Bioinformatics

Bioinformatics

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1-20 of 384 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.171282.1
Research Article metrics AWAITING PEER REVIEW
’Spanscriptomics’: towards bioinformatics training materials in Spanish.
[version 1; peer review: awaiting peer review]
Jurgi Giraud, Stefana Dreptate, Wendi Bacon, The Galaxy Community
Peer Reviewers Invited
  • Funder
  • Company of Biologists
PUBLISHED 20 Oct 2025
https://doi.org/10.12688/f1000research.129581.2
Software Tool Article metrics
Revised
AmpSeqR: an R package for amplicon deep sequencing data analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Jiru Han, Jacob E. Munro, Melanie Bahlo
Peer Reviewers Eduardo Castro-Nallar; Cristian Koepfli and Gustavo Da Silva; Patrick Murigu Kamau Njage
  • Funders
  • Institute Infrastructure Support Scheme (IRIISS)
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 17 Oct 2025
https://doi.org/10.12688/f1000research.163212.2
Data Note metrics
Revised
CD4+ T-cell transcription factors as early predictors of phenoconversion in idiopathic rapid eye movement sleep behaviour disorder
[version 2; peer review: 1 approved, 1 approved with reservations]
Monica Pinoli, Michele Terzaghi, Franca Marino, Cristoforo Comi, Maurizio Versino, Marco Cosentino
Peer Reviewers Tommaso Schirinzi; Adawiya J. Haider
LATEST VERSION PUBLISHED 06 Oct 2025
https://doi.org/10.12688/f1000research.157465.2
Research Article metrics
Revised
Exploring acenocoumarol and silodosin in non-small cell lung cancer: Insights into EGFR-linked signaling mechanisms
[version 2; peer review: 1 approved with reservations, 1 not approved]
Swastika Maity, Krishnaprasad Baby, Bharath Harohalli Byregowda, Megh Pravin Vithalkar, Usha Y Nayak, K Sreedhara Ranganath Pai, Yogendra Nayak
Peer Reviewers Tyler Beyett; Chandan Shivamallu
  • Funders
  • Science and Engineering Research Board
  • Indian Council of Medical Research
LATEST VERSION PUBLISHED 23 Sep 2025
https://doi.org/10.12688/f1000research.29032.3
Method Article metrics
Revised
Sustainable data analysis with Snakemake
[version 3; peer review: 2 approved]
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vieira, Christian Meesters, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Jake VanCampen, Venkat Malladi, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Peer Reviewers Michael Reich; Caroline C. Friedel
  • Funders
  • Netherlands Organisation for Scientific Research (NWO)
  • Deutsche Stiftung für Herzforschung
  • Google LLC
  • United States National Science Foundation Graduate Research Fellowship Program (NSF-GRFP)
LATEST VERSION PUBLISHED 23 Sep 2025
https://doi.org/10.12688/f1000research.168245.1
Software Tool Article metrics AWAITING PEER REVIEW
Computational Modeling and Visualization of Ischemic Effects on an Advanced Purkinje Network
[version 1; peer review: awaiting peer review]
Laiba Khan, Maham khan, Nijat Rzayev, Mahmood ahmad, Joanne Lac
Peer Reviewers Invited
PUBLISHED 18 Sep 2025
https://doi.org/10.12688/f1000research.164530.1
Research Article metrics AWAITING PEER REVIEW
Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human.
[version 1; peer review: awaiting peer review]
Olivier Gandrillon
Peer Reviewers Invited
  • Funder
  • Ligue Contre le Cancer
PUBLISHED 11 Sep 2025
https://doi.org/10.12688/f1000research.168786.1
Software Tool Article metrics
Identification of Viral Variants from Functional Genomics Data
[version 1; peer review: 1 approved with reservations]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Dóra Tombácz
  • Funder
  • Deutsche Forschungsgemeinschaft
PUBLISHED 18 Aug 2025
https://doi.org/10.12688/f1000research.139476.2
Research Article metrics
Revised
Epigenetic germline variants predict cancer prognosis and risk and distribute uniquely in topologically associating domains
[version 2; peer review: 1 approved, 1 approved with reservations]
Shervin Goudarzi, Meghana Pagadala, Adam Klie, James V Talwar, Hannah Carter
Peer Reviewers Charu Mehta; Chiara Herzog
  • Funders
  • National Institutes of Health, National Cancer Institute
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 24 Jul 2025
https://doi.org/10.12688/f1000research.166855.1
Software Tool Article metrics
KICA: A MATLAB package for high-throughput analysis of calcium and voltage imaging data from cardiac cells
[version 1; peer review: 1 approved with reservations]
Satya N.V Arjunan, Anton Shpak, George W. Parker, Adam P. Hill
Peer Reviewers Amelia S Power and Amanda Groenewald
  • Funders
  • Targeted Translation Research Accelerator
  • New South Wales Office for Health and Medical Research
PUBLISHED 17 Jul 2025
https://doi.org/10.12688/f1000research.154432.2
Research Article metrics
Revised
Deep learning neural network development for the classification of bacteriocin sequences produced by lactic acid bacteria
[version 2; peer review: 4 approved]
Lady L. González, Isaac Arias-Serrano, Fernando Villalba-Meneses, Paulo Navas-Boada, Jonathan Cruz-Varela
Peer Reviewers John J. Georrge; Alaa Kareem Niamah; Ismail Erol; Cristóbal Joel González-Pérez
LATEST VERSION PUBLISHED 20 Jun 2025
https://doi.org/10.12688/f1000research.155223.2
