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https://doi.org/10.12688/f1000research.9794.1
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The ISMARA client
[version 1; peer review: 2 approved]
Panu Artimo, Séverine Duvaud, Mikhail Pachkov, Vassilios Ioannidis, Erik van Nimwegen, Heinz Stockinger
Peer Reviewers Carsten O. Daub; Josep Lluís Gelpi
  • Funders
  • Swiss State Secretariat for Education, Research and Innovation
  • Universität Basel
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 15 Dec 2016
https://doi.org/10.12688/f1000research.10221.1
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Integration of EGA secure data access into Galaxy
[version 1; peer review: 2 approved]
Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln
Peer Reviewers Hervé Ménager; Anton Nekrutenko
  • Funders
  • ELIXIR
  • ELIXIR-EXCELERATE
  • CTMM-TraIT
  • European Molecular Biology Laboratory
PUBLISHED 12 Dec 2016
https://doi.org/10.12688/f1000research.8935.3
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Revised
Bringing your tools to CyVerse Discovery Environment using Docker
[version 3; peer review: 3 approved]
Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav Merchant, Eric Lyons
Peer Reviewers Steven B Cannon; Thomas S. B. Schmidt; Robert Cannon
LATEST VERSION PUBLISHED 05 Dec 2016
https://doi.org/10.12688/f1000research.6139.3
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Revised
MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data
[version 3; peer review: 1 approved, 2 approved with reservations]
Damien Correia, Olivia Doppelt-Azeroual, Jean-Baptiste Denis, Mathias Vandenbogaert, Valérie Caro
Peer Reviewers Peter Li; Manuel Corpas and Benedikt Rauscher; Saskia Hiltemann
LATEST VERSION PUBLISHED 01 Dec 2016
https://doi.org/10.12688/f1000research.9619.1
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Recent advances in the medical treatment of breast cancer
[version 1; peer review: 2 approved]
Daniel A. Vorobiof
Peer Reviewers István Láng; Stephen R Johnston
PUBLISHED 29 Nov 2016
https://doi.org/10.12688/f1000research.10255.1
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Divergent pattern of genomic variation in Plasmodium falciparum and P. vivax
[version 1; peer review: 2 approved with reservations]
Preeti Goel, Gajinder Pal Singh
Peer Reviewers Richard D. Pearson; Charles J. Woodrow and Ipsita Sinha
  • Funders
  • University Grants Commission of India
  • Wellcome Trust/DBT India Alliance
PUBLISHED 25 Nov 2016
https://doi.org/10.12688/f1000research.10116.1
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Dynamics of tRNA fragments and their targets in aging mammalian brain
[version 1; peer review: 2 approved]
Spyros Karaiskos, Andrey Grigoriev
Peer Reviewers Tatiana V. Tatarinova; Laura Kamenetzky and Natalia Macchiaroli
PUBLISHED 24 Nov 2016
https://doi.org/10.12688/f1000research.9821.1
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A guide and best practices for R/Bioconductor tool integration in Galaxy
[version 1; peer review: 1 approved, 1 approved with reservations]
Nitesh Turaga, Mallory A. Freeberg, Dannon Baker, John Chilton, Galaxy Team, Anton Nekrutenko, James Taylor
Peer Reviewers Paul A. Stewart and Dekai Rohlsen; Houtan Noushmehr and Tiago Silva
PUBLISHED 24 Nov 2016
https://doi.org/10.12688/f1000research.9708.1
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Differentially correlated genes in co-expression networks control phenotype transitions
[version 1; peer review: 1 approved, 2 approved with reservations]
Lina D. Thomas, Dariia Vyshenska, Natalia Shulzhenko, Anatoly Yambartsev, Andrey Morgun
Peer Reviewers Thiago M. Venancio; Andrei Zinovyev; Fabrício Martins Lopes
  • Funders
  • Fundação de Amparo à Pesquisa do Estado de São Paulo
  • National Science Foundation
PUBLISHED 22 Nov 2016
