Bioinformatics

Bioinformatics

Methods and Tools

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21-40 of 81 ARTICLES
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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.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.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
https://doi.org/10.12688/f1000research.149237.1
Software Tool Article metrics
ZARP: A user-friendly and versatile RNA-seq analysis workflow
[version 1; peer review: 2 approved with reservations]
Maria Katsantoni, Foivos Gypas, Christina J Herrmann, Dominik Burri, Maciej Bąk, Paula Iborra, Krish Agarwal, Meriç Ataman, Máté Balajti, Noè Pozzan, Niels Schlusser, Youngbin Moon, Aleksei Mironov, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
Peer Reviewers Silvia Liu; Bo Li
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • National Center of Competence in Research RNA & Disease
PUBLISHED 24 May 2024
https://doi.org/10.12688/f1000research.145486.1
Research Article metrics
Negligible effects of read trimming on the accuracy of germline short variant calling in the human genome
[version 1; peer review: 2 approved with reservations]
Yury Barbitoff, Alexander Predeus
Peer Reviewers Dharma Varapula; Xihao Li and Muqing Zhou
PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.134465.2
Research Article metrics
Revised
Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Alex Kipnyargis, Eucharia Kenya, Fathiya Khamis, Romano Mwirichia
Peer Reviewers Marianne Haines; Srijak Bhatnagar; Cristiano Pedroso-Roussado; Addis Simachew
  • Funder
  • National Research Fund, Kenya
LATEST VERSION PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.127348.2
Software Tool Article metrics
Revised
CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes
[version 2; peer review: 1 approved, 2 approved with reservations]
Jianqiang Sun, Xi Fu, Wei Cao
Peer Reviewers Eric Soler and Mohammad Salma; Xueyi Dong; Alexander Zelikovsky and Bikram Sahoo
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 30 Apr 2024
https://doi.org/10.12688/f1000research.140624.3
Opinion Article metrics
Revised
Creating cloud platforms for supporting FAIR data management in biomedical research projects.
[version 3; peer review: 2 approved]
Marcel Jentsch, Valentin Schneider-Lunitz, Ulrike Taron, Martin Braun, Naveed Ishaque, Harald Wagener, Christian Conrad, Sven Twardziok
Peer Reviewers Anna Bernasconi; Joseph Bonello
  • Funders
  • Bundesministerium für Bildung und Forschung
  • HORIZON EUROPE European Research Council
LATEST VERSION PUBLISHED 29 Apr 2024
https://doi.org/10.12688/f1000research.125325.2
Software Tool Article metrics
Revised
Librarian: A quality control tool to analyse sequencing library compositions
[version 2; peer review: 2 approved, 1 approved with reservations]
Kartavya Vashishtha, Caroline Gaud, Simon Andrews, Christel Krueger
Peer Reviewers Andrew Keniry; Konstantin Okonechnikov; Karim Gharbi
  • Funder
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 24 Jan 2024
https://doi.org/10.12688/f1000research.135250.2
Software Tool Article metrics
Revised
DrosOMA: the Drosophila Orthologous Matrix browser
[version 2; peer review: 4 approved]
Antonin Thiébaut, Adrian M. Altenhoff, Giulia Campli, Natasha Glover, Christophe Dessimoz, Robert M. Waterhouse
Peer Reviewers Berend Snel; Daofeng Li; Jung-Wan Mok; Elise Parey
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 Jan 2024
https://doi.org/10.12688/f1000research.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.131861.2
Research Article metrics
Revised
Single-cell transcriptional uncertainty landscape of cell differentiation
[version 2; peer review: 2 approved]
Nan Papili Gao, Olivier Gandrillon, András Páldi, Ulysse Herbach, Rudiyanto Gunawan
Peer Reviewers Alessandro Giuliani; Geneviève Dupont
  • Funders
  • Swiss National Science Foundation
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 20 Jul 2023
https://doi.org/10.12688/f1000research.132587.2
Software Tool Article metrics
Revised
CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system
[version 2; peer review: 2 approved]
Sergio Hidalgo, Joanna C Chiu
Peer Reviewers Abhilash Lakshman; Daniel J. Cavanaugh
  • Funders
  • Pew Charitable Trusts
  • National Institute of Diabetes and Digestive and Kidney Diseases
LATEST VERSION PUBLISHED 19 Jun 2023
https://doi.org/10.12688/f1000research.132538.1
Research Article metrics
Discordant results among major histocompatibility complex binding affinity prediction tools
[version 1; peer review: 2 approved with reservations, 1 not approved]
Austin Nguyen, Abhinav Nellore, Reid F. Thompson
Peer Reviewers André Leier; Michael E Birnbaum; Nikolaos G Sgourakis and Sagar Gupta
PUBLISHED 07 Jun 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.122949.2
Software Tool Article metrics
Revised
DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
[version 2; peer review: 2 approved]
Miriam Riquelme-Perez, Fernando Perez-Sanz, Jean-François Deleuze, Carole Escartin, Eric Bonnet, Solène Brohard
Peer Reviewers Hélène Hirbec; Wenbin Guo
  • Funder
  • PhD fellowship from the CEA (Amont-Aval).
LATEST VERSION PUBLISHED 24 Mar 2023
https://doi.org/10.12688/f1000research.128091.2
Software Tool Article metrics
Revised
SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
[version 2; peer review: 2 approved]
Nachida Tadrent, Franck Dedeine, Vincent Hervé
Peer Reviewers Célio Dias Santos Júnior; Aram Mikaelyan
  • Funders
  • Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
  • Université de Tours
  • Centre National de la Recherche Scientifique
  • European Regional Development Fund
LATEST VERSION PUBLISHED 27 Feb 2023
https://doi.org/10.12688/f1000research.128982.1
Software Tool Article metrics
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE)
[version 1; peer review: 2 approved]
Yuda Munarko, Anand Rampadarath, David Nickerson
Peer Reviewers Socrates Dokos; Garima Malik
  • Funders
  • National Institutes of Health
  • Aotearoa Foundation
  • Auckland Bioengineering Institute
PUBLISHED 10 Feb 2023
21-40 of 81 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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