Bioinformatics

Bioinformatics

Methods and Tools

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41-60 of 69 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.53214.4
Research Article metrics
Revised
Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences
[version 4; peer review: 2 approved, 1 approved with reservations]
Onega Ulianova, Yury Saltykov, Sergey Ulyanov, Sergey Zaytsev, Alexander Ulyanov, Valentina Feodorova
Peer Reviewers Oleg Angelsky; Alexey Bashkatov and Claudia Zenkova; Dmitry A. Zimnyakov
  • Funder
  • Russian Foundation for Basic Research
LATEST VERSION PUBLISHED 22 Jun 2022
https://doi.org/10.12688/f1000research.121775.1
Software Tool Article metrics
eXNVerify: coverage analysis for long and short-read sequencing data in clinical context
[version 1; peer review: 2 approved, 1 approved with reservations]
Sebastian Porębski, Tomasz Stokowy
Peer Reviewers Zebin Zhang; Xueyi Dong; Wouter De Coster
  • Funders
  • Bergen Research Foundation
  • Research Council of Norway
  • Silesian University of Technology
PUBLISHED 13 Jun 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.121486.1
Method Article metrics
Ensemble method for cluster number determination and algorithm selection in unsupervised learning
[version 1; peer review: 2 approved with reservations, 1 not approved]
Antoine Zambelli
Peer Reviewers Dong Huang; Ana Estela Antunes da Silva; Luca Coraggio
PUBLISHED 25 May 2022
https://doi.org/10.12688/f1000research.114698.1
Method Article metrics
DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning
[version 1; peer review: 1 approved, 1 approved with reservations]
Jesús Fernando Cevallos Moreno, Peyman Zarrineh, Aminael Sánchez-Rodríguez, Massimo Mecella
Peer Reviewers Wanding Zhou; Tallulah Andrews and Boris Tchatchoua Ngassam
  • Funders
  • Universidad Técnica Particular de Loja
  • ELIS Innovation Hub
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 13 May 2022
https://doi.org/10.12688/f1000research.110936.1
Research Article metrics
TReNCo: Topologically associating domain (TAD) aware regulatory network construction
[version 1; peer review: 2 not approved]
Christopher Bennett, Viren Amin, Daehwan Kim, Murat Can Cobanoglu, Venkat Malladi
Peer Reviewers Junbai Wang; Sonika Tyagi
  • Funders
  • National Institute of General Medical Sciences
  • Cancer Prevention and Research Institute of Texas
PUBLISHED 14 Apr 2022
https://doi.org/10.12688/f1000research.76154.1
Software Tool Article metrics
IsoAligner: dynamic mapping of amino acid positions across protein isoforms
[version 1; peer review: 2 approved with reservations]
Jacob Hanimann, Holger Moch, Martin Zoche, Abdullah Kahraman
Peer Reviewers James D Stephenson; Laurens van de Wiel
PUBLISHED 31 Mar 2022
https://doi.org/10.12688/f1000research.83714.1
Software Tool Article metrics
pTITAN2: Permutation of treatment labels and Threshold Indicator Taxa ANalysis
[version 1; peer review: 1 approved, 1 not approved]
Stephanie Figary, Peter DeWitt, Naomi Detenbeck
Peer Reviewers Cajo J. F. ter Braak; Jonathan A Walter
  • Funder
  • U.S. Environmental Protection Agency
PUBLISHED 02 Mar 2022
https://doi.org/10.12688/f1000research.75243.1
Software Tool Article metrics
SASCRiP: A Python workflow for preprocessing UMI count-based scRNA-seq data
[version 1; peer review: 2 approved with reservations]
Darisia Moonsamy, Nikki Gentle
Peer Reviewers Fabiola Curion and Luke Zappia; Fangming Xie
  • Funder
  • National Research Foundation
PUBLISHED 15 Feb 2022
https://doi.org/10.12688/f1000research.79530.1
Software Tool Article metrics
bit: a multipurpose collection of bioinformatics tools
[version 1; peer review: 2 not approved]
Michael Lee
Peer Reviewers Kai Zhang; Georges Hattab
PUBLISHED 31 Jan 2022
https://doi.org/10.12688/f1000research.76004.1
