Bioinformatics

Bioinformatics

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341-360 of 384 ARTICLES
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https://doi.org/10.12688/f1000research.7587.2
Editorial metrics NOT PEER REVIEWED
Update
The ELIXIR channel in F1000Research
[version 2; peer review: not peer reviewed]
Niklas Blomberg, Arlindo Oliveira, Barend Mons, Bengt Persson, Inge Jonassen
LATEST VERSION PUBLISHED 04 May 2016
https://doi.org/10.12688/f1000research.8288.1
Software Tool Article metrics
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
[version 1; peer review: 3 approved]
Eric Moyer, Megan Hagenauer, Matthew Lesko, Felix Francis, Oscar Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby
Peer Reviewers John Didion; Sahar Al Seesi; Tomasz Adamusiak
PUBLISHED 13 Apr 2016
https://doi.org/10.12688/f1000research.7118.2
Software Tool Article metrics
Revised
DREAMTools: a Python package for scoring collaborative challenges
[version 2; peer review: 1 approved, 2 approved with reservations]
Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Alberto de la Fuente, Mehmet Gönen, Steven M. Hill, Bruce Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez
Peer Reviewers Konrad Hinsen; Rafael Najmanovich; Nicola J. Mulder
LATEST VERSION PUBLISHED 08 Apr 2016
https://doi.org/10.12688/f1000research.7408.2
Research Article metrics
Revised
Transcription factor motif quality assessment requires systematic comparative analysis
[version 2; peer review: 2 approved]
Caleb Kipkurui Kibet, Philip Machanick
Peer Reviewers Trevor W. Siggers; Jan Grau
LATEST VERSION PUBLISHED 14 Mar 2016
https://doi.org/10.12688/f1000research.7911.1
Research Article metrics
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources
[version 1; peer review: 3 approved]
David Bousfield, Johanna McEntyre, Sameer Velankar, George Papadatos, Alex Bateman, Guy Cochrane, Jee-Hyub Kim, Florian Graef, Vid Vartak, Blaise Alako, Niklas Blomberg
Peer Reviewers Mark Parsons; Timothy W. Clark; Ben Johnson
PUBLISHED 11 Feb 2016
https://doi.org/10.12688/f1000research.8051.1
Editorial metrics NOT PEER REVIEWED
ISCB’s initial reaction to New England Journal of Medicine editorial on data sharing
[version 1; peer review: not peer reviewed]
Alfonso Valencia, Scott Markel, Bruno Gaeta, Terry Gaasterland, Thomas Lengauer, Bonnie Berger, Christine Orengo
PUBLISHED 11 Feb 2016
https://doi.org/10.12688/f1000research.7591.1
Research Article metrics
Computational identification of signaling pathways in protein interaction networks
[version 1; peer review: 2 approved with reservations]
Angela U. Makolo, Temitayo A. Olagunju
Peer Reviewers Winston A. Hide; Lynn Fink
PUBLISHED 30 Dec 2015
https://doi.org/10.12688/f1000research.6852.2
Software Tool Article metrics
Revised
CyAnimator: Simple Animations of Cytoscape Networks
[version 2; peer review: 3 approved]
John H. Morris, Dhameliya Vijay, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
Peer Reviewers Giovanni Scardoni; Nathan Salomonis; Piet Molenaar
LATEST VERSION PUBLISHED 30 Dec 2015
https://doi.org/10.12688/f1000research.7647.1
Software Tool Article metrics
CausalTrail: Testing hypothesis using causal Bayesian networks
[version 1; peer review: 2 approved]
Daniel Stöckel, Florian Schmidt, Patrick Trampert, Hans-Peter Lenhof
Peer Reviewers Maxime Gasse; Vishakh Hegde
PUBLISHED 30 Dec 2015
https://doi.org/10.12688/f1000research.6804.3
Software Tool Article metrics
Revised
Social Network: a Cytoscape app for visualizing co-authorship networks
[version 3; peer review: 1 approved, 2 approved with reservations]
Victor Kofia, Ruth Isserlin, Alison M.J. Buchan, Gary D. Bader
Peer Reviewers Michael Bales and Terrie Wheeler; Jiang Bian; Shahadat Uddin
LATEST VERSION PUBLISHED 23 Dec 2015
https://doi.org/10.12688/f1000research.5754.2
Software Tool Article metrics
Revised
G-Links: a gene-centric link acquisition service
[version 2; peer review: 2 approved]
Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
Peer Reviewers Mark A. Ragan and Sriganesh Srihari; Kenji Satou
LATEST VERSION PUBLISHED 18 Nov 2015
https://doi.org/10.12688/f1000research.6656.2
Software Tool Article metrics
Revised
NetMatchStar: an enhanced Cytoscape network querying app
[version 2; peer review: 2 approved]
Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Peer Reviewers Xifeng Yan; Shaillay Dogra
LATEST VERSION PUBLISHED 03 Nov 2015
https://doi.org/10.12688/f1000research.6030.2
Software Tool Article metrics
Revised
AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
[version 2; peer review: 2 approved]
Michael Considine, Hilary Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael Ochs, Elana Fertig
Peer Reviewers Subha Madhavan; Matthew McCall
LATEST VERSION PUBLISHED 21 Oct 2015
https://doi.org/10.12688/f1000research.6925.1
Software Tool Article metrics
GOsummaries: an R Package for Visual Functional Annotation of Experimental Data
[version 1; peer review: 2 approved]
Raivo Kolde, Jaak Vilo
Peer Reviewers Shaillay Dogra; Hilary Ann Coller
PUBLISHED 18 Aug 2015
https://doi.org/10.12688/f1000research.6877.1
Editorial metrics NOT PEER REVIEWED
Highlights of the first ISCB Student Council Symposium in Africa 2015
[version 1; peer review: not peer reviewed]
Yassine Souilmi, Imane Allali, Oussama Badad, Chinmay Kumar Dwibedi
PUBLISHED 17 Aug 2015
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]
Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
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]
Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards
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]
John H. Morris, Samad Lotia, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Alexander R. Pico, Thomas E Ferrin
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]
Indika Kahanda, Christopher Funk, Karin Verspoor, Asa Ben-Hur
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]
Farzana Rahman, Rohit Farmer, Sayoni Das, Fatima Vayani, Mehedi Hassan
PUBLISHED 16 Jun 2015
341-360 of 384 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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