Bioinformatics

Machine learning ensemble identifies distinct age-related response to spaceflight in mammary tissue

1. James A. Casaletto
2. Tyler Zhao
3. Jay Yeung
4. Amaan Ansari
5. Ayush Raj
6. Arnav Mishra
7. Amber Fry
8. Kathryn Sun
9. Sofia Lendahl
10. Willy Guan
11. Abigail Lee
12. Lauren M. Sanders
13. Sylvain V. Costes

Reviewed by PREreview

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

1. Giuseppe Deganutti
2. Ludovico Pipitò
3. Roxana M Rujan
4. Tal Weizmann
5. Peter Griffin
6. Antonella Ciancetta
7. Stefano Moro
8. Christopher A Reynolds

• Curated by eLife

  eLife Assessment

  This study describes an improved adaptive sampling approach, multiple-walker Supervised Molecular Dynamics (mwSuMD), and its application to G protein-coupled receptors (GPCRs), which are the most abundant membrane proteins and key targets for drug discovery. The manuscript provides solid evidence that the mwSuMD approach can assist in the sampling of complex binding processes, leading to useful findings for GPCR activity, including resolution of interactions not seen experimentally. The method has the potential to have broad applicability in structural biology and pharmacology.

Reviewed by eLife

Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing

1. Masaaki Uematsu
2. Jeremy M Baskin

• Curated by eLife

  eLife Assessment

  This study provides an important computational tool for analyzing and deconvoluting a pool of plasmids sequenced without barcoding using nanopore long-read sequencing. The tool, which has been convincingly validated, is readily available to scientists interested in rapid and cost-effective verification of plasmid sequences as well as in scaling up analysis by pooling samples within barcodes.

Reviewed by eLife

Healthy microbiome - moving towards functional interpretation

1. Kinga Zielińska
2. Klas I. Udekwu
3. Witold Rudnicki
4. Alina Frolova
5. Paweł P Łabaj

Reviewed by GigaScience

Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spider

1. Guoqing Zhang
2. Yiru Wang
3. Hongcen Jiang
4. Yi Wang

Reviewed by GigaScience

A network regularized linear model to infer spatial expression pattern for single cell

1. Chaohao Gu
2. Hu Chen
3. Zhandong Liu

• Curated by eLife

  eLife Assessment

  The study is useful for advancing spatial transcriptomics through its novel regression-based linear model (glmSMA) that integrates single-cell RNA-seq with spatial reference atlases, though its methodological framework remains incomplete regarding spatial communication applications and feature dependence. The approach demonstrates notable utility by enabling higher-resolution cell mapping across multiple biological systems and spatial platforms compared to existing tools.

Reviewed by eLife

Systematic discovery of directional regulatory motifs associated with human insulator sites

1. Naoki Osato
2. Michiaki Hamada

Reviewed by Review Commons

ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation’s Functional Effect

1. Moritz Glaser
2. Johannes Brägelmann

Reviewed by Arcadia Science

Inferring protein from mRNA concentrations using convolutional neural networks

1. Patrick Maximilian Schwehn
2. Pascal Falter-Braun

Reviewed by preLights

In Silico Toxicity Assessment of Organophosphates: A DFT and Molecular Docking Study on Their Interaction with Human Serum Albumin (HSA)

1. Tanya Singh
2. Nisha Shankhwar
3. Neeta Raj Sharma
4. Anil Kumar
5. Awadhesh Kumar Verma

Reviewed by PREreview