Bioinformatics

A knowledge-based distance metric highlights underperformance of variant effect predictors on gain-of-function missense variants

1. Lukas Gerasimavicius
2. Joseph A. Marsh

Reviewed by Arcadia Science

Cellpose-SAM: superhuman generalization for cellular segmentation

1. Marius Pachitariu
2. Michael Rariden
3. Carsen Stringer

Reviewed by Arcadia Science

Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing

1. Kevin Stachelek
2. Bhavana Bhat
3. David Cobrinik

• Curated by GigaByte

  Editors Assessment:

  This paper presents Chevreul, a new open-source R Bioconductor (meta-)package for processing and integration of scRNA-seq data from cDNA end-counting, full-length short-read or long-read protocols. Alongside a R Shiny app for easy visualization, formatting, and analysis for exploratory analyses of scRNA-seq data processed in the SingleCellExperiment Bioconductor or Seurat formats. The name of the tool is inspired by the colour theorist Michel-Eugène Chevreul and the optical illusion of the same name. To demonstrate the use of Chevreul, the authors provide a sample analysis, which helps to demonstrate how users can visualize a wide range of parameters, enabling transparent and reproducible scRNA-seq analyses. Peer review also pushing the author to provide extensive guidance materials to assist with use. Being implemented in R, the R package and integrated Shiny application are freely available under an open-source MIT license in Bioconductor and their GitHub page here: https://github.com/cobriniklab/chevreul

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Machine Learning and Network Analysis to Predict Hypothetical Protein Functions of Aeromonas hydrophila

1. Harun Pirim
2. Zaidur Rahman
3. Saviz Saei
4. Sangam Gyawali
5. Mohammad Marufuzzaman
6. Nazanin Tajik
7. Hasan Tekedar

Reviewed by Arcadia Science

The lipocone superfamily, a unifying theme in metabolism of lipids, peptidoglycan and exopolysaccharides, inter-organismal conflicts and immunity

1. A Maxwell Burroughs
2. Gianlucca G Nicastro
3. L Aravind

• Curated by eLife

  eLife Assessment

  This fundamental study presents a compelling and comprehensive analysis of the newly defined Lipocone superfamily, offering unprecedented insights into the evolutionary origins of Wnt proteins. The authors provide evidence that this superfamily evolved from membrane proteins. The work is exemplary in its use of sequence analysis and structural modeling and will be of broad interest to researchers studying protein evolution and enzymology.

  [Editors' note: this paper was reviewed by Review Commons.]

Reviewed by eLife

Systematic discovery of directional regulatory motifs associated with human insulator sites

1. Naoki Osato
2. Michiaki Hamada

Reviewed by Review Commons

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