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https://doi.org/10.12688/f1000research.9751.2
Software Tool Article metrics
Revised
dot-app: a Graphviz-Cytoscape conversion plug-in
[version 2; peer review: 4 approved]
Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak
Peer Reviewers Eric Bonnet; Matthias König; David J. Lynn and John Salamon; Giovanni Scardoni
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 10 Jul 2017
https://doi.org/10.12688/f1000research.9259.2
Software Tool Article metrics
Revised
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
[version 2; peer review: 2 approved]
Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J.A. Fijneman, Sanne Abeln
Peer Reviewers Tobias Marschall; Angel Rubio
LATEST VERSION PUBLISHED 06 Jul 2017
https://doi.org/10.12688/f1000research.11718.1
Opinion Article metrics
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action
[version 1; peer review: 3 approved]
Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble
Peer Reviewers Erin A. Becker; Anelda P. van der Walt and Juan Steyn; Laurent Gatto
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 03 Jul 2017
https://doi.org/10.12688/f1000research.11168.2
Software Tool Article metrics
Revised
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data
[version 2; peer review: 2 approved]
Jesper Eisfeldt, Francesco Vezzi, Pall Olason, Daniel Nilsson, Anna Lindstrand
Peer Reviewers Giuseppe Narzisi and Wayne Clarke; Bud Mishra
  • Funders
  • Marianne and Marcus Wallenberg Foundation
  • Vetenskapsrådet
  • Erik Rönnberg Foundation
  • Nilsson Ehle Donations
  • Svenska Sällskapet för Medicinsk Forskning
  • Hjärnfonden
  • Harald and Greta Jeanssons Foundation
  • Stockholms Läns Landsting
LATEST VERSION PUBLISHED 30 Jun 2017
https://doi.org/10.12688/f1000research.11997.1
Software Tool Article metrics
valr: Reproducible genome interval analysis in R
[version 1; peer review: 2 approved]
Kent A. Riemondy, Ryan M. Sheridan, Austin Gillen, Yinni Yu, Christopher G. Bennett, Jay R. Hesselberth
Peer Reviewers Robert A. Amezquita; Ryan K. Dale
  • Funders
  • U.S. National Library of Medicine
  • National Institutes of Health
  • Colorado Office of Economic Development and International Trade
  • BioFrontiers Institute, University of Colorado Boulder
  • University of Colorado
PUBLISHED 29 Jun 2017
https://doi.org/10.12688/f1000research.11588.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11587.1
Editorial metrics NOT PEER REVIEWED
2017 Outstanding Contributions to ISCB Award: Fran Lewitter
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11586.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Overton Prize: Christoph Bock
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11585.1
Editorial metrics NOT PEER REVIEWED
2017 ISCB Innovator Award: Aviv Regev
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11379.1
Review metrics
Chemical genetics and strigolactone perception
[version 1; peer review: 2 approved]
Shelley Lumba, Michael Bunsick, Peter McCourt
Peer Reviewers David C Nelson; Steven Smith
  • Funder
  • National Science & Engineering Research Council of Canada
PUBLISHED 22 Jun 2017
https://doi.org/10.12688/f1000research.8996.2
Study Protocol metrics
Revised
Automated analysis of retinal imaging using machine learning techniques for computer vision
[version 2; peer review: 2 approved]
Jeffrey De Fauw, Pearse Keane, Nenad Tomasev, Daniel Visentin, George van den Driessche, Mike Johnson, Cian O Hughes, Carlton Chu, Joseph Ledsam, Trevor Back, Tunde Peto, Geraint Rees, Hugh Montgomery, Rosalind Raine, Olaf Ronneberger, Julien Cornebise
Peer Reviewers Yit Yang; Sandrine Zweifel
  • Funder
  • DeepMind
LATEST VERSION PUBLISHED 22 Jun 2017
https://doi.org/10.12688/f1000research.11355.2
Software Tool Article metrics
Revised
Arkas: Rapid reproducible RNAseq analysis
[version 2; peer review: 2 approved]
