Bioinformatics

ImmCellTyper facilitates systematic mass cytometry data analysis for deep immune profiling

1. Jing Sun
2. Desmond Choy
3. Nicolas Sompairac
4. Shirin Jamshidi
5. Michele Mishto
6. Shahram Kordasti

• Curated by eLife

  eLife assessment

  ImmCellTyper presents a useful toolkit for CyTOF data analysis, integrating BinaryClust for semi-supervised clustering and cell type annotation. The evidence supporting the findings is convincing, with appropriate and validated methodology. This tool will be helpful to researchers in immunology and cytometry, offering a robust solution for cell type identification and differential analysis.

Reviewed by eLife

MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

1. Tao Feng
2. Shufang Wu
3. Hongwei Zhou
4. Zhencheng Fang

Reviewed by GigaScience

Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

1. Kari Lavikka
2. Jaana Oikkonen
3. Yilin Li
4. Taru Muranen
5. Giulia Micoli
6. Giovanni Marchi
7. Alexandra Lahtinen
8. Kaisa Huhtinen
9. Rainer Lehtonen
10. Sakari Hietanen
11. Johanna Hynninen
12. Anni Virtanen
13. Sampsa Hautaniemi

Reviewed by GigaScience

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

Pathway activation model for personalized prediction of drug synergy

1. Quang Thinh Trac
2. Yue Huang
3. Tom Erkers
4. Päivi Östling
5. Anna Bohlin
6. Albin Österroos
7. Mattias Vesterlund
8. Rozbeh Jafari
9. Ioannis Siavelis
10. Helena Bäckvall
11. Santeri Kiviluoto
12. Lukas M Orre
13. Mattias Rantalainen
14. Janne Lehtiö
15. Sören Lehmann
16. Olli Kallioniemi
17. Yudi Pawitan
18. Trung Nghia Vu

• Curated by eLife

  eLife assessment

  This study presents a valuable report on a machine-learning tool for predicting synergistic drug combinations for cancer treatment. However, the evidence supporting the claims of the authors is incomplete, as the reported model shows some evidence of overfitting, and the claims of the authors could be strengthened if additional validation experiments were performed. The work will be of interest to oncologists and medical biologists working on cancer.

Reviewed by eLife

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

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