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https://doi.org/10.12688/f1000research.11417.1
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Bacterial vaginosis
[version 1; peer review: 2 approved]
Phillip Hay
Peer Reviewers Amanda Lewis; Catriona Bradshaw
PUBLISHED 27 Sep 2017
https://doi.org/10.12688/f1000research.12223.1
Method Article metrics
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
[version 1; peer review: 1 approved, 2 approved with reservations]
Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe
Peer Reviewers Davide Risso; Alejandro Reyes; Nick Schurch
  • Funder
  • National Institutes of Health
PUBLISHED 24 Aug 2017
https://doi.org/10.12688/f1000research.12332.1
Opinion Article metrics
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training
[version 1; peer review: 2 approved]
Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
Peer Reviewers Jason J. Williams; Kim T. Gurwitz
  • Funder
  • ELIXIR-EXCELERATE
PUBLISHED 24 Aug 2017
https://doi.org/10.12688/f1000research.12168.1
Method Article metrics
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
[version 1; peer review: 2 approved]
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J. Dylan Spalding, Sanne Abeln
Peer Reviewers Hervé Ménager; Gilbert S. Omenn
  • Funders
  • CTMM-TraIT
  • Horizon 2020
PUBLISHED 16 Aug 2017
https://doi.org/10.12688/f1000research.11543.1
Review metrics
Co-evolution techniques are reshaping the way we do structural bioinformatics
[version 1; peer review: 2 approved]
Saulo de Oliveira, Charlotte Deane
Peer Reviewers David Baker; Johannes Söding
  • Funder
  • Engineering and Physical Sciences Research Council
PUBLISHED 25 Jul 2017
https://doi.org/10.12688/f1000research.11495.1
Review metrics
New frontiers in metabolomics: from measurement to insight
[version 1; peer review: 3 approved]
Eli Riekeberg, Robert Powers
Peer Reviewers Brent Winston; Uwe Christians; Christoph Steinbeck
  • Funders
  • Nebraska Research Council
  • Nebraska Tobacco Settlement Biomedical Research Development Fund
  • Nebraska Center for Integrated Biomolecular Communication Systems Biology Core (NIH National Institute of General Medical Sciences)
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 19 Jul 2017
https://doi.org/10.12688/f1000research.10750.2
Review metrics
Revised
General guidelines for biomedical software development
[version 2; peer review: 2 approved]
Luis Bastiao Silva, Rafael C. Jimenez, Niklas Blomberg, José Luis Oliveira
Peer Reviewers João P. G. L. M.  Rodrigues; Victor Maojo
  • Funders
  • European Federation of Pharmaceutical Industries and Associations
  • Horizon 2020
LATEST VERSION PUBLISHED 12 Jul 2017
https://doi.org/10.12688/f1000research.11251.2
Research Article metrics
Revised
Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections
[version 2; peer review: 2 approved]
Sapan Mandloi, Saikat Chakrabarti
Peer Reviewers Anna Panchenko; Ramanathan Sowdhamini
  • Funder
  • Council for Scientific and Industrial Research
LATEST VERSION PUBLISHED 07 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.10962.1
Review metrics
Recent advances in methods to assess the activity of the kinome
[version 1; peer review: 3 approved]
Maria Radu, Jonathan Chernoff
Peer Reviewers Roger Daly; David Adams; Ed Manser
  • Funders
  • Congressionally Directed Medical Research Programs
  • National Cancer Institute
PUBLISHED 26 Jun 2017
https://doi.org/10.12688/f1000research.11823.1
Research Article metrics
Analytical challenges of untargeted GC-MS-based metabolomics and the critical issues in selecting the data processing strategy
[version 1; peer review: 2 approved]
Ting-Li Han, Yang Yang, Hua Zhang, Kai P. Law
Peer Reviewers Feng Zhu; Jianguo Xia
PUBLISHED 22 Jun 2017
https://doi.org/10.12688/f1000research.11837.1
Opinion Article metrics
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR
[version 1; peer review: 4 approved, 1 approved with reservations]
L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo, B. Overduin, S-A Sansone, M. Thurston, M.R. Viant, C.L. Winder, C.A. Goble, C.P. Ponting, G. Rustici
Peer Reviewers Michelle D. Brazas; Patricia M. Palagi; Celia W.G. van Gelder; Nicola J. Mulder; Manuel Corpas
  • Funders
  • Horizon 2020
  • Biotechnology and Biological Sciences Research Council
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.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.11221.1
Review metrics
Screening and identification of novel biologically active natural compounds
[version 1; peer review: 2 approved]
David Newman
Peer Reviewers Roger G. Linington; Rolf Müller
PUBLISHED 05 Jun 2017
https://doi.org/10.12688/f1000research.10896.1
Review metrics
Recent advances in microbial fermentation for dairy and health
[version 1; peer review: 3 approved]
Daragh Hill, Ivan Sugrue, Elke Arendt, Colin Hill, Catherine Stanton, R Paul Ross
Peer Reviewers Willem M de Vos; Pratyoosh Shukla; Miguel A. Alvarez
  • Funders
  • Science Foundation Ireland
  • JPI Food Processing for Health funded ‘Longlife'
PUBLISHED 26 May 2017
https://doi.org/10.12688/f1000research.9690.1
Review metrics
Nanoparticle-based drug delivery systems: What can they really do in vivo?
[version 1; peer review: 3 approved]
Yi-Feng Wang, Lu Liu, Xue Xue, Xing-Jie Liang
Peer Reviewers Kenneth A. Dawson; Zhen Gu; Xiaoyuan (Shawn) Chen
  • Funders
  • Chinese Academy of Sciences
  • National Distinguished Young Scholars
  • Bureau of International Cooperation, Chinese Academy of Sciences
  • Natural Science Foundation
PUBLISHED 16 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
https://doi.org/10.12688/f1000research.10625.1
Review metrics
Inducing death in tumor cells: roles of the inhibitor of apoptosis proteins
[version 1; peer review: 3 approved]
Darren Finlay, Peter Teriete, Mitchell Vamos, Nicholas D. P. Cosford, Kristiina Vuori
Peer Reviewers Craig M Walsh; Domagoj Vucic; Robert G Korneluk and Eric C LaCasse
  • Funder
  • NIH
PUBLISHED 27 Apr 2017
https://doi.org/10.12688/f1000research.10998.1
Review metrics
Recent advances in the management and understanding of macular degeneration
[version 1; peer review: 2 approved]
Sepehr Bahadorani, Michael Singer
Peer Reviewers Jorge G. Arroyo; Ron A. Adelman
PUBLISHED 20 Apr 2017
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