in the cryoEM data processing workflow. This work will be of particular interest and useful to groups interested in understanding the molecular basis of nutrient sensing, cellular metabolism, and structural regulation of enzyme activity.

Reviewed by eLife

Macroscopic Analyses of RNA-Seq Data to Reveal Chromatin Modifications in Aging and Disease

1. Achal Mahajan
2. Francesca Ratti
3. Ban Wang
4. Hana El-Samad
5. James H Kaufman
6. Vishrawas Gopalakrishnan

• Curated by eLife

  eLife Assessment

  This valuable study analyzes aging-related chromatin changes through the lens of intra-chromosomal gene correlation length, which is a novel computational metric that captures spatial correlations in gene expression along the chromosome. The authors propose that this metric reflects chromatin structure and can serve as a proxy for its changes during aging. While currently the strength of evidence is somewhat incomplete, if revised with further supporting data, this work will provide a systems-level understanding of aging and genome regulation, which is predicted to have a substantive impact on the field.

Reviewed by eLife

Restoring data balance via generative models of T cell receptors for antigen-binding prediction

1. Emanuele Loffredo
2. Mauro Pastore
3. Simona Cocco
4. Rémi Monasson

• Curated by eLife

  eLife Assessment

  This valuable study introduces a data augmentation approach based on generative unsupervised models to address data imbalance in immune receptor modeling. Support for the findings is solid, showing that the use of generated data increases the performance of downstream supervised prediction tasks, e.g., TCR-peptide interaction prediction. However, the validation, mainly relying on synthetic data, could be completed, especially regarding unseen epitopes, and given the exclusive focus on CDR3β. The results should be of interest to the communities working on immunology and biological sequence data analysis.

Reviewed by eLife

The Demodifier: a tool for screening modification-induced alternate peptide taxonomy in palaeoproteomics

1. Miranda Evans

Reviewed by Peer Community in Archaeology

Unbiased whole genome comparison of Pan paniscus (bonobo) and Homo sapiens (human) through a novel sequence match-based approach

1. Christof Rosler
2. Derick DuFriend
3. Evonn Annor
4. Rita Njoroge
5. Elena Davis
6. Ywahae Law Anthem
7. Celestino Velásquez
8. William P. Ranahan
9. Matthew H. Goelzer
10. Stephen Wheat
11. Julianna A. Goelzer

Reviewed by Arcadia Science