Bioinformatics

Bioinformatics

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241-260 of 378 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.17976.2
Software Tool Article metrics
Revised
TFutils: Data structures for transcription factor bioinformatics
[version 2; peer review: 2 approved, 1 not approved]
Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin Raby, Vincent Carey
Peer Reviewers Lihua Julie Zhu, Haibo Liu and Rui Li; Giovanna Ambrosini, Philipp Bucher and Rui Li; Kevin Ernst and Matthew T. Weirauch
  • Funders
  • National Institute of Allergy and Infectious Diseases
  • National Heart, Lung, and Blood Institute
  • National Cancer Institute
LATEST VERSION PUBLISHED 17 May 2019
https://doi.org/10.12688/f1000research.18458.2
Software Tool Article metrics
Revised
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
[version 2; peer review: 2 approved]
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Peer Reviewers Marta Szachniuk; Jerome Waldispühl and Roman Sarrazin-Gendron
  • Funder
  • Austrian Science Fund
LATEST VERSION PUBLISHED 23 Apr 2019
https://doi.org/10.12688/f1000research.15091.2
Research Note metrics
Revised
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach
[version 2; peer review: 2 approved with reservations]
Pedro Morell Miranda, Francesca Bertolini, Haja N. Kadarmideen
Peer Reviewers Yasir Suhail; Manikandan Narayanan
  • Funders
  • Technical University of Denmark, DTU Bioinformatics
  • The Danish Independent Research Council
LATEST VERSION PUBLISHED 17 Apr 2019
https://doi.org/10.12688/f1000research.16252.3
Method Article metrics
Revised
Improved inference of chromosome conformation from images of labeled loci
[version 3; peer review: 2 approved]
Brian C. Ross, James C. Costello
Peer Reviewers Ewan Birney and Carl Barton; Marco Cosentino Lagomarsino and Vittore Scolari
  • Funders
  • Boettcher Foundation
  • Cancer League of Colorado
  • National Institutes of Health
LATEST VERSION PUBLISHED 28 Mar 2019
https://doi.org/10.12688/f1000research.17139.3
Software Tool Article metrics
Revised
Radtools: R utilities for convenient extraction of medical image metadata
[version 3; peer review: 2 approved]
Pamela H. Russell, Debashis Ghosh
Peer Reviewers Andrey Fedorov; Volker Schmid
  • Funder
  • Cancer Center, University of Colorado
LATEST VERSION PUBLISHED 25 Mar 2019
https://doi.org/10.12688/f1000research.15140.2
Opinion Article metrics
Revised
Recommendations for the packaging and containerizing of bioinformatics software
[version 2; peer review: 2 approved, 1 approved with reservations]
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol
Peer Reviewers Ka Yee Yeung and Daniel Kristiyanto; Monther Alhamdoosh; Evan Floden
  • Funders
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 20 Mar 2019
https://doi.org/10.12688/f1000research.16198.2
Software Tool Article metrics
Revised
scClustViz – Single-cell RNAseq cluster assessment and visualization
[version 2; peer review: 2 approved]
Brendan T. Innes, Gary D. Bader
Peer Reviewers Martin Hemberg and Tallulah Andrews; Michael Steinbaugh
  • Funder
  • Canada First Research Excellence Fund
LATEST VERSION PUBLISHED 12 Mar 2019
https://doi.org/10.12688/f1000research.17149.2
Research Article metrics
Revised
Hub genes in a pan-cancer co-expression network show potential for predicting drug responses
[version 2; peer review: 2 approved]
Francisco Azuaje, Tony Kaoma, Céline Jeanty, Petr V. Nazarov, Arnaud Muller, Sang-Yoon Kim, Gunnar Dittmar, Anna Golebiewska, Simone P. Niclou
Peer Reviewers Elizabeth A. Coker; Therese Commes
  • Funders
  • Fonds National de la Recherche Luxembourg
  • Ministère de l'Education Nationale, de l'Enseignement Superieur et de la Recherche
LATEST VERSION PUBLISHED 05 Mar 2019
https://doi.org/10.12688/f1000research.18357.1
Opinion Article metrics
Advancing the international data science workforce through shared training and education
[version 1; peer review: 1 approved, 1 approved with reservations]
John Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi
Peer Reviewers Ariel Rokem; David N. Kennedy and Julianna F. Bates
  • Funder
  • National Institutes of Health
PUBLISHED 04 Mar 2019
https://doi.org/10.12688/f1000research.17739.1
Editorial metrics NOT PEER REVIEWED
Nurturing tomorrow’s leaders: The ISCB Student Council Symposia in 2018
[version 1; peer review: not peer reviewed]
Daniele Parisi, Gabriel J. Olguín-Orellana, Eli J. Draizen, Nilson Da Rocha Coimbra, Nikolaos Papadopoulos, Susanne Kirchen, Yvonne Saara Gladbach, Numrah Fadra, Nazeefa Fatima, Aishwarya Alex Namasivayam, Sayane Shome, Dan DeBlasio, Alexander M. Monzon, Farzana Rahman, R. Gonzalo Parra
