Bioinformatics

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

1. Randy Heiland
2. Daniel Bergman
3. Blair Lyons
4. Grant Waldow
5. Julie Cass
6. Heber Lima da Rocha
7. Marco Ruscone
8. Vincent Noël
9. Paul Macklin

• Curated by GigaByte

  Editors Assessment:

  This paper presents a new tool to make using PhysiCell easier, which is an open-source, physics-based multicellular simulation framework with a very wide user base. PhysiCell Studio is a graphical tool that makes it easier to build, run, and visualize PhysiCell models. Over time, it has evolved from being a GUI to include many additional functionalities, and can be used as desktop and cloud versions. This paper outlines the many features and functions, the design and development process behind it, and deployment instructions. Peer review improved the organisation of the various repositories and adding both a requirements.txt and environment.yml files. Looking to the future the developers are planning to add new features based on community feedback and contributions, and this paper presents the many code repositories if readers wish to contribute to the development process.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients

1. Renato Santos
2. Víctor Moreno-Torres
3. Ilduara Pintos
4. Octavio Corral
5. Carmen de Mendoza
6. Vicente Soriano
7. Manuel Corpas

• Curated by GigaByte

  Editors Assessment:

  Many studies have explored the genetic determinants of COVID-19 severity, these GWAS studies using microarrays or expensive whole-genome sequencing (WGS). Low-coverage WGS data can be imputed using reference panels to enhance resolution and statistical power while maintaining much lower costs, but imputation accuracy is difficult to balance. This work demonstrates how to address these challenges utilising the GLIMPSE1 algorithm, a less resource-intensive tool that produces more accurate imputed data than its predecessors. Generating a dataset containing 79 imputed low-coverage WGS samples from patients with severe COVID-19 symptoms during the initial wave of the SARS-CoV-2 pandemic in Spain. The validation of this imputation and filtering process shows that GLIMPSE1 can be confidently used to impute variants with minor allele frequency up to approximately 2%. After peer review the authors clarified and provided more validation and statistics and figures to help convince this approach was valid. This work showcasing the viability of using low-coverage WGS imputation to generate data for the study of disease-related genetic markers, alongside a validation methodology to ensure the accuracy of the data produced. Helping inspire confidence and encouraging others to deploy similar approaches to other infectious diseases, genetic disorders, or population-based genetic studies. Particularly in large-scale genomic projects and resource-limited settings where sequencing at higher coverage could prove to be prohibitively expensive.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome

1. Chao Yang
2. Zhenmiao Zhang
3. Yufen Huang
4. Xuefeng Xie
5. Herui Liao
6. Jin Xiao
7. Werner Pieter Veldsman
8. Kejing Yin
9. Xiaodong Fang
10. Lu Zhang

Reviewed by GigaScience

Hecatomb: An End-to-End Research Platform for Viral Metagenomics

1. Michael J. Roach
2. Sarah J. Beecroft
3. Kathie A. Mihindukulasuriya
4. Leran Wang
5. Anne Paredes
6. Kara Henry-Cocks
7. Lais Farias Oliveira Lima
8. Elizabeth A. Dinsdale
9. Robert A. Edwards
10. Scott A. Handley

Reviewed by GigaScience

ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection

1. Justin Chu
2. Jiazhen Rong
3. Xiaowen Feng
4. Heng Li

Reviewed by GigaScience

MDverse, shedding light on the dark matter of molecular dynamics simulations

1. Johanna KS Tiemann
2. Magdalena Szczuka
3. Lisa Bouarroudj
4. Mohamed Oussaren
5. Steven Garcia
6. Rebecca J Howard
7. Lucie Delemotte
8. Erik Lindahl
9. Marc Baaden
10. Kresten Lindorff-Larsen
11. Matthieu Chavent
12. Pierre Poulain

• Curated by eLife

  eLife assessment

  The study presents a valuable tool for searching molecular dynamics simulation data, making such datasets accessible for open science. The authors provide convincing evidence that it is possible to identify noteworthy molecular dynamics simulation datasets and that their analysis can produce information of value to the community.

Reviewed by eLife

Circulating small extracellular vesicle RNA profiling for the detection of T1a stage colorectal cancer and precancerous advanced adenoma

1. Li Min
2. Fanqin Bu
3. Jingxin Meng
4. Xiang Liu
5. Qingdong Guo
6. Libo Zhao
7. Zhi Li
8. Xiangji Li
9. Shengtao Zhu
10. Shutian Zhang

• Curated by eLife

  eLife assessment

  This study presents a useful description of RNA in extracellular vesicles (EV-RNAs) and highlights the potential to develop biomarkers for the early detection of colorectal cancer (CRC) and precancerous adenoma (AA). The data were analysed using overall solid methodology and would benefit from further validation of predicted lncRNAs and biomarker validation at each stage of CRC/AA to evaluate the potential application to early detection of CRC and AA.

Reviewed by eLife

GTalign: spatial index-driven protein structure alignment, superposition, and search

1. Mindaugas Margelevičius

Reviewed by Arcadia Science

Robust virtual staining of landmark organelles

1. Ziwen Liu
2. Eduardo Hirata-Miyasaki
3. Soorya Pradeep
4. Johanna Rahm
5. Christian Foley
6. Talon Chandler
7. Ivan Ivanov
8. Hunter Woosley
9. Tiger Lao
10. Akilandeswari Balasubramanian
11. Rita Marreiros
12. Chad Liu
13. Manu Leonetti
14. Ranen Aviner
15. Carolina Arias
16. Adrian Jacobo
17. Shalin B. Mehta

Reviewed by Arcadia Science

Prediction of Anti‐Freezing Proteins From Their Evolutionary Profile

1. Nishant Kumar
2. Shubham Choudhury
3. Nisha Bajiya
4. Sumeet Patiyal
5. Gajendra P. S. Raghava

Reviewed by Arcadia Science