Bioinformatics

Bioinformatics

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121-140 of 389 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.122840.1
Software Tool Article metrics
vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework
[version 1; peer review: 1 approved, 2 approved with reservations]
V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Jianye Ge, August E. Woerner, Meng Huang, Bruce Budowle, Stephen D. Turner
Peer Reviewers Ardalan Naseri; Gianluca Della Vedova; Cristiane Taniguti
  • Funders
  • Center for Human Identification, University of North Texas Health Science Center
  • National Institute of Justice, Office of Justice Programs, U.S. Department of Justice
PUBLISHED 11 Jul 2022
https://doi.org/10.12688/f1000research.118761.1
Software Tool Article metrics
MAFDash: An easy-to-use dashboard builder for mutation data
[version 1; peer review: 2 not approved]
Ashish Jain, Mayank Tandon
Peer Reviewers Sigve Nakken; Heiko Brennenstuhl
  • Funder
  • National Cancer Institute, National Institutes of Health
PUBLISHED 06 Jul 2022
https://doi.org/10.12688/f1000research.75471.3
Correspondence metrics
Revised
Positional weight matrices have sufficient prediction power for analysis of noncoding variants
[version 3; peer review: 2 approved]
Alexandr Boytsov, Sergey Abramov, Vsevolod J. Makeev, Ivan V. Kulakovskiy
Peer Reviewers Victor G. Levitsky; Philip Machanick
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 04 Jul 2022
https://doi.org/10.12688/f1000research.53842.2
Opinion Article metrics
Revised
Python for gene expression
[version 2; peer review: 2 approved]
Leonid Bystrykh
Peer Reviewers Sergio Peignier; Yasha Hasija
LATEST VERSION PUBLISHED 23 Jun 2022
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.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
121-140 of 389 ARTICLES
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