Bioinformatics

Real-time transcriptomic profiling in distinct experimental conditions

1. Tamer Butto
2. Stefan Pastore
3. Max Müller
4. Kaushik Viswanathan Iyer
5. Marko Jörg
6. Julia Brechtel
7. Stefan Mündnich
8. Anna Wierczeiko
9. Kristina Friedland
10. Mark Helm
11. Marie-Luise Winz
12. Susanne Gerber

• Curated by eLife

  eLife Assessment

  This useful study presents a real-time transcriptomics analysis, with the aim of providing rapid access to sequenced data to reduce the costs associated with Oxford Nanopore long-read technology. The revised manuscript demonstrates the utilities with four sets of experiments with convincing evidence.

Reviewed by eLife

Pan-tissue transcriptome analysis reveals sex-dimorphic human aging

1. Siqi Wang
2. Danyue Dong
3. Xin Li
4. Zefeng Wang

• Curated by eLife

  eLife Assessment

  In this study Wang et. al. mined publicly available RNA-seq data from The Genotype-Tissue Expression (GTEx) database spanning multiple tissues to ask the question of how transcriptomes are changed with age and in both sexes. The authors provide solid evidence reporting widespread gene expression changes and alternative splicing events that vary in an age- and sex-dependent manner. An important finding is that many of these changes coincide with the time sex hormones begin to decline; additionally, the rate of aging is faster in males than in females.

Reviewed by eLife

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

1. Shuya Ikeda
2. Zhaonan Zou
3. Hidemasa Bono
4. Yuki Moriya
5. Shuichi Kawashima
6. Toshiaki Katayama
7. Shinya Oki
8. Tazro Ohta

Reviewed by GigaScience

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

1. Murilo Caminotto Barbosa
2. João Fernando Marques da Silva
3. Leonardo Cardoso Alves
4. Robert D Finn
5. Alexandre Rossi Paschoal

Reviewed by GigaScience

Analysis-ready VCF at Biobank scale using Zarr

1. Eric Czech
2. Will Tyler
3. Tom White
4. Ben Jeffery
5. Timothy R Millar
6. Benjamin Elsworth
7. Jérémy Guez
8. Jonny Hancox
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