Bioinformatics

Bioinformatics

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361-380 of 389 ARTICLES
https://doi.org/10.12688/f1000research.6767.1
Software Tool Article metrics
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
[version 1; peer review: 2 approved]
Peer Reviewers Sergey Nepomnyachiy; Guanming Wu
PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.6773.1
Software Tool Article metrics
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks
[version 1; peer review: 2 approved]
Peer Reviewers Ulrich Stelzl; Srikrishna Subramanian and Gurmeet Kaur
PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.4392.2
Software Tool Article metrics
Update
setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges
[version 2; peer review: 3 approved]
Peer Reviewers Jiguang Wang; Thomas Kelder; Tamara Munzner
LATEST VERSION PUBLISHED 05 Aug 2015
https://doi.org/10.12688/f1000research.6670.1
Research Article metrics
PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources
[version 1; peer review: 2 approved]
Peer Reviewers Peter N. Robinson; Shaillay Dogra
PUBLISHED 16 Jul 2015
https://doi.org/10.12688/f1000research.6616.1
Editorial metrics NOT PEER REVIEWED
Highlights of the 1st Student Symposium of the ISCB RSG UK
[version 1; peer review: not peer reviewed]
PUBLISHED 16 Jun 2015
https://doi.org/10.12688/f1000research.6037.2
Research Note metrics
Revised
Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
[version 2; peer review: 2 approved]
Peer Reviewers Martin Kennedy; Thomas Hoenen
LATEST VERSION PUBLISHED 20 May 2015
https://doi.org/10.12688/f1000research.6148.2
Research Article metrics
Revised
Theoretical modelling of epigenetically modified DNA sequences
[version 2; peer review: 2 approved]
Peer Reviewers Célia Fonseca Guerra; Katja Petzold
LATEST VERSION PUBLISHED 06 May 2015
https://doi.org/10.12688/f1000research.6038.1
Editorial metrics NOT PEER REVIEWED
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus
[version 1; peer review: not peer reviewed]
PUBLISHED 15 Jan 2015
https://doi.org/10.12688/f1000research.4510.2
Software Tool Article metrics
Revised
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters
[version 2; peer review: 2 approved]
Peer Reviewers Alexander Lex; Jose Villaveces
LATEST VERSION PUBLISHED 28 Oct 2014
https://doi.org/10.12688/f1000research.3928.2
Software Tool Article metrics
Update
edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
[version 2; peer review: 3 approved]
Peer Reviewers James W. MacDonald; Ross Lazarus; Sumit Deswal
LATEST VERSION PUBLISHED 21 Oct 2014
https://doi.org/10.12688/f1000research.5412.1
Software Tool Article metrics
Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding
[version 1; peer review: 2 not approved]
Peer Reviewers Nathan Alexander; Kenneth De Jong
PUBLISHED 07 Oct 2014
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]
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]
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]
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]
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]
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]
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]
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]
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]
Peer Reviewers Nathan Salomonis; Florian Markowetz
PUBLISHED 01 Jul 2014
361-380 of 389 ARTICLES
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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