Bioinformatics

Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids

1. Kyoung Jo
2. Zong-Yuan Liu
3. Gauri Patel
4. Zhiyuan Yu
5. LiAng Yao
6. Seth Teague
7. Craig Johnson
8. Jason Spence
9. Idse Heemskerk

• Curated by eLife

  eLife Assessment

  This work is an important contribution to understanding the role of FGF signaling in the induction of primitive-like cells in a 2D system of human gastrulation. The authors provide compelling evidence showing that endogenous FGF ligands, acting through FGF receptors localized basolaterally, are determinant in the acquisition of specific cell fates. These observations will be of broad relevance to the FGF field.

Reviewed by eLife

Computational Engineering of a Therapeutic Antibody to Inhibit Multiple Mutants of HER2 Without Compromising Inhibition of the Canonical HER2

1. Sapir Peled
2. Julia Guez-Haddad
3. Nevet Zur Biton
4. Guy Nimrod
5. Sharon Fischman
6. Yair Fastman
7. Yanay Ofran

• Curated by eLife

  eLife assessment

  In this important manuscript, the authors used unbiased approaches to identify somatic mutations in publicly available databases that would disrupt clinically approved antibodies targeting HER2. Using a solid combination of both computational and experimental approaches they identify mutations that could restore therapeutic antibody sensitivity in a series of disease-relevant model systems. Additional cell-based and in vivo assays would strengthen the work and increase the translational and potential clinical relevance of the proposed work.

Reviewed by eLife

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

1. Robert van Dijk
2. John Arevalo
3. Mehrtash Babadi
4. Anne E. Carpenter
5. Shantanu Singh

Reviewed by Review Commons

gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

1. Muzaffer Arikan
2. Thilo Muth

Reviewed by GigaScience

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

1. Nathan J LeRoy
2. Oleksandr Khoroshevskyi
3. Aaron O’Brien
4. Rafał Stępień
5. Alip Arslan
6. Nathan C Sheffield

Reviewed by GigaScience

Omada: robust clustering of transcriptomes through multiple testing

1. Sokratis Kariotis
2. Pei Fang Tan
3. Haiping Lu
4. Christopher J Rhodes
5. Martin R Wilkins
6. Allan Lawrie
7. Dennis Wang

Reviewed by GigaScience

Effective structure-aware protein alignment via residue-level contrastive learning

1. Ronghui You
2. Ziye Wang
3. Kunpeng Liu
4. Wei Zheng
5. Qiqige Wuyun
6. Yuhao Yi
7. Shanfeng Zhu

Reviewed by Arcadia Science

Protein Set Transformer: a protein-based genome language model to power high-diversity viromics

1. Cody Martin
2. Anthony Gitter
3. Karthik Anantharaman

Reviewed by Arcadia Science

Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python

1. Julian Bender
2. Wignand W. D. Mühlhäuser
3. Johannes P. Zimmerman
4. Friedel Drepper
5. Bettina Warscheid

Reviewed by Arcadia Science

GenomeDelta: detecting recent transposable element invasions without repeat library

1. Riccardo Pianezza
2. Anna Haider
3. Robert Kofler

Reviewed by Arcadia Science