Bioinformatics

ASPEN: Robust detection of allelic dynamics in single cell RNA-seq

1. Veronika Petrova
2. Muqing Niu
3. Thomas Vierbuchen
4. Emily S Wong

Reviewed by Review Commons

Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models

1. Yasha Ektefaie
2. Andrew Shen
3. Lavik Jain
4. Maha Farhat
5. Marinka Zitnik

Reviewed by Arcadia Science

SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework

1. Yichao Hua
2. Linqian Weng
3. Fang Zhao
4. Florian Rambow

Reviewed by GigaScience

Micro𝕊plit: Semantic Unmixing of Fluorescent Microscopy Data

1. Ashesh Ashesh
2. Federico Carrara
3. Igor Zubarev
4. Vera Galinova
5. Melisande Croft
6. Melissa Pezzotti
7. Daozheng Gong
8. Francesca Casagrande
9. Elisa Colombo
10. Stefania Giussani
11. Elena Restelli
12. Eugenia Cammarota
13. Juan Manuel Battagliotti
14. Nikolai Klena
15. Moises Di Sante
16. Raghabendra Adhikari
17. Daniel Feliciano
18. Gaia Pigino
19. Elena Taverna
20. Oliver Harschnitz
21. Nicola Maghelli
22. Norbert Scherer
23. Damian Edward Dalle Nogare
24. Joran Deschamps
25. Francesco Pasqualini
26. Florian Jug

Reviewed by Arcadia Science

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation

1. Nihit Aggarwal
2. Johanna Elena Schmitz
3. Lukas Laufer
4. Sven Rahmann
5. Jörn Walter
6. Abdulrahman Salhab

Reviewed by Arcadia Science

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

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