Bioinformatics

Bioinformatics

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1-20 of 377 ARTICLES
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https://doi.org/10.12688/f1000research.168786.1
Software Tool Article metrics AWAITING PEER REVIEW
Identification of Viral Variants from Functional Genomics Data
[version 1; peer review: awaiting peer review]
Florian Röckl, Caroline C. Friedel
Peer Reviewers Invited
  • 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 AWAITING PEER REVIEW
KICA: A MATLAB package for high-throughput analysis of calcium and voltage imaging data from cardiac cells
[version 1; peer review: awaiting peer review]
Satya N.V Arjunan, Anton Shpak, George W. Parker, Adam P. Hill
Peer Reviewers Invited
  • 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
https://doi.org/10.12688/f1000research.153698.1
Software Tool Article metrics
scRICA: An R package for multiple-sample single-cell RNA-seq data integrative comparative analysis
[version 1; peer review: 1 approved with reservations, 1 not approved]
Yan Li, Jason Shapiro, Qiaoshan Lin, Qing Gong, Michiko Ryu, Mengjie Chen
Peer Reviewers Pedro L Baldoni; Sebastiaan Valkiers
  • Funders
  • University of Chicago
  • National Institutes of Health
  • Institute for Translational Medicine
PUBLISHED 20 Jan 2025
https://doi.org/10.12688/f1000research.130618.2
Research Article metrics
Revised
In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease 
[version 2; peer review: 3 approved, 1 not approved]
Phaniendra Alugoju, Vishwambar Vishnu Bhandare, Vishal S. Patil, Krishna Swamy V. K. D, Prem Kumar Borugadda, Tewin Tencomnao
Peer Reviewers Sailu Sarvagalla; Yassir Boulaamane and Iman Touati; Abdul Rajjak Shaikh; James Adams
  • Funder
  • Thailand Science Research and Innovation Fund Chulalongkorn University
LATEST VERSION PUBLISHED 16 Dec 2024
https://doi.org/10.12688/f1000research.131014.3
Software Tool Article metrics
Revised
RBP-Tar – a searchable database for experimental RBP binding sites
[version 3; peer review: 2 approved, 4 approved with reservations]
Katarina Gresova, Tomas Racek, Vlastimil Martinek, David Cechak, Radka Svobodova, Panagiotis Alexiou
Peer Reviewers Xiaoyong Pan; Clifford A Meyer; Michiel Stock; Eric Van Nostrand; M. J. Nishanth; Zhi-Ping Liu
  • Funders
  • ELIXIR-CZ
  • Ministry of Education, Youth and Sports of the Czech Republic
  • MEYS
  • Horizon europe
LATEST VERSION PUBLISHED 25 Nov 2024
https://doi.org/10.12688/f1000research.157160.1
Software Tool Article metrics
BEpipeR: a user-friendly, flexible, and scalable data synthesis pipeline for the Biodiversity Exploratories and other research consortia
[version 1; peer review: 1 approved with reservations, 1 not approved]
Marcel Glück, Oliver Bossdorf, Henri A. Thomassen
Peer Reviewers Elliot Gould; Matthias Grenié
  • Funder
  • Deutsche Forschungsgemeinschaft
PUBLISHED 24 Oct 2024
https://doi.org/10.12688/f1000research.73999.3
Research Article metrics
Revised
A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.
[version 3; peer review: 2 approved, 1 approved with reservations]
Rizone Al Hasib, Md. Chayan Ali, Md. Shahedur Rahman, Md. Mafizur Rahman, Fee Faysal Ahmed, Md. Abdullah Al Mashud, Md. Azizul Islam, Mohammad Abu Hena Mostofa Jamal
Peer Reviewers Thi Thanh Binh Nguyen; Rituraj Purohit; Behrooz sadeghi kalani
  • Funder
  • Ministry of Science and Technology, Government of the People’s Republic of Bangladesh
LATEST VERSION PUBLISHED 07 Oct 2024
https://doi.org/10.12688/f1000research.152290.2
Software Tool Article metrics
Revised
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG
[version 2; peer review: 2 approved, 1 approved with reservations]
Jeferyd Yepes-García, Laurent Falquet
Peer Reviewers Abraham Gihawi; Fotis Baltoumas; Juliette Hayer
  • Funders
  • Centenary Research Fund of the University of Fribourg
  • Fondation de Recherche en Biochimie, Epalinges, Switzerland
LATEST VERSION PUBLISHED 23 Sep 2024
https://doi.org/10.12688/f1000research.142843.2
Research Article metrics
Revised
In silico analysis of molecular mimicry between human aquaporin 3, Aspergillus fumigatus aquaporin and aquaporins from allergic sources
[version 2; peer review: 2 approved]
Andrés Sánchez, Yaquelin Padilla, Adriana Lorduy, Jorge Sanchez, Marlon Munera, Claudia Baena, Carlos Bernal, Juan Urrego
Peer Reviewers Celso Eduardo Olivier; Elizabeth Garcia
LATEST VERSION PUBLISHED 12 Sep 2024
1-20 of 377 ARTICLES
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