Bioinformatics

Bioinformatics

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121-140 of 384 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.54685.2
Opinion Article metrics
Revised
Introducing R as a smart version of calculators enables beginners to explore it on their own
[version 2; peer review: 3 approved]
Krishna Choudhary, Alexander R. Pico
Peer Reviewers Lex Nederbragt; Yasha Hasija; Rayna M Harris
  • Funders
  • UCSF Bakar Computational Health Sciences Institute
  • Gladstone Institutes
LATEST VERSION PUBLISHED 21 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.109895.4
Research Article metrics
Revised
Duration of dry and humidified incubation of single-step embryo culture medium and oxygen tension during sham culture do not alter medium composition.
[version 4; peer review: 2 approved]
Aswathi Cheredath, Shubhashree Uppangala, Gitanjali Asampille, Vani Lakshmi R., David Joseph, Keyur Raval, Nagana Gowda G. A., Guruprasad Kalthur, Satish Kumar Adiga
Peer Reviewers Erode N. Prabhakaran; Borut Kovačič and Peter Slatinšek
  • Funders
  • Science and Engineering Research Board
  • Manipal Academy of Higher Education
LATEST VERSION PUBLISHED 30 May 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.109080.2
Opinion Article metrics
Revised
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
[version 2; peer review: 2 approved]
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul J. Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
Peer Reviewers Boas Pucker and Alenka Hafner; Micha M. Bayer
  • Funders
  • ELIXIR
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 19 May 2022
https://doi.org/10.12688/f1000research.51868.3
Method Article metrics
Revised
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo
[version 3; peer review: 2 approved]
Benjamin Mayer, Meike Schwan, Kai M. Thormann, Peter L. Graumann
Peer Reviewers Massimiliano Lucidi; Janos Kriston-Vizi and Qing Hsuan Ong
  • Funder
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 17 May 2022
https://doi.org/10.12688/f1000research.73600.2
Software Tool Article metrics
Revised
Doublet identification in single-cell sequencing data using scDblFinder
[version 2; peer review: 2 approved]
Pierre-Luc Germain, Aaron Lun, Carlos Garcia Meixide, Will Macnair, Mark D. Robinson
Peer Reviewers Zev J. Gartner and Chris McGinnis; Dennis Kostka and Hannah Schriever
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 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.108835.2
Software Tool Article metrics
Revised
SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline
[version 2; peer review: 2 approved, 1 approved with reservations]
John Krapohl, Brett E. Pickett
Peer Reviewers Tobias Jakobi; Michael J Roach; Lauren Mak
LATEST VERSION PUBLISHED 28 Apr 2022
https://doi.org/10.12688/f1000research.110351.1
Brief Report metrics
High-quality genome assembly of a Pestalotiopsis fungus using DIY-friendly methods
[version 1; peer review: 3 approved with reservations]
Joshua L. McGinnis, Daniel J. Giguere
Peer Reviewers Paula Maria Moolhuijzen; Huzefa A Raja; Sinem Beyhan
  • Funder
  • Mitacs
PUBLISHED 20 Apr 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.54449.2
Research Article metrics
Revised
Philympics 2021: Prophage Predictions Perplex Programs
[version 2; peer review: 1 approved, 1 approved with reservations]
Michael J. Roach, Katelyn McNair, Maciej Michalczyk, Sarah K Giles, Laura K Inglis, Evan Pargin, Jakub Barylski, Simon Roux, Przemysław Decewicz, Robert A. Edwards
Peer Reviewers Franklin Nobrega; Karthik Anantharaman and Kristopher Kieft
  • Funder
  • NIH National Institute Of Diabetes And Digestive And Kidney Diseases
LATEST VERSION PUBLISHED 08 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.51494.2
Method Article metrics
Revised
The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Zoey R. Werbin, Briana Hackos, Jorge Lopez-Nava, Michael C. Dietze, Jennifer M. Bhatnagar
Peer Reviewers Naupaka Zimmerman; William Nelson; Olubukola Oluranti Babalola
  • Funder
  • National Science Foundation
LATEST VERSION PUBLISHED 23 Mar 2022
https://doi.org/10.12688/f1000research.39214.2
Opinion Article metrics
Revised
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing
[version 2; peer review: 1 approved, 2 approved with reservations]
Mauro Petrillo, Marco Fabbri, Dafni Maria Kagkli, Maddalena Querci, Guy Van den Eede, Erik Alm, Derya Aytan-Aktug, Salvador Capella-Gutierrez, Catherine Carrillo, Alessandro Cestaro, Kok-Gan Chan, Teresa Coque, Christoph Endrullat, Ivo Gut, Paul Hammer, Gemma L. Kay, Jean-Yves Madec, Alison E. Mather, Alice Carolyn McHardy, Thierry Naas, Valentina Paracchini, Silke Peter, Arthur Pightling, Barbara Raffael, John Rossen, Etienne Ruppé, Robert Schlaberg, Kevin Vanneste, Lukas M. Weber, Henrik Westh, Alexandre Angers-Loustau
Peer Reviewers Rene Hendriksen; Anna Abramova and Marcus Wenne; Enrico Lavezzo and Emilio Ispano
  • Funders
  • Biotechnology and Biological Sciences Research Counci
  • European Commission
LATEST VERSION PUBLISHED 16 Mar 2022
https://doi.org/10.12688/f1000research.84360.1
Review metrics
Automated human chromosome segmentation and feature extraction: Current trends and prospects
[version 1; peer review: 2 approved with reservations]
Umaya Bhashini Balagalla, Jagath Samarabandu, Akila Subasinghe
Peer Reviewers Mousami Munot; Lamiaa Elrefae
PUBLISHED 11 Mar 2022
https://doi.org/10.12688/f1000research.74024.1
Research Article metrics
eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain
[version 1; peer review: 2 approved]
Sirarat Sarntivijai, Niklas Blomberg, Katharina B. Lauer, Katharine Briggs, Thomas Steger-Hartmann, Johan van der Lei, John-Michael Sauer, Richard Liwski, Miranda Mourby, Montse Camprubi, The eTRANSAFE Consortium
Peer Reviewers Merran Smith; Ishwar Chandramouliswaran
  • Funders
  • Innovative Medicines Initiative
  • Horizon 2020
PUBLISHED 07 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.23790.2
Method Article metrics
Revised
How to build phylogenetic species trees with OMA
[version 2; peer review: 2 approved]
David Dylus, Yannis Nevers, Adrian M. Altenhoff, Antoine Gürtler, Christophe Dessimoz, Natasha M. Glover
Peer Reviewers Jianbo Xie; Denis Baurain
  • Funders
  • Swiss National Science Foundation
  • Swiss Institute of Bioinformatics
LATEST VERSION PUBLISHED 28 Feb 2022
121-140 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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    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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    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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