Software Tool Article metrics
skater: an R package for SNP-based kinship analysis, testing, and evaluation
[version 1; peer review: 2 approved, 1 approved with reservations]
Stephen D. Turner, V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Carlos Acevedo, Jianye Ge, August E. Woerner, Bruce Budowle
Peer Reviewers Wei-Min Chen; Magnus Dehli Vigeland; Amy L. Williams
  • Funder
  • National Institute of Justice
PUBLISHED 07 Jan 2022
https://doi.org/10.12688/f1000research.73641.1
Software Tool Article metrics
PlotXpress, a webtool for normalization and visualization of reporter expression data
[version 1; peer review: 3 approved]
Elias Brandorff, Marc Galland, Joachim Goedhart
Peer Reviewers Lorena Pantano Rubino; Guillaume Jacquemet; Vincent J. Lynch
PUBLISHED 08 Nov 2021
https://doi.org/10.12688/f1000research.54159.1
Opinion Article metrics
Perspectives on automated composition of workflows in the life sciences
[version 1; peer review: 2 approved]
Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Peer Reviewers Pinar Alper; Rafael Ferreira da Silva
  • Funder
  • European Commission Horizon 2020 Framework Programme
PUBLISHED 07 Sep 2021
https://doi.org/10.12688/f1000research.51755.2
Review metrics
Revised
Calcium imaging analysis – how far have we come?
[version 2; peer review: 3 approved]
Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, Marta Zlatic
Peer Reviewers Christopher Rowlands and Isabell Whiteley; William Zeiger; Anubhuti Goel
LATEST VERSION PUBLISHED 26 Aug 2021
https://doi.org/10.12688/f1000research.27214.2
Software Tool Article metrics
Revised
iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
[version 2; peer review: 2 approved]
Ahmad Rajeh, Kyle Wolf, Courtney Schiebout, Nabeel Sait, Tim Kosfeld, Richard J. DiPaolo, Tae-Hyuk Ahn
Peer Reviewers Shuo-Wang Qiao and Ying Yao; Se-Ran Jun
  • Funder
  • Federal Bureau of Investigations
LATEST VERSION PUBLISHED 29 Jun 2021
https://doi.org/10.12688/f1000research.52460.1
Software Tool Article metrics
scNetViz: from single cells to networks using Cytoscape
[version 1; peer review: 2 approved]
Krishna Choudhary, Elaine C. Meng, J. Javier Diaz-Mejia, Gary D. Bader, Alexander R. Pico, John H. Morris
Peer Reviewers Luca Pinello; Kenji Kamimoto
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.50857.2
Brief Report metrics
Revised
Interactive SARS-CoV-2 mutation timemaps
[version 2; peer review: 3 approved]
René L. Warren, Inanc Birol
Peer Reviewers Ingo Ebersberger and Ruben Iruegas; Takahiko Koyama; Jale Moradi
  • Funders
  • National Institute for Health Research
  • Genome Canada
LATEST VERSION PUBLISHED 03 Jun 2021
https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.27062.2
Software Tool Article metrics
Revised
SAPHIR: a Shiny application to analyze tissue section images
[version 2; peer review: 2 approved]
Elodie Germani, Hugues Lelouard, Mathieu Fallet
Peer Reviewers Mahmoud Ahmed; Seth Winfree
  • Funders
  • Agence Nationale de la Recherche
  • Aix-Marseille University
  • Fondation pour la Recherche Médicale
  • Centre National de la Recherche Scientifique and Institut National de la Santé et de la Recherche Médicale
LATEST VERSION PUBLISHED 08 Apr 2021
41-60 of 69 ARTICLES
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  • Methods and Tools
    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
  • Genetics and Genomics
    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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    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
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    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
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    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
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