Bioinformatics

Bioinformatics

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361-380 of 389 ARTICLES
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https://doi.org/10.12688/f1000research.6767.1
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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Editorial metrics NOT PEER REVIEWED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[version 1; peer review: not peer reviewed]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
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]
Ron Ammar, Tara A. Paton, Dax Torti, Adam Shlien, Gary D. Bader
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]
Alexandra Teresa Pires Carvalho, Maria Leonor Gouveia, Charan Raju Kanna, Sebastian K. T. S. Wärmländer, Jamie Platts, Shina Caroline Lynn Kamerlin
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]
Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost
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]
Keiichiro Ono, Barry Demchak, Trey Ideker
Peer Reviewers Alexander Lex; Jose Villaveces
LATEST VERSION PUBLISHED 28 Oct 2014
https://doi.org/10.12688/f1000research.3928.2
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Update
edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
[version 2; peer review: 3 approved]
Zhiyin Dai, Julie M. Sheridan, Linden J. Gearing, Darcy L. Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O'Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Peer Reviewers James W. MacDonald; Ross Lazarus; Sumit Deswal
LATEST VERSION PUBLISHED 21 Oct 2014
https://doi.org/10.12688/f1000research.5412.1
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Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding
[version 1; peer review: 2 not approved]
Michael Scott Brown, Tommy Bennett, James A. Coker
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]
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
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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
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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
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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
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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
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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
361-380 of 389 ARTICLES
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