Review metrics
Revised
Selecting differential splicing methods: Practical considerations for short-read RNA sequencing
[version 2; peer review: 2 approved, 3 approved with reservations]
Ben J. Draper, Mark J. Dunning, David C. James
Peer Reviewers Stefano Donega; Charlotte Capitanchik; Julia Olivieri; Zhaoqi Liu; Monica Salinas and Juan Valcarcel
  • Funders
  • Lonza Biologics plc
  • University of Sheffield
LATEST VERSION PUBLISHED 30 May 2025
https://doi.org/10.12688/f1000research.145391.3
Research Article metrics
Revised
Molecular docking studies and molecular dynamic simulation analysis: To identify novel ATP-competitive inhibition of Glycogen synthase kinase-3β for Alzheimer’s disease
[version 3; peer review: 2 approved, 1 approved with reservations, 1 not approved]
Suggala Ramya Shri, Yogendra Nayak, Sreedhara Ranganath Pai
Peer Reviewers Qingchun Zhao; Jigna Samir Shah; Shvetank Bhatt; Sachchida Rai and Payal Singh
  • Funder
  • Indian Council of Medical Research
LATEST VERSION PUBLISHED 27 May 2025
https://doi.org/10.12688/f1000research.140273.3
Research Article metrics
Revised
Predicting gene expression changes upon epigenomic drug treatment
[version 3; peer review: 4 approved, 2 not approved]
Piyush Agrawal, Vishaka Gopalan, Monjura Afrin Rumi, Sridhar Hannenhalli
Peer Reviewers Angelika Merkel; Daiqing Liao and Zhiguang Huo; Sukhen Das Mandal; Indrakant K. Singh; Vivek Dhar Dwivedi; Ashwini Kumar
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 02 May 2025
https://doi.org/10.12688/f1000research.160063.2
Software Tool Article metrics
Revised
mimicINT: A workflow for microbe-host protein interaction inference
[version 2; peer review: 2 approved, 1 approved with reservations]
Sébastien A. Choteau, Kevin Maldonado, Aurélie Bergon, Marceau Cristianini, Mégane Boujeant, Lilian Drets, Christine Brun, Lionel Spinelli, Andreas Zanzoni
Peer Reviewers Ylva Ivarsson; Sobia Idrees; Leandro Simonetti
  • Funders
  • Excellence Initiative of Aix-Marseille University - A*MIDEX
  • Agence Nationale de la Recherche
  • Fondation pour la Recherche Médicale
  • European Union’s Horizon 2020 Research and Innovation Programme
LATEST VERSION PUBLISHED 28 Mar 2025
https://doi.org/10.12688/f1000research.162719.1
Software Tool Article metrics
The EpiFusion Analysis Framework for joint phylodynamic and epidemiological analysis of outbreak characteristics
[version 1; peer review: 2 approved, 1 approved with reservations]
Ciara Judge, Oliver Brady, Sarah Hill
Peer Reviewers Vijaykrishna Dhanasekaran and Ruopeng Xie; Claire Guinat; Leo A Featherstone
  • Funders
  • National Universities of Ireland Denis Phelan Scholarship
  • Medical Research Council
  • Wellcome Trust
  • Bloomsbury Colleges PhD Studentship
PUBLISHED 28 Mar 2025
https://doi.org/10.12688/f1000research.161076.1
Software Tool Article metrics
ShinyCellPlus: an improved ShinyCell application for the interactive visualization of single cell dat
[version 1; peer review: 2 approved with reservations]
Drew Moore, Bryan Granger, Stefano Berto
Peer Reviewers Valdemaras Petrošius; Pierre-Luc Germain
  • Funder
  • National Institute of General Medical Sciences
PUBLISHED 27 Mar 2025
https://doi.org/10.12688/f1000research.155657.2
Research Article metrics
Revised
Molecular docking and MD simulation approach to identify potential phytochemical lead molecule against triple negative breast cancer
[version 2; peer review: 1 approved, 2 approved with reservations]
Pranaya Sankaranarayanan, Dicky John Davis G, Abhinand PA, M Manikandan, Arabinda Ghosh
Peer Reviewers Shiek S S J Ahmed; Yutian Zou; Indiraleka Muthiah
  • Funder
  • Sri Ramachandra Institute of Higher Education and Research (Deemed to be University)
LATEST VERSION PUBLISHED 18 Mar 2025
https://doi.org/10.12688/f1000research.76068.5
Research Article metrics
Revised
Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
[version 5; peer review: 2 approved, 2 approved with reservations, 1 not approved]
Soichi Osozawa, John Wakabayashi
Peer Reviewers Sungsik Kong; David A Duchêne; Fan Song; Jacek Szwedo; Christopher H Dietrich
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 14 Feb 2025
https://doi.org/10.12688/f1000research.127142.3
Software Tool Article metrics
Revised
Med-ImageTools: An open-source Python package for robust data processing pipelines and curating medical imaging data
[version 3; peer review: 2 approved]
Sejin Kim, Michal Kazmierski, Kevin Qu, Jacob Peoples, Minoru Nakano, Vishwesh Ramanathan, Joseph Marsilla, Mattea Welch, Amber Simpson, Benjamin Haibe-Kains
Peer Reviewers Rachel Sparks; Johann Faouzi
  • Funders
  • Canadian Cancer Society
  • Canadian Institutes of Health Research
LATEST VERSION PUBLISHED 07 Feb 2025
1-20 of 384 ARTICLES
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    The Methods and Tools Gateway Area will allow researchers to publish outputs concerning both the application and research into the use of various computational methods to analyse quantities of biological data for a range of different results, including predictions and discoveries. Read more keyboard_arrow_right
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