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https://doi.org/10.12688/f1000research.9227.2
Research Article metrics
Revised
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
[version 2; peer review: 2 approved, 1 approved with reservations, 1 not approved]
Javier Ramiro-Garcia, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, Hauke Smidt
Peer Reviewers Thomas S. B. Schmidt; Julien Tremblay; Fiona Fouhy; George Watts and Bonnie L Hurwitz
  • Funders
  • Top Institute Food and Nutrition
  • European Community’s Seventh Framework Program
LATEST VERSION PUBLISHED 23 Nov 2018
https://doi.org/10.12688/f1000research.15486.2
Method Article metrics
Revised
Identifying communities from multiplex biological networks by randomized optimization of modularity
[version 2; peer review: 3 approved, 1 approved with reservations]
Gilles Didier, Alberto Valdeolivas, Anaïs Baudot
Peer Reviewers Emre Guney; Lenore J. Cowen; Yasir Suhail; Arda Halu
  • Funders
  • Excellence Initiative of Aix- Marseille University
  • French “Plan Cancer 2009–2013”
  • Centre National de la Recherche Scientifique
LATEST VERSION PUBLISHED 22 Nov 2018
https://doi.org/10.12688/f1000research.16409.2
Software Tool Article metrics
Revised
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2
[version 2; peer review: 2 approved]
Jesper L.V. Maag
Peer Reviewers Helder I. Nakaya; Saskia Freytag
LATEST VERSION PUBLISHED 20 Nov 2018
https://doi.org/10.12688/f1000research.15868.1
Review metrics
Making progress in a rare disease: emerging therapeutics in soft tissue sarcomas
[version 1; peer review: 2 approved]
Jennifer Choe, Richard Riedel
Peer Reviewers Shreyaskumar Patel; Bernd Kasper
PUBLISHED 02 Nov 2018
https://doi.org/10.12688/f1000research.16680.1
Software Tool Article metrics
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
[version 1; peer review: 1 approved, 2 approved with reservations]
Gaurav S. Kandlikar, Zachary J. Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J.B. Kraft, Jordan Moberg-Parker, Joshua Sprague, David J. Kushner, Emily E. Curd
Peer Reviewers Tristan Cordier; Holly M. Bik; Niklaus J. Grünwald and Zach Foster
  • Funders
  • University of California President’s Research Catalyst Awards
  • National Science Foundation
PUBLISHED 01 Nov 2018
https://doi.org/10.12688/f1000research.13349.2
Method Article metrics PEER REVIEW DISCONTINUED
Revised
Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation
[version 2; peer review: peer review discontinued]
Darrell O. Ricke, Steven Schwartz
Peer Reviewers Invited
  • Funder
  • Assistant Secretary of Defense for Research & Engineering
LATEST VERSION PUBLISHED 31 Oct 2018
https://doi.org/10.12688/f1000research.16301.2
Software Tool Article metrics
Revised
Increasing workflow development speed and reproducibility with Vectools
[version 2; peer review: 2 approved]
Tyler Weirick, Raphael Müller, Shizuka Uchida
Peer Reviewers Yutaka Saito; Dimitar Vassilev
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Gheens Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.15393.1
Review metrics
Recent advances in lung transplantation
[version 1; peer review: 2 approved]
Keith C Meyer
Peer Reviewers Donald Hayes; Matthew G Hartwig
  • Funder
  • Partial support from George and Julie Mosher Pulmonary Research Fund
PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.14385.1
Review metrics
What is the hologenome concept of evolution?
