Bioinformatics

Bioinformatics

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121-140 of 377 ARTICLES
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 in 
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
https://doi.org/10.12688/f1000research.94159.1
Software Tool Article metrics
miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies
[version 1; peer review: 2 approved with reservations]
Andreas Diendorfer, Kseniya Khamina, Marianne Pultar, Matthias Hackl
Peer Reviewers Kristian Almstrup, Nina Mørup and Ailsa Maria Main; Francisco J. Enguita
  • Funder
  • Innovative Medicines Initiative 2
PUBLISHED 24 Feb 2022
https://doi.org/10.12688/f1000research.28352.2
Method Article metrics
Revised
Methods for sequencing the pandemic: benefits of rapid or high-throughput processing
[version 2; peer review: 2 approved]
Megan L. Folkerts, Darrin Lemmer, Ashlyn Pfeiffer, Danielle Vasquez, Chris French, Amber Jones, Marjorie Nguyen, Brendan Larsen, W. Tanner Porter, Krystal Sheridan, Jolene R. Bowers, David M. Engelthaler
Peer Reviewers Bronwyn L. MacInnis; Keith Crandall
  • Funders
  • Arizona Department of Health Services
  • The NARBHA institute
LATEST VERSION PUBLISHED 21 Feb 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.107925.1
Software Tool Article metrics
NIFtHool: an informatics program for identification of NifH proteins using deep neural networks
[version 1; peer review: 2 approved]
Jefferson Daniel Suquilanda-Pesántez, Evelyn Dayana Aguiar Salazar, Diego Almeida-Galárraga, Graciela Salum, Fernando Villalba-Meneses, Marco Esteban Gudiño Gomezjurado
Peer Reviewers Juan Onofre Orozco-López; Lorena Isabel Barona López
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.26452.1
Software Tool Article metrics
Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence
[version 1; peer review: 1 approved, 1 approved with reservations]
Brett E. Pickett, Ryan Connor, Tamiru Berhanu-Denka, Sherry Bhalla, Vyacheslav Brover, Michael James Chambers, Kumardeep Chaudhary, Ousmane H. Cissé, Allissa Dillman, Moamen M. Elmassry, Michael Feldgarden, Eric Holloway, Xin Huang, William Klimke, Catarina Inês Mendes, S. Elizabeth Norred, Jonathan Parkinson, Samantha Sevilla, Monica Garcia Solache, Defne Surujon, Udana Torian, Vadim Zalunin, Ben Busby
Peer Reviewers Rick Stevens and James Davis; Kevin Tyler
  • Funders
  • Fundação para a Ciência e a Tecnologia
  • Scientific and Technological Research Council of Turkey
  • Intramural Research Program of the National Library of Medicine
PUBLISHED 09 Feb 2022
https://doi.org/10.12688/f1000research.28225.2
Research Article metrics
Revised
Human Proteinase 3, an important autoantigen of c-ANCA associated vasculitis, shares cross-reactive epitopes with serine protease allergens from mites: an in silico analysis
[version 2; peer review: 1 approved, 2 approved with reservations]
Emiro Buendía, Múnera Marlon, Orlando Parra, María Sánchez, Andrés Sánchez, Jorge Sánchez, Diego Viasus
Peer Reviewers Chandrabose Selvaraj; Tomas Erban; Hiroshi Tanaka
  • Funder
  • Fondo Nacional de Financiamiento para la Ciencia, la Tecnología y la Innovación
LATEST VERSION PUBLISHED 03 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
121-140 of 377 ARTICLES
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