Bioinformatics

Alleviating cell-free DNA sequencing biases with optimal transport

1. Antoine Passemiers
2. Tatjana Jatsenko
3. Adriaan Vanderstichele
4. Pieter Busschaert
5. An Coosemans
6. Dirk Timmerman
7. Diether Lambrechts
8. Daniele Raimondi
9. Joris Robert Vermeesch
10. Yves Moreau

• Curated by eLife

  eLife assessment

  This study presents a useful computational data preprocessing methodology for de-biasing/denoising high-throughput genomic signals using optimal transport techniques. The evidence supporting the claims of the authors is, however, in parts incomplete, with a partially insufficient experimental setup for validation. The method needs to be be compared with other algorithms, using datasets that demonstrate broad applicability of the algorithm presented. The work could be of interest to scientists in the field of computational genomics.

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 Arıkan
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 Stepień
5. Alip Arslan
6. Nathan C. Sheffield

Reviewed by GigaScience

Omada: Robust clustering of transcriptomes through multiple testing

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

Reviewed by GigaScience

Structure-aware protein sequence alignment using contrastive learning

1. Ronghui You
2. Yuhao Yi
3. 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

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. Although the authors illustrate the compelling utility of this approach with three diverse experimental setups, issues with study design and analysis result in incomplete supporting evidence.

Reviewed by eLife

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