Bioinformatics

Analysis-ready VCF at Biobank scale using Zarr

1. Eric Czech
2. Timothy R. Millar
3. Will Tyler
4. Tom White
5. Benjamin Elsworth
6. Jérémy Guez
7. Jonny Hancox
8. Ben Jeffery
9. Konrad J. Karczewski
10. Alistair Miles
11. Sam Tallman
12. Per Unneberg
13. Rafal Wojdyla
14. Shadi Zabad
15. Jeff Hammerbacher
16. Jerome Kelleher

Reviewed by GigaScience

The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

1. Terence Li
2. Marcus Alvarez
3. Cuining Liu
4. Kevin Abuhanna
5. Yu Sun
6. Jason Ernst
7. Kathrin Plath
8. Brunilda Balliu
9. Chongyuan Luo
10. Noah Zaitlen

• Curated by eLife

  eLife Assessment

  This study introduces ambisim, a rigorously validated and well-documented simulation framework that enables the generation of synthetic, genotype-aware single-cell RNA and ATAC sequencing datasets under realistic conditions. The authors provide solid evidence of its utility by benchmarking multiple demultiplexing methods and proposing a new variant consistency metric. While the tool is valuable for guiding method selection, the interpretation of the new metric requires further clarification.

Reviewed by eLife

The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation

1. Kyle Swanson
2. Wesley Wu
3. Nash L. Bulaong
4. John E. Pak
5. James Zou

Reviewed by PREreview

Multivariate Mutual Information based Feature Selection for Predicting Histone Post-Translational Modifications in Epigenetic Datasets

1. V. K. Dhanasekhar
2. Sibi Raj B. Pillai
3. Nithya Ramakrishnan

Reviewed by Arcadia Science

The role of induced polarization in drug discovery applications

1. Ashraf Mohamed
2. Bernard R. Brooks
3. Muhamed Amin

Reviewed by PREreview

Have protein-ligand cofolding methods moved beyond memorisation?

1. Peter Škrinjar
2. Jérôme Eberhardt
3. Gerardo Tauriello
4. Torsten Schwede
5. Janani Durairaj

Reviewed by PREreview, Arcadia Science

AI-Guided Discovery and Optimization of Antimicrobial Peptides Through Species-Aware Language Model

1. Daehun Bae
2. Minsang Kim
3. Jiwon Seo
4. Hojung Nam

Reviewed by Arcadia Science

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models

1. Charles W. J. Pugh
2. Paulina G. Nuñez-Valencia
3. Mafalda Dias
4. Jonathan Frazer

Reviewed by Arcadia Science

External validation of machine learning models—registered models and adaptive sample splitting

1. Giuseppe Gallitto
2. Robert Englert
3. Balint Kincses
4. Raviteja Kotikalapudi
5. Jialin Li
6. Kevin Hoffschlag
7. Ulrike Bingel
8. Tamas Spisak

Reviewed by GigaScience

Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset

1. Maximillian Wess
2. Maria K. Andersen
3. Elise Midtbust
4. Juan Carlos Cabellos Guillem
5. Trond Viset
6. Øystein Størkersen
7. Sebastian Krossa
8. Morten Beck Rye
9. May-Britt Tessem

Reviewed by GigaScience