Bioinformatics

Bioinformatics

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21-40 of 389 ARTICLES
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 in 
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
https://doi.org/10.12688/f1000research.140344.2
Research Article metrics
Revised
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
[version 2; peer review: 2 approved]
Friederike Hanssen, Gisela Gabernet, Famke Bäuerle, Bianca Stöcker, Felix Wiegand, Nicholas H. Smith, Christian Mertes, Avirup Guha Neogi, Leon Brandhoff, Anna Ossowski, Janine Altmueller, Kerstin Becker, Andreas Petzold, Marc Sturm, Tyll Stöcker, Sugirthan Sivalingam, Fabian Brand, Axel Schmidt, Andreas Buness, Alexander J. Probst, Susanne Motameny, Johannes Köster
Peer Reviewers Justin M. Zook; Kez Cleal
  • Funders
  • German Federal Ministry for Education and Research
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 12 Sep 2024
https://doi.org/10.12688/f1000research.153895.1
Opinion Article metrics
From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure
[version 1; peer review: 3 approved with reservations]
Bogdan Mirăuță, Cătălina Zenoaga-Barbăroșie, Monica Abrudan, Marius Mihășan, Mădălina Giurgiu, Daria Mihalachi, Michalis-Daniel Lazăr, RSBI Members, Horia L. Banciu
Peer Reviewers Francis Ouellette; Federico Zambelli; Carol Goble
  • Funder
  • EEA Grants/Norway Grants (Bioinformatics Capacity Building Human Genomics, an RSBI and ELIXIR Norway bilateral project)
PUBLISHED 03 Sep 2024
https://doi.org/10.12688/f1000research.131134.2
Research Article metrics
Revised
Improving genomic prediction of rhizomania resistance in sugar beet (Beta vulgaris L.) by implementing epistatic effects and feature selection
[version 2; peer review: 1 approved with reservations, 3 not approved]
Thomas Martin Lange, Felix Heinrich, Friedrich Kopisch-Obuch, Harald Keunecke, Mehmet Gültas, Armin O. Schmitt
Peer Reviewers J Mitchell McGrath; Muhammad Massub Tehseen; Daniela Holtgräwe; Chenggen Chu
LATEST VERSION PUBLISHED 28 Aug 2024
https://doi.org/10.12688/f1000research.150115.1
Research Article metrics
Unraveling the Interplay of Autophagy Genes and KLF3/KLF8 in Colorectal Cancer Metastasis: A Bioinformatics and cellular Exploration
[version 1; peer review: 1 approved with reservations, 1 not approved]
Eglal Mahgoub, Jalal Taneera, Samrein B. Ahmed, shirin hafezi, Thenmozhi Venkatachalam, Mahmood Hachim, Nabil Sulaiman, Rifat Hamoudi, Maha Saber-Ayad
Peer Reviewers Aamir Ahmed; Mohammad Azhar Aziz
  • Funders
  • University of Sharjah
  • Mohammed Bin Rashid University of Medicine and Health Sciences
PUBLISHED 30 Jul 2024
https://doi.org/10.12688/f1000research.139356.2
Research Article metrics
Revised
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
[version 2; peer review: 3 approved]
James Fleming, Pia Merete Eriksen, Torsten Hugo Struck
Peer Reviewers Paul Zaharias; Xianzhao Kan; Anthony K. Redmond
  • Funders
  • Norges Forskningsråd
  • Norwegian Metacenter for Computational Science
LATEST VERSION PUBLISHED 10 Jul 2024
https://doi.org/10.12688/f1000research.134956.2
Research Article metrics
Revised
In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein
[version 2; peer review: 3 approved]
Kishore Krishna Kumaree, Naga Venkata Anusha Anthikapalli, Anchalee Prasansuklab
Peer Reviewers Arumugam Vijaya Anand; Luis Marquez-Dominguez; Tiratha Raj Singh
  • Funder
  • Second Century Fund (C2F) Postdoctoral Fellowship, Chulalongkorn University
LATEST VERSION PUBLISHED 25 Jun 2024
https://doi.org/10.12688/f1000research.122924.2
Software Tool Article metrics
Revised
Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics
[version 2; peer review: 2 approved, 2 approved with reservations]
Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita, Takeshi Fujino, Tsuyoshi Hachiya, Yuichi Kodama, Takatomo Fujisawa, Osamu Ogasawara, Atsushi Shimizu, Masanori Arita, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta
Peer Reviewers Justin M. Wozniak; Iacopo Colonnelli; Denis Yuen; Stephen R. Piccolo
  • Funders
  • JSPS KAKENHI
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
  • Japan Science and Technology Agency
LATEST VERSION PUBLISHED 24 Jun 2024
21-40 of 389 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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    The Genetics & Genomics Gateway Area will enable researchers to publish content related to the analysis, storage and accessibility of DNA, RNA and protein sequences. This analysis can be conducted in a variety of ways, including comparison of sequences and relationships, identification of functions, and recognition of patterns across the samples. Read more keyboard_arrow_right
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