Bioinformatics

Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

1. Eva Aßmann
2. Shelesh Agrawal
3. Laura Orschler
4. Sindy Böttcher
5. Susanne Lackner
6. Martin Hölzer

Reviewed by GigaScience

Peptipedia v2.0: A peptide sequence database and user-friendly web platform. A major update

1. Gabriel Cabas-Mora
2. Anamaría Daza
3. Nicole Soto-García
4. Valentina Garrido
5. Diego Alvarez
6. Marcelo Navarrete
7. Lindybeth Sarmiento-Varón
8. Julieta H. Sepúlveda Yañez
9. Mehdi D. Davari
10. Frederic Cadet
11. Álvaro Olivera-Nappa
12. Roberto Uribe-Paredes
13. David Medina-Ortiz

Reviewed by Arcadia Science

Multiple Protein Structure Alignment at Scale with FoldMason

1. Cameron L.M. Gilchrist
2. Milot Mirdita
3. Martin Steinegger

Reviewed by Arcadia Science

Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus

1. Xin Zhang
2. Iseult Leahy
3. Jérȏme Collemare
4. Michael F. Seidl

Reviewed by Arcadia Science

DAGIP: alleviating cell-free DNA sequencing biases with optimal transport

1. Antoine Passemiers
2. Stefania Tuveri
3. Tatjana Jatsenko
4. Adriaan Vanderstichele
5. Pieter Busschaert
6. An Coosemans
7. Dirk Timmerman
8. Sabine Tejpar
9. Peter Vandenberghe
10. Diether Lambrechts
11. Daniele Raimondi
12. Joris Robert Vermeesch
13. 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 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