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 in 
https://doi.org/10.12688/f1000research.130530.2
Software Tool Article metrics
Revised
scANANSE gene regulatory network and motif analysis of single-cell clusters
[version 2; peer review: 2 approved]
Jos G.A. Smits, Julian A. Arts, Siebren Frölich, Rebecca R. Snabel, Branco M.H. Heuts, Joost H.A. Martens, Simon J. van Heeringen, Huiqing Zhou
Peer Reviewers Kenji Kamimoto; Marouen Ben Guebila
  • Funders
  • NWO grant 016 Vidi
  • NWO-ALW
  • ZonMw Open
LATEST VERSION PUBLISHED 29 Nov 2023
https://doi.org/10.12688/f1000research.125924.3
Method Article metrics
Revised
Gaidai reliability method for long-term coronavirus modelling
[version 3; peer review: 1 approved, 3 approved with reservations]
Oleg Gaidai, Ping Yan, Yihan Xing, JingXiang Xu, Yu Wu
Peer Reviewers Oluwakemi E Abiodun; Adnan Khan; Md. Ashraful Babu; Eduard Campillo-Funollet
LATEST VERSION PUBLISHED 21 Nov 2023
https://doi.org/10.12688/f1000research.132899.1
Research Article metrics
Identification of informative genes and sub-pathways using Improved Differential Expression Analysis for Pathways (iDEAP) for cancer classification
[version 1; peer review: 1 approved, 1 approved with reservations]
Nurul Athirah Nasarudin, Mohd Saberi Mohamad, Zalmiyah Zakaria, Richard O. Sinnott, Fatma Al Jasmi, Noura Al Dhaheri
Peer Reviewers Suhaila Zainudin; Nora Muda
  • Funder
  • Strategic Research Program, United Arab Emirates University
PUBLISHED 06 Nov 2023
https://doi.org/10.12688/f1000research.126839.3
Method Article metrics
Revised
Manual annotation of Drosophila genes: a Genomics Education Partnership protocol
[version 3; peer review: 2 approved]
Chinmay P. Rele, Katie M. Sandlin, Wilson Leung, Laura K. Reed
Peer Reviewers Terence D. Murphy; Madeline Crosby
  • Funders
  • National Institute of General Medical Sciences of the National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 13 Oct 2023
https://doi.org/10.12688/f1000research.130458.2
Software Tool Article metrics
Revised
Numerical Scheme for Compartmental Models: New Matlab Software Codes for Numerical Simulation
[version 2; peer review: 2 approved]
Samuel Okyere, Joseph Ackora-Prah, Ebenezer Bonyah, Samuel Akwasi Adarkwa
Peer Reviewers Belela Samuel Kotola; Shewafera Wondimagegnhu Teklu
LATEST VERSION PUBLISHED 25 Sep 2023
https://doi.org/10.12688/f1000research.134526.1
Research Article metrics
Benchmarking graph representation learning algorithms for detecting modules in molecular networks
[version 1; peer review: 1 approved, 1 approved with reservations]
Zhiwei Song, Brittany Baur, Sushmita Roy
Peer Reviewers Claude Pasquier and Nina Singlan; Renming Liu
  • Funders
  • James S. McDonnell Foundation
  • National Human Genome Research Institute
PUBLISHED 07 Aug 2023
https://doi.org/10.12688/f1000research.125579.1
Research Article metrics
Cell-type classification of cancer single-cell RNA-seq data using the Subsemble ensemble-based machine learning classifier
[version 1; peer review: 3 approved with reservations]
David Chen, Parisa Shooshtari
Peer Reviewers Saskia Freytag; Yue Cao; Zhixiang Ren
  • Funders
  • Children's Health Research Institute
  • Ontario Institute for Cancer Research
  • Natural Sciences and Engineering Research Council of Canada
  • NSERC Undergraduate Student Research Award
PUBLISHED 14 Apr 2023
https://doi.org/10.12688/f1000research.111658.2
Software Tool Article metrics
Revised
GRAPE: genomic relatedness detection pipeline
[version 2; peer review: 2 approved]
Alexander Medvedev, Mikhail Lebedev, Andrew Ponomarev, Mikhail Kosaretskiy, Dmitriy Osipenko, Alexander Tischenko, Egor Kosaretskiy, Hui Wang, Dmitry Kolobkov, Vitalina Chamberlain-Evans, Ruslan Vakhitov, Pavel Nikonorov
Peer Reviewers Ying Zhou; Ardalan Naseri
  • Funder
  • GenX Global Limited
LATEST VERSION PUBLISHED 13 Apr 2023
https://doi.org/10.12688/f1000research.126463.2
Software Tool Article metrics
Revised
A2TEA: Identifying trait-specific evolutionary adaptations
[version 2; peer review: 2 approved]
Tyll Stöcker, Carolin Uebermuth-Feldhaus, Florian Boecker, Heiko Schoof
Peer Reviewers Manuel Aranda and Octavio Salazar Moya; Rahul Siddharthan
LATEST VERSION PUBLISHED 12 Apr 2023
https://doi.org/10.12688/f1000research.128656.1
Method Article metrics
Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups
[version 1; peer review: 1 approved with reservations, 1 not approved]
Samuel Moix, Natasha Glover, Sina Majidian