  • Funder
  • International Society for Computational Biology
PUBLISHED 09 Jan 2019
https://doi.org/10.12688/f1000research.17518.1
Software Tool Article metrics
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
[version 1; peer review: 2 approved]
Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey
Peer Reviewers Dennis J. Hazelett; Sheila Reynolds
  • Funders
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jan 2019
https://doi.org/10.12688/f1000research.9005.3
Software Tool Article metrics
Revised
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
[version 3; peer review: 3 approved]
Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Peer Reviewers James W. MacDonald; Maria A. Doyle; Jovana Maksimovic
  • Funders
  • Australian Government NHMRC IRIISS
  • State Government Operational Infrastructure Support
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 28 Dec 2018
https://doi.org/10.12688/f1000research.17315.1
Method Article metrics
Rapid identification of novel protein families using similarity searches
[version 1; peer review: 2 approved]
Matt Jeffryes, Alex Bateman
Peer Reviewers Daniel J. Rigden; Desmond G Higgins
  • Funder
  • European Molecular Biology Laboratory
PUBLISHED 24 Dec 2018
https://doi.org/10.12688/f1000research.15809.2
Research Article metrics
Revised
Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
[version 2; peer review: 3 approved]
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Peer Reviewers Joshua W. K. Ho; Shila Ghazanfar; Stephanie C Hicks
  • Funder
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 19 Dec 2018
https://doi.org/10.12688/f1000research.14509.2
Opinion Article metrics
Revised
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
[version 2; peer review: 2 approved]
Alexandre Angers-Loustau, Mauro Petrillo, Johan Bengtsson-Palme, Thomas Berendonk, Burton Blais, Kok-Gan Chan, Teresa M. Coque, Paul Hammer, Stefanie Heß, Dafni M. Kagkli, Carsten Krumbiegel, Val F. Lanza, Jean-Yves Madec, Thierry Naas, Justin O'Grady, Valentina Paracchini, John W.A. Rossen, Etienne Ruppé, Jessica Vamathevan, Vittorio Venturi, Guy Van den Eede
Peer Reviewers Enrico Lavezzo and Giorgio Palù; Jason C. Kwong
  • Funder
  • European Commission
LATEST VERSION PUBLISHED 07 Dec 2018
https://doi.org/10.12688/f1000research.16338.1
Software Tool Article metrics
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
[version 1; peer review: 2 approved]
Clarence K. Mah, Jill P. Mesirov, Lukas Chavez
Peer Reviewers Robert  Ivanek; Aris Floratos
  • Funder
  • National Institutes of Health
PUBLISHED 05 Dec 2018
https://doi.org/10.12688/f1000research.16301.2
Software Tool Article metrics
Revised
Increasing workflow development speed and reproducibility with Vectools
[version 2; peer review: 2 approved]
Tyler Weirick, Raphael Müller, Shizuka Uchida
Peer Reviewers Yutaka Saito; Dimitar Vassilev
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Gheens Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.16605.1
Software Tool Article metrics
KnetMaps: a BioJS component to visualize biological knowledge networks
[version 1; peer review: 3 approved, 1 approved with reservations]
Ajit Singh, Christopher J. Rawlings, Keywan Hassani-Pak
Peer Reviewers Ian Dunham and Gareth Peat; Chia-Yi Cheng; Nicholas J. Provart; Ramil Mauleon
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 17 Oct 2018
https://doi.org/10.12688/f1000research.16290.1
Method Article metrics
A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens
[version 1; peer review: 2 approved with reservations]
Daniel E. Carlin, Forrest Kim, Trey Ideker, Jill P. Mesirov
Peer Reviewers Shouhong Guang; Xiaowei Wang
  • Funder
  • National Human Genome Research Institute
PUBLISHED 12 Oct 2018
https://doi.org/10.12688/f1000research.16415.1
Method Article metrics
Large-scale protein function prediction using heterogeneous ensembles
[version 1; peer review: 2 approved]
Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Peer Reviewers Guoxian Yu; Predrag Radivojac
  • Funders
  • International Business Machines Corporation
  • Intelligence Advanced Research Projects Activity
  • National Institutes of Health
PUBLISHED 28 Sep 2018
241-260 of 378 ARTICLES
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Gateway Areas
  • 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
  • Transcriptomics
    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
  • Proteomics
    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
  • Metagenomics
    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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