Anthony R. Colombo, Timothy J. Triche Jr, Giridharan Ramsingh
Peer Reviewers Harold Pimentel; Ted Abel and Marie Gaine
  • Funders
  • Stop Cancer
  • Illumina
  • Tower Cancer Research Foundation
  • Leukemia and Lymphoma Society
LATEST VERSION PUBLISHED 21 Jun 2017
https://doi.org/10.12688/f1000research.11407.1
Opinion Article metrics
Four simple recommendations to encourage best practices in research software
[version 1; peer review: 3 approved]
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Peer Reviewers Roberto Di Cosmo; Gregory V. Wilson; Stefanie Betz
  • Funders
  • ELIXIR-EXCELERATE
  • EMBL-ABR
  • Netherlands eScience Center
  • CORBEL
  • Software Sustainability Institute
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.10427.2
Research Note metrics
Revised
Insights for conducting real-time focus groups online using a web conferencing service
[version 2; peer review: 2 approved]
James Kite, Philayrath Phongsavan
Peer Reviewers Sarah Collard and Edwin Roland van Teijlingen; Marita Hefler
  • Funder
  • Sydney School of Public Health, University of Sydney
LATEST VERSION PUBLISHED 12 Jun 2017
https://doi.org/10.12688/f1000research.11429.1
Research Article metrics
Community and Code: Nine Lessons from Nine NESCent Hackathons
[version 1; peer review: 1 approved, 1 approved with reservations]
Arlin Stoltzfus, Michael Rosenberg, Hilmar Lapp, Aidan Budd, Karen Cranston, Enrico Pontelli, Shann Oliver, Rutger A. Vos
Peer Reviewers Eva Amsen; Cameron Neylon
  • Funder
  • National Evolutionary Synthesis Center
PUBLISHED 06 Jun 2017
https://doi.org/10.12688/f1000research.11638.1
Method Article metrics
Semantics for interoperability of distributed data and models: Foundations for better-connected information
[version 1; peer review: 2 approved with reservations]
Ferdinando Villa, Stefano Balbi, Ioannis N. Athanasiadis, Caterina Caracciolo
Peer Reviewers Carol Goble; Pier Luigi Buttigieg
  • Funders
  • Horizon 2020
  • Ecosystem Services for Poverty Alleviation
  • National Science Foundation
PUBLISHED 17 May 2017
https://doi.org/10.12688/f1000research.11317.1
Software Tool Article metrics
ogttMetrics: Data structures and algorithms for oral glucose tolerance tests
[version 1; peer review: 1 approved with reservations]
Benjamin J. Stubbs, Keith Frankston, Marcel Ramos, Nancy Laranjo, Frank M. Sacks, Vincent J. Carey
Peer Reviewers Antti Honkela
  • Funders
  • National Institute of Diabetes and Digestive and Kidney Diseases
  • National Cancer Institute
PUBLISHED 16 May 2017
https://doi.org/10.12688/f1000research.10742.2
Software Tool Article metrics
Revised
haploR: an R package for querying web-based annotation tools
[version 2; peer review: 3 approved]
Ilya Y. Zhbannikov, Konstantin Arbeev, Svetlana Ukraintseva, Anatoliy I. Yashin
Peer Reviewers Garrett M. Dancik; Claudia Vitolo and Estibaliz Gascon; Stephanie M. Gogarten
  • Funder
  • National Institute on Aging
LATEST VERSION PUBLISHED 15 May 2017
https://doi.org/10.12688/f1000research.9417.3
Research Note metrics
Revised
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning
[version 3; peer review: 2 approved]
Eliseos J. Mucaki, Katherina Baranova, Huy Q. Pham, Iman Rezaeian, Dimo Angelov, Alioune Ngom, Luis Rueda, Peter K. Rogan
Peer Reviewers Elana J. Fertig; Chun-Wei Tung
LATEST VERSION PUBLISHED 12 May 2017
https://doi.org/10.12688/f1000research.10335.2
Software Tool Article metrics
Revised
Cluster Flow: A user-friendly bioinformatics workflow tool
[version 2; peer review: 3 approved]
Philip Ewels, Felix Krueger, Max Käller, Simon Andrews
Peer Reviewers Alastair R. W. Kerr and Shaun Webb; Stephen Taylor and Jelena Telenius; David R. Powell
  • Funders
  • Science for Life Laboratory
  • National Genomics Infrastructure
  • Babraham Institute
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 02 May 2017
701-720 of 1,017 ARTICLES
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