Bioinformatics

Bioinformatics

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361-378 of 378 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.4680.2
Software Tool Article metrics
Revised
shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
[version 2; peer review: 2 approved]
Jean-Philippe Fortin, Elana Fertig, Kasper Hansen
Peer Reviewers Timothy J. Triche; Tiffany J. Morris
LATEST VERSION PUBLISHED 19 Sep 2014
https://doi.org/10.12688/f1000research.4431.2
Software Tool Article metrics
Revised
ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis
[version 2; peer review: 2 approved]
Guanming Wu, Eric Dawson, Adrian Duong, Robin Haw, Lincoln Stein
Peer Reviewers Hamid Bolouri; Nikolaus Schultz and B. Arman Aksoy
LATEST VERSION PUBLISHED 12 Sep 2014
https://doi.org/10.12688/f1000research.4492.2
Software Tool Article metrics
Revised
Cytoscape: the network visualization tool for GenomeSpace workflows
[version 2; peer review: 3 approved]
Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael Smoot, Trey Ideker, Jill P. Mesirov
Peer Reviewers Aris Floratos; Gabriela Bindea and Bernhard Mlecnik; Jan Aerts
LATEST VERSION PUBLISHED 26 Aug 2014
https://doi.org/10.12688/f1000research.4996.1
Research Article metrics
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes
[version 1; peer review: 2 approved]
Jennifer Wyffels, Benjamin L. King, James Vincent, Chuming Chen, Cathy H. Wu, Shawn W. Polson
Peer Reviewers Kevin Feldheim; Ed Heist
PUBLISHED 12 Aug 2014
https://doi.org/10.12688/f1000research.4830.1
Software Tool Article metrics
Explain your data by Concept Profile Analysis Web Services
[version 1; peer review: 2 approved with reservations]
Kristina Hettne, Reinout van Schouwen, Eleni Mina, Eelke van der Horst, Mark Thompson, Rajaram Kaliyaperumal, Barend Mons, Erik van Mulligen, Jan A. Kors, Marco Roos
Peer Reviewers Karin Verspoor; Naoaki Okazaki
PUBLISHED 25 Jul 2014
https://doi.org/10.12688/f1000research.4572.1
Software Tool Article metrics
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
[version 1; peer review: 2 approved]
Jason Montojo, Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
Peer Reviewers Giovanni Scardoni; Rosalba Giugno
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4521.1
Software Tool Article metrics
BridgeDb app: unifying identifier mapping services for Cytoscape
[version 1; peer review: 2 approved]
Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
Peer Reviewers Benno Schwikowski; Olivier Elemento
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4460.1
Software Tool Article metrics
enhancedGraphics: a Cytoscape app for enhanced node graphics
[version 1; peer review: 2 approved]
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
Peer Reviewers Lars Juhl Jensen; Piet Molenaar
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4536.1
Software Tool Article metrics
Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results
[version 1; peer review: 2 approved]
Ruth Isserlin, Daniele Merico, Veronique Voisin, Gary D. Bader
Peer Reviewers Nathan Salomonis; Florian Markowetz
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.4642.1
Editorial metrics NOT PEER REVIEWED
The Cytoscape app article collection
[version 1; peer review: not peer reviewed]
Alexander R Pico, Gary D Bader, Barry Demchak, Oriol Guitart Pla, Timothy Hull, William Longabaugh, Christian Lopes, Samad Lotia, Piet Molenaar, Jason Montojo, John H Morris, Keiichiro Ono, Benno Schwikowski, David Welker, Trey Ideker
PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.3-47.v2
Software Tool Article metrics
Revised
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences
[version 2; peer review: 2 approved]
Leyla Garcia, Guy Yachdav, Maria-Jesus Martin
Peer Reviewers Jim Procter; Andreas Prlic
LATEST VERSION PUBLISHED 09 Apr 2014
https://doi.org/10.12688/f1000research.3-8.v2
Software Tool Article metrics
Revised
Validation of predicted mRNA splicing mutations using high-throughput transcriptome data
[version 2; peer review: 4 approved]
Coby Viner, Stephanie N. Dorman, Ben C. Shirley, Peter K. Rogan
Peer Reviewers Stefania Bortoluzzi; Francesc Xavier Roca; Liliana D. Florea; Peter N. Robinson
LATEST VERSION PUBLISHED 07 Apr 2014
https://doi.org/10.12688/f1000research.3-56.v1
Editorial metrics NOT PEER REVIEWED
The BioJS article collection of open source components for biological data visualisation
[version 1; peer review: not peer reviewed]
Manuel Corpas
PUBLISHED 13 Feb 2014
https://doi.org/10.12688/f1000research.3-54.v1
Software Tool Article metrics
DNAContentViewer a BioJS component to visualise GC/AT Content
[version 1; peer review: 2 approved with reservations]
Anil S. Thanki, Shabhonam Caim, Manuel Corpas, Robert P. Davey
Peer Reviewers Dan Schwartz and Joseph O'Shea; Matúš Kalaš
PUBLISHED 13 Feb 2014
https://doi.org/10.12688/f1000research.3-50.v1
Software Tool Article metrics
PPI layouts: BioJS components for the display of Protein-Protein Interactions
[version 1; peer review: 2 approved]
Gustavo A. Salazar, Ayton Meintjes, Nicola Mulder
Peer Reviewers Laurent Gatto; Hagen Blankenburg
PUBLISHED 13 Feb 2014
https://doi.org/10.12688/f1000research.2-264.v1
Software Tool Article metrics
illuminaio: An open source IDAT parsing tool for Illumina microarrays
[version 1; peer review: 2 approved]
Mike L Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Peer Reviewers Jan Oosting; Tiffany J. Morris
PUBLISHED 04 Dec 2013
https://doi.org/10.12688/f1000research.2-188.v2
Research Article metrics
Revised
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
[version 2; peer review: 2 approved]
Liliana Florea, Li Song, Steven L Salzberg
Peer Reviewers Manuel Corpas; Peter N. Robinson
LATEST VERSION PUBLISHED 21 Nov 2013
https://doi.org/10.12688/f1000research.2-68.v1
Software Tool Article metrics
The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics
[version 1; peer review: 2 approved]
Matthew E Berginski, Shawn M Gomez
Peer Reviewers Jonathan Jones; Kenneth Yamada
PUBLISHED 04 Mar 2013
361-378 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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