Peer Reviewers Xinyi Guo; Gavin Conant
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 12 Apr 2023
https://doi.org/10.12688/f1000research.130443.1
Research Article metrics
Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning
[version 1; peer review: 2 approved]
Margaux Aubel, Lars Eicholt, Erich Bornberg-Bauer
Peer Reviewers Caroline Weisman; Isabelle Callebaut
  • Funder
  • Volkswagen Foundation
PUBLISHED 29 Mar 2023
https://doi.org/10.12688/f1000research.131522.1
Research Article metrics
Seasonal effects decouple SARS-CoV-2 haplotypes worldwide
[version 1; peer review: 2 approved]
Tre Tomaszewski, Muhammad Asif Ali, Kelsey Caetano-Anollés, Gustavo Caetano-Anollés
Peer Reviewers Francisco Solano Muñoz; Kyung Mo Kim
  • Funders
  • National Centre for Supercomputing Applications
  • Office of Research and Office of International Programs, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign
  • National Institute of Food and Agriculture
PUBLISHED 13 Mar 2023
https://doi.org/10.12688/f1000research.130105.1
Research Article metrics
Determination of pharmacological activity of bioactives in Allium sativum using computational analysis
[version 1; peer review: 2 approved with reservations]
Stephen Ouma, Richard Kagia, Faith Kamakia
Peer Reviewers Rahadian Zainul; Sandeep Kumar
PUBLISHED 09 Feb 2023
https://doi.org/10.12688/f1000research.129490.1
Research Article metrics
Toblerone: detecting exon deletion events in cancer using RNA-seq
[version 1; peer review: 2 approved]
Andrew Lonsdale, Andreas Halman, Lauren Brown, Hansen Kosasih, Paul Ekert, Alicia Oshlack
Peer Reviewers Katherine Pillman; Matt Field
  • Funder
  • National Health and Medical Research Council
PUBLISHED 03 Feb 2023
https://doi.org/10.12688/f1000research.52791.3
Software Tool Article metrics
Revised
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
[version 3; peer review: 2 approved]
Balazs Bohar, David Fazekas, Matthew Madgwick, Luca Csabai, Marton Olbei, Tamás Korcsmáros, Mate Szalay-Beko
Peer Reviewers John H. Morris; Nadezhda Doncheva
  • Funders
  • Earlham Institute
  • Biotechnology and Biological Sciences Research Council
  • Quadram Institute Bioscience
LATEST VERSION PUBLISHED 12 Jan 2023
https://doi.org/10.12688/f1000research.123934.1
Software Tool Article metrics
ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data
[version 1; peer review: 1 approved, 1 not approved]
Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane
Peer Reviewers Sujeevan Ratnasingham; Begoña Aguado and Sandra Gonzalez
  • Funder
  • Horizon 2020 Research and Innovation Action
PUBLISHED 13 Sep 2022
https://doi.org/10.12688/f1000research.122775.1
Method Article metrics
Spatial transcriptomics dimensionality reduction using wavelet bases
[version 1; peer review: 3 approved with reservations, 1 not approved]
Zhuoyan Xu, Kris Sankaran
Peer Reviewers Ben Fulcher; André F Rendeiro; Nguyen Quoc Khanh Le; Shixiong Zhang
  • Funders
  • Office of Science
  • National Science Foundation
PUBLISHED 12 Sep 2022
https://doi.org/10.12688/f1000research.75471.3
Correspondence metrics
Revised
Positional weight matrices have sufficient prediction power for analysis of noncoding variants
[version 3; peer review: 2 approved]
Alexandr Boytsov, Sergey Abramov, Vsevolod J. Makeev, Ivan V. Kulakovskiy
Peer Reviewers Victor G. Levitsky; Philip Machanick
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 04 Jul 2022
https://doi.org/10.12688/f1000research.18553.2
Research Article metrics
Revised
Impact of pathogenic mutations of the GLUT1 glucose transporter on solute carrier dynamics using ComDYN enhanced sampling
[version 2; peer review: 2 approved, 1 approved with reservations]
Halima Mouhib, Akiko Higuchi, Sanne Abeln, Kei Yura, K. Anton Feenstra
Peer Reviewers Lucie Delemotte; Jocelyne Vreede; Lívia Maria Ferreira Sobrinho
  • Funders
  • European Molecular Biology Organization
  • Ministry of Education, Culture, Sports, Science and Technology
LATEST VERSION PUBLISHED 13 Jun 2022
https://doi.org/10.12688/f1000research.53961.3
Brief Report metrics
Revised
All neurons can perform linearly non-separable computations
[version 3; peer review: 2 approved]
Romain D. Cazé
Peer Reviewers Athanasia Papoutsi and Spyridon Chavlis; Balazs B Ujfalussy
  • Funder
  • Centre National de la Recherche Scientifique
LATEST VERSION PUBLISHED 08 Jun 2022
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