https://doi.org/10.12688/f1000research.10040.1
Research Article metrics
YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools
[version 1; peer review: 2 approved, 1 not approved]
Sandeep Chakraborty, Pedro J. Martínez-García, Abhaya M. Dandekar
Peer Reviewers Carmen Cuadrado and Africa Sanchiz; Margaret E Staton and Miriam Payá Milans; Nic Herndon
PUBLISHED 17 Nov 2016
https://doi.org/10.12688/f1000research.7035.2
Research Article metrics
Revised
RNA-Seq workflow: gene-level exploratory analysis and differential expression
[version 2; peer review: 2 approved]
Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber
Peer Reviewers Davide Risso; Zhijin Wu
LATEST VERSION PUBLISHED 17 Nov 2016
https://doi.org/10.12688/f1000research.9511.1
Review metrics
Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens
[version 1; peer review: 3 approved]
Sushant Bangru, Auinash Kalsotra
Peer Reviewers Graziano Pesole; Emanuele Buratti; Gordon Carmichael
  • Funders
  • March of Dimes Foundation
  • Center for Advanced Study, University of Illinois at Urbana-Champaign
  • National Institutes of Health
PUBLISHED 14 Nov 2016
https://doi.org/10.12688/f1000research.8986.2
Research Article metrics
Revised
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
[version 2; peer review: 3 approved]
Ben J. Callahan, Kris Sankaran, Julia A. Fukuyama, Paul J. McMurdie, Susan P. Holmes
Peer Reviewers Leo Lahti; Zachary Charlop-Powers; Nandita R. Garud
LATEST VERSION PUBLISHED 02 Nov 2016
https://doi.org/10.12688/f1000research.9501.2
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Revised
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
[version 2; peer review: 3 approved, 2 approved with reservations]
Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni
Peer Reviewers Diana H.P. Low; Hongkai Ji; Andrew McDavid; David duVerle; Antonio Rausell
LATEST VERSION PUBLISHED 31 Oct 2016
https://doi.org/10.12688/f1000research.9484.2
Research Note metrics
Revised
Analysis of morphine responses in mice reveals a QTL on Chromosome 7
[version 2; peer review: 2 approved]
Wim E. Crusio, Esha Dhawan, Elissa J. Chesler, Anna Delprato
Peer Reviewers Clarissa Parker; Robert Gerlai
LATEST VERSION PUBLISHED 27 Oct 2016
https://doi.org/10.12688/f1000research.9615.1
Review metrics
Bacteriocin production: a relatively unharnessed probiotic trait?
[version 1; peer review: 2 approved]
James W. Hegarty, Caitriona M. Guinane, R. Paul Ross, Colin Hill, Paul D. Cotter
Peer Reviewers Michael Chikindas; Antonio Galvez
PUBLISHED 27 Oct 2016
https://doi.org/10.12688/f1000research.8950.3
Data Note metrics
Revised
High quality, small molecule-activity datasets for kinase research
[version 3; peer review: 2 approved]
Rajan Sharma, Stephan C. Schürer, Steven M. Muskal
Peer Reviewers George Nicola; Sorin Avram
LATEST VERSION PUBLISHED 26 Oct 2016
https://doi.org/10.12688/f1000research.7403.1
Review metrics
Current strategies to treat tuberculosis
[version 1; peer review: 2 approved]
Anthony T. Podany, Susan Swindells
Peer Reviewers Andreas Diacon; Digby Warner
PUBLISHED 26 Oct 2016
https://doi.org/10.12688/f1000research.9241.1
Review metrics
Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome
[version 1; peer review: 4 approved]
Pedro Morgado, Dipak Manna, Upinder Singh
Peer Reviewers Lesly Temesvari; Sudha Bhattacharya; Sharon Reed; Tomoyoshi Nozaki
PUBLISHED 26 Oct 2016
https://doi.org/10.12688/f1000research.9357.2
Software Tool Article metrics
Revised
Genomic variant annotation workflow for clinical applications
[version 2; peer review: 2 approved]
Thomas Thurnherr, Franziska Singer, Daniel J. Stekhoven, Niko Beerenwinkel
Peer Reviewers Christopher Southan; Ankush Sharma and Md. Sahidul Islam
LATEST VERSION PUBLISHED 24 Oct 2016
461-480 of 631 ARTICLES
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