[version 1; peer review: 2 approved]
J. Jeffrey Morris
Peer Reviewers Seth Bordenstein; Kevin R Theis
  • Funder
  • National Science Foundation
PUBLISHED 19 Oct 2018
https://doi.org/10.12688/f1000research.16516.1
Method Article metrics
Orchestrating a community-developed computational workshop and accompanying training materials
[version 1; peer review: 2 approved]
Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron
Peer Reviewers Ewy Mathe; Kevin Blighe
  • Funders
  • Horizon 2020
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 17 Oct 2018
https://doi.org/10.12688/f1000research.13197.2
Software Tool Article metrics
Revised
Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform
[version 2; peer review: 2 approved]
Ryan A. Miller, Peter Woollard, Egon L. Willighagen, Daniela Digles, Martina Kutmon, Antonis Loizou, Andra Waagmeester, Stefan Senger, Chris T. Evelo
Peer Reviewers Augustin Luna; Yi-An Chen
  • Funder
  • Innovative Medicines Initiative Joint Undertaking
LATEST VERSION PUBLISHED 12 Oct 2018
https://doi.org/10.12688/f1000research.15398.3
Method Article metrics
Revised
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
[version 3; peer review: 3 approved]
Michael I. Love, Charlotte Soneson, Rob Patro
Peer Reviewers Kristoffer Vitting-Seerup and Malte Thodberg; Alicia Oshlack and Marek Cmero; Nick Schurch
  • Funders
  • National Institute of Environmental Health Sciences
  • National Cancer Institute
  • National Human Genome Research Institute
  • National Science Foundation
LATEST VERSION PUBLISHED 01 Oct 2018
https://doi.org/10.12688/f1000research.15789.2
Software Tool Article metrics
Revised
TRGAted: A web tool for survival analysis using protein data in the Cancer Genome Atlas.
[version 2; peer review: 2 approved]
Nicholas Borcherding, Nicholas L. Bormann, Andrew P. Voigt, Weizhou Zhang
Peer Reviewers Jean Claude Zenklusen; Austin Gillen
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 01 Oct 2018
https://doi.org/10.12688/f1000research.16415.1
Method Article metrics
Large-scale protein function prediction using heterogeneous ensembles
[version 1; peer review: 2 approved]
Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Peer Reviewers Guoxian Yu; Predrag Radivojac
  • Funders
  • International Business Machines Corporation
  • Intelligence Advanced Research Projects Activity
  • National Institutes of Health
PUBLISHED 28 Sep 2018
https://doi.org/10.12688/f1000research.16310.1
Research Article metrics
Design and implementation of semester long project and problem based bioinformatics course
[version 1; peer review: 3 approved with reservations]
Geetha Saarunya, Bert Ely
Peer Reviewers Russell Schwartz; Mark A. Pauley; Allegra Via
PUBLISHED 25 Sep 2018
https://doi.org/10.12688/f1000research.14956.1
Review metrics
Recent advances in ankylosing spondylitis: understanding the disease and management
[version 1; peer review: 2 approved]
Leticia Garcia-Montoya, Hanna Gul, Paul Emery
Peer Reviewers Nigil Haroon; Michael Ward
PUBLISHED 21 Sep 2018
https://doi.org/10.12688/f1000research.16058.1
Research Article metrics
Computational genome-wide identification of heat shock protein genes in the bovine genome
[version 1; peer review: 2 approved, 1 approved with reservations]
Oyeyemi O. Ajayi, Sunday O. Peters, Marcos De Donato, Sunday O. Sowande, Fidalis D.N. Mujibi, Olanrewaju B. Morenikeji, Bolaji N. Thomas, Matthew A. Adeleke, Ikhide G. Imumorin
Peer Reviewers José Luis Martínez-Guitarte; Ankit K. Rochani; Anurag Sharma
  • Funders
  • U.S. Department of Agriculture
  • Cornell University Agricultural Experiment Station
  • United States Agency for International Development
  • National Institute of Food and Agriculture
  • Zoetis
PUBLISHED 20 Sep 2018
https://doi.org/10.12688/f1000research.14940.1
Review metrics
Recent advances in understanding and managing infantile colic
[version 1; peer review: 2 approved]
Siel Daelemans, Linde Peeters, Bruno Hauser, Yvan Vandenplas
Peer Reviewers J Marc Rhoads; Francesco Savino
PUBLISHED 07 Sep 2018
https://doi.org/10.12688/f1000research.8219.2
Data Note metrics
Revised
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis
[version 2; peer review: 2 approved]
Elise Ruark, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, Nazneen Rahman
Peer Reviewers Richard Bagnall; Brad Chapman and Oliver Hofmann
  • Funder
  • Institute of Cancer Research
LATEST VERSION PUBLISHED 05 Sep 2018
https://doi.org/10.12688/f1000research.15333.1
Review metrics
Recent Breakthroughs and Ongoing Limitations in Cryptosporidium Research
[version 1; peer review: 3 approved]
Seema Bhalchandra, Daviel Cardenas, Honorine D. Ward
Peer Reviewers Xian-Ming Chen; Boris Striepen and Elizabeth English; Robin Gasser
PUBLISHED 03 Sep 2018
341-360 of 631 ARTICLES
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