Bioinformatics

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 development of glmSMA represents a valuable advancement in spatial transcriptomics analysis, offering a mathematically robust regression-based approach that achieves higher-resolution mapping of single-cell RNA sequencing data to spatial locations than existing methods. The evidence is convincing, as the authors demonstrate the method's superiority by formulating it as a convex optimization problem that ensures stable solutions, coupled with successful validation across multiple biological systems. The rigorous mathematical framework and validation across diverse tissues enable precise spatial mapping of cellular heterogeneity at enhanced resolution.

Reviewed by eLife

The structural context of mutations in proteins predicts their effect on antibiotic resistance

1. Anna G Green
2. Mahbuba Tasmin
3. Roger Vargas
4. Maha R Farhat

• Curated by eLife

  eLife Assessment

  This valuable study leverages a large global dataset of tens of thousands of tuberculosis samples to place recurrent protein-coding mutations into their three-dimensional structural context, offering an expanded view of how antibiotic resistance emerges compared to traditional genetic analyses alone. The strength of evidence is convincing, supported by the scale and breadth of the dataset and the systematic structural analysis, although some of the assumptions made in the the modeling approach are only partially supported. Overall, the work will be of broad interest to researchers studying microbial evolution, antibiotic resistance, and structure-function relationships in pathogens.

Reviewed by eLife

Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

1. Manuel Lafond
2. Celine Scornavacca

Reviewed by Peer Community in Evolutionary Biology

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

1. Zhanghan Ni
2. Troy Osborn
3. Juntao Zhong
4. Adrian Gonzalez
5. Will Puzella
6. Aya Klos
7. Bryan Le
8. Alec Leonetti
9. Joanne S Boden
10. Eva E Stueeken
11. Rika E Anderson

Reviewed by Arcadia Science

Direct Comparative Analyses of 10X Genomics Chromium and Smart-Seq2

1. Xiliang Wang
2. Yao He
3. Qiming Zhang
4. Xianwen Ren
5. Zemin Zhang

Reviewed by PREreview

pyRootHair: Machine Learning Accelerated Software for High-Throughput Phenotyping of Plant Root Hair Traits

1. Ian Tsang
2. Lawrence Percival-Alwyn
3. Stephen Rawsthorne
4. James Cockram
5. Fiona Leigh
6. Jonathan A. Atkinson

Reviewed by GigaScience

EMImR: a Shiny application for identifying transcriptomic and epigenomic changes

1. Hiba Ben Aribi
2. Careen Naitore
3. Farah Ayadi
4. Souheila Guerbouj
5. Olaitan I. Awe

• Curated by GigaByte

  Editors Assessment:

  Coded and written up as part of the African Society for Bioinformatics and Computational Biology (ASBCB) Omicscodeathons, EMImR is a novel Shiny application for transcriptomic and epigenomic change identification and correlation wrapped up using a combination of Bioconductor and CRAN packages. Case studies are on publicly available GEO data corresponding to sequencing data of human blood cell samples of multiple sclerosis patients to demonstrate how the tool works. And a documentation and videos are provided. Peer review and the study highlighting the usefulness of the developed tool for analyzing transcriptomic and epigenomic data.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

1. Simon Holzinger
2. Leo Schmutterer
3. Victoria Marie Rothe
4. Maria Theresia Watzlowik
5. Uwe Schwartz
6. Gernot Längst

Reviewed by Review Commons

TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing

1. Jiachen Li
2. Zhe Wang
3. Hong-Bin Shen
4. Ye Yuan

• Curated by eLife

  eLife Assessment

  This study presents a valuable tool named TSvelo, a computational framework for RNA velocity inference that models transcriptional regulation and gene-specific splicing. The evidence supporting the claims of the authors is solid, although elaboration of the computational benchmark and datasets would have strengthened the study. The work will be of interest to computational scientists working in the field of RNA biology.

Reviewed by eLife

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

1. Markus Hoffmann
2. Lina-Liv Willruth
3. Alexander Dietrich
4. Hye Kyung Lee
5. Ludwig Knabl
6. Nico Trummer
7. Jan Baumbach
8. Priscilla A. Furth
9. Lothar Hennighausen
10. Markus List

Reviewed by Rapid Reviews Infectious Diseases