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https://doi.org/10.12688/f1000research.16198.2
Software Tool Article metrics
Revised
scClustViz – Single-cell RNAseq cluster assessment and visualization
[version 2; peer review: 2 approved]
Brendan T. Innes, Gary D. Bader
Peer Reviewers Martin Hemberg and Tallulah Andrews; Michael Steinbaugh
  • Funder
  • Canada First Research Excellence Fund
LATEST VERSION PUBLISHED 12 Mar 2019
https://doi.org/10.12688/f1000research.15613.2
Software Tool Article metrics
Revised
EpiLog: A software for the logical modelling of epithelial dynamics
[version 2; peer review: 3 approved]
Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya
Peer Reviewers Stefano Nichele; Alejandro F. Villaverde and David Henriques; Arnau Montagud
  • Funders
  • Fundação para a Ciência e a Tecnologia
  • Fundação Calouste Gulbenkian
LATEST VERSION PUBLISHED 11 Mar 2019
https://doi.org/10.12688/f1000research.16715.3
Research Article metrics
Revised
Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations
[version 3; peer review: 2 approved]
Dominik Sidler, Marc Lehner, Simon Frasch, Michael Cristófol-Clough, Sereina Riniker
Peer Reviewers Bojan Zagrovic and Daniel Braun; Nico. F. A. van der Vegt
  • Funders
  • Eidgenössische Technische Hochschule Zürich
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 08 Mar 2019
https://doi.org/10.12688/f1000research.17979.1
Research Article metrics
The impact of the open-access status on journal indices: a review of medical journals
[version 1; peer review: 3 approved, 1 approved with reservations]
Saif Aldeen AlRyalat, Mohammad Saleh, Mohammad Alaqraa, Alaa Alfukaha, Yara Alkayed, Maryann Abaza, Hadeel Abu Saa, Mohamed Alshamiry
Peer Reviewers Ernesto Roldan-Valadez; Suneet Sood; Deeb N. Salem; Sung-Tae Hong
PUBLISHED 07 Mar 2019
https://doi.org/10.12688/f1000research.15997.1
Review metrics
Recent advances in biomedical simulations: a manifesto for model engineering
[version 1; peer review: 3 approved]
Joseph L. Hellerstein, Stanley Gu, Kiri Choi, Herbert M. Sauro
Peer Reviewers Robert Hoehndorf; Shuichi Onami; Martin Meier-Schellersheim
  • Funders
  • Gordon and Betty Moore Foundation
  • Alfred P. Sloan Foundation
  • NIH
  • NIAID
PUBLISHED 05 Mar 2019
https://doi.org/10.12688/f1000research.16613.2
Research Article metrics
Revised
False signals induced by single-cell imputation
[version 2; peer review: 4 approved]
Tallulah S. Andrews, Martin Hemberg
Peer Reviewers Simone Tiberi; Jean Fan; Charlotte Soneson; Stephanie C Hicks
  • Funders
  • Chan Zuckerberg Initiative
  • Wellcome Trust
LATEST VERSION PUBLISHED 05 Mar 2019
https://doi.org/10.12688/f1000research.18357.1
Opinion Article metrics
Advancing the international data science workforce through shared training and education
[version 1; peer review: 1 approved, 1 approved with reservations]
John Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola Mulder, Caroline O'Driscoll, Crystal Stewart, Sonika Tyagi
Peer Reviewers Ariel Rokem; David N. Kennedy and Julianna F. Bates
  • Funder
  • National Institutes of Health
PUBLISHED 04 Mar 2019
https://doi.org/10.12688/f1000research.17669.1
Software Tool Article metrics
shiny-pred: a server for the prediction of protein disordered regions
[version 1; peer review: 1 approved with reservations, 1 not approved]
Mauricio Oberti, Iosif Vaisman
Peer Reviewers Jinbo Xu; Appadurai Rajeswari and Anand Srivastava
PUBLISHED 28 Feb 2019
https://doi.org/10.12688/f1000research.15949.2
Software Tool Article metrics
Revised
The Mega2R package: R tools for accessing and processing genetic data in common formats
[version 2; peer review: 3 approved]
Robert V. Baron, Justin R. Stickel, Daniel E. Weeks
Peer Reviewers Dajiang J. Lui; Alejandro Q. Nato, Jr.; Derek Gordon
  • Funders
  • The University of Pittsburgh
  • National Institutes of Health
LATEST VERSION PUBLISHED 25 Feb 2019
https://doi.org/10.12688/f1000research.17916.1
Method Article metrics
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
[version 1; peer review: 1 approved, 2 approved with reservations]
Kimon Froussios, Kira Mourão, Gordon Simpson, Geoffrey J. Barton, Nicholas Schurch
Peer Reviewers Sophie Shaw; James P. B. Lloyd; Michael I. Love
  • Funders
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 24 Feb 2019
https://doi.org/10.12688/f1000research.14591.2
