Bioinformatics

Bioinformatics

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241-260 of 389 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.16454.2
Research Article metrics
Revised
Large-scale analysis of B-cell epitopes of envelope: Implications for Zika vaccine and immunotherapeutic development
[version 2; peer review: 2 approved]
Iman Almansour, Rahaf Alfares, Halah Aljofi
Peer Reviewers Meirong Jia; Sunil K Joshi
  • Funder
  • Imam Abdulrahman Bin Faisal University
LATEST VERSION PUBLISHED 27 Jun 2019
https://doi.org/10.12688/f1000research.18142.2
Software Tool Article metrics
Revised
Visualization of the small RNA transcriptome using seqclusterViz
[version 2; peer review: 2 approved]
Lorena Pantano, Francisco Pantano, Eulalia Marti, Shannan Ho Sui
Peer Reviewers Xavier Bofill-De Ros; Stefan Scholten
LATEST VERSION PUBLISHED 27 Jun 2019
https://doi.org/10.12688/f1000research.19592.1
Software Tool Article metrics
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
[version 1; peer review: 3 approved]
Aurora S. Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
Peer Reviewers Fuhai Li; Aritro Nath; Tero Aittokallio and Ziaurrehman Tanoli
  • Funder
  • National Institutes of Health
PUBLISHED 20 Jun 2019
https://doi.org/10.12688/f1000research.19013.1
Method Article metrics
de.NBI Cloud federation through ELIXIR AAI
[version 1; peer review: 2 approved, 1 not approved]
Peter Belmann, Björn Fischer, Jan Krüger, Michal Procházka, Helena Rasche, Manuel Prinz, Maximilian Hanussek, Martin Lang, Felix Bartusch, Benjamin Gläßle, Jens Krüger, Alfred Pühler, Alexander Sczyrba
Peer Reviewers Enol Fernández-del-Castillo; Dixie Baker; Volker P. Brendel
  • Funder
  • Bundesministerium für Bildung und Forschung
PUBLISHED 10 Jun 2019
https://doi.org/10.12688/f1000research.19410.1
Software Tool Article metrics
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
[version 1; peer review: 2 approved, 1 approved with reservations]
Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin T. Morgan, Sean Davis
Peer Reviewers Simina M. Boca; Mike Smith; Henrik Bengtsson
  • Funders
  • EU H2020 Personalizing Health and Care Program
  • Intramural Research Program, National Institutes of Health
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 29 May 2019
https://doi.org/10.12688/f1000research.15830.2
Software Tool Article metrics
Revised
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
[version 2; peer review: 2 approved]
Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael M. Reich, Jill P. Mesirov
Peer Reviewers Timothy Tickle; Joshua Batson
  • Funders
  • Silicon Valley Community Foundation
  • National Institutes of Health
LATEST VERSION PUBLISHED 29 May 2019
https://doi.org/10.12688/f1000research.19221.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Innovator Award recognizes William Stafford Noble
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19220.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Overton Prize: Christophe Dessimoz
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19219.1
Editorial metrics NOT PEER REVIEWED
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19218.1
Editorial metrics NOT PEER REVIEWED
2019 Outstanding Contributions to ISCB awarded to Barb Bryant
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
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
241-260 of 389 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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