Research Article metrics
Clinical trial
Revised
A study update newsletter or Post-it® note did not increase postal questionnaire response rates in a falls prevention trial: an embedded randomised factorial trial
[version 2; peer review: 2 approved]
Sara Rodgers, Illary Sbizzera, Sarah Cockayne, Caroline Fairhurst, Sarah E. Lamb, Wesley Vernon, Judith Watson, Catherine Hewitt, David J. Torgerson
Peer Reviewers Shaun P. Treweek; Phil J. Edwards and Benjamin Woolf
  • Funders
  • National Institute for Health Research
  • York Trials Unit
LATEST VERSION PUBLISHED 19 Feb 2019
https://doi.org/10.12688/f1000research.17693.1
Research Note metrics
Massive open online courses on biomedical informatics
[version 1; peer review: 2 not approved]
Cender Udai Quispe-Juli, Victor Hugo Moquillaza-Alcántara, Katherine Arapa-Apaza
Peer Reviewers Edward Meinert; Tharindu Liyanagunawardena
  • Funder
  • Fondo Nacional de Desarrollo Científico y Tecnológico
PUBLISHED 14 Feb 2019
https://doi.org/10.12688/f1000research.17207.1
Review metrics
Recent advances in gene function prediction using context-specific coexpression networks in plants
[version 1; peer review: 2 approved]
Chirag Gupta, Andy Pereira
Peer Reviewers Ross Sozzani and Natalie Clark; Marek Mutwil
  • Funder
  • National Science Foundation
PUBLISHED 05 Feb 2019
https://doi.org/10.12688/f1000research.17125.1
Method Article metrics
Projection layers improve deep learning models of regulatory DNA function
[version 1; peer review: 1 approved, 1 approved with reservations]
Alex Hawkins-Hooker, Henry Kenlay, John E. Reid
Peer Reviewers David R. Kelley; Qin Ma
  • Funder
  • Medical Research Council
PUBLISHED 05 Feb 2019
https://doi.org/10.12688/f1000research.18002.1
Software Tool Article metrics
Epidemic curves made easy using the R package incidence
[version 1; peer review: 1 approved, 2 approved with reservations]
Zhian N. Kamvar, Jun Cai, Juliet R.C. Pulliam, Jakob Schumacher, Thibaut Jombart
Peer Reviewers Benjamin M. Bolker; Quirine ten Bosch; Bertrand Sudre
  • Funders
  • Global Challenges Research Fund (GCRF)
  • United Kingdom Department of Health and Social Care
  • National Institute for Health Research - Health Protection Research Unit for Modelling Methodology
PUBLISHED 31 Jan 2019
https://doi.org/10.12688/f1000research.16771.2
Research Article metrics
Revised
Key Concepts for assessing claims about treatment effects and making well-informed treatment choices
[version 2; peer review: 3 approved]
Andrew D. Oxman, Iain Chalmers, Astrid Austvoll-Dahlgren, Informed Health Choices group
Peer Reviewers Catherine Mathews; Richard Lehman; David Henry and Paulina Stehlik
  • Funders
  • National Institute for Health Research
  • Research Council of Norway
LATEST VERSION PUBLISHED 23 Jan 2019
https://doi.org/10.12688/f1000research.17615.1
Opinion Article metrics
What is reproducibility?
[version 1; peer review: 3 approved with reservations]
Gerben ter Riet, Bram W.C. Storosum, Aeilko H. Zwinderman
Peer Reviewers Steven N. Goodman; C. Glenn Begley; Ksenija Bazdaric
PUBLISHED 09 Jan 2019
https://doi.org/10.12688/f1000research.16148.2
Research Article metrics
Revised
Relative effectiveness of a full versus reduced version of the ‘Smoke Free’ mobile application for smoking cessation: an exploratory randomised controlled trial
[version 2; peer review: 2 approved]
David Crane, Harveen Kaur Ubhi, Jamie Brown, Robert West
Peer Reviewers Erica Cruvinel; Jonathan B Bricker
  • Funder
  • Cancer Research UK
LATEST VERSION PUBLISHED 09 Jan 2019
https://doi.org/10.12688/f1000research.16450.2
Software Tool Article metrics
Revised
Improve your Galaxy text life: The Query Tabular Tool
[version 2; peer review: 3 approved]
James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap, Timothy J. Griffin
Peer Reviewers Daniel Blankenberg; Maria A. Doyle; Margaret E Staton
  • Funders
  • National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 09 Jan 2019
https://doi.org/10.12688/f1000research.17518.1
Software Tool Article metrics
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
[version 1; peer review: 2 approved]
Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey
Peer Reviewers Dennis J. Hazelett; Sheila Reynolds
  • Funders
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jan 2019
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