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https://doi.org/10.12688/f1000research.18435.1
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Interaction of N-3-oxododecanoyl homoserine lactone with transcriptional regulator LasR of Pseudomonas aeruginosa: Insights from molecular docking and dynamics simulations
[version 1; peer review: 1 approved, 1 approved with reservations, 1 not approved]
Hovakim Grabski, Lernik Hunanyan, Susanna Tiratsuyan, Hrachik Vardapetyan
Peer Reviewers Jon Paczkowski; Faizul Azam; Kapil Dave
  • Funder
  • Russian-Armenian University
PUBLISHED 22 Mar 2019
https://doi.org/10.12688/f1000research.17084.1
Review metrics
The Application of Omics Technologies to Study Axon Regeneration and CNS Repair
[version 1; peer review: 3 approved]
Andrea Tedeschi, Phillip G Popovich
Peer Reviewers Melissa R Andrews; Shuxin Li; Simone Di Giovanni
  • Funders
  • Marina Romoli Onlus Association
  • Ray W. Poppleton Endowment
  • The Ohio Sate University Discovery Themes Initiative - Chronic Brain Injury
  • National Institutes of Health
  • Craig H. Neilsen Foundation
PUBLISHED 20 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.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.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.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.14960.2
Research Article metrics
Revised
Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules
[version 2; peer review: 2 approved]
Guilherme Duarte Ramos Matos, David L. Mobley
Peer Reviewers Lillian T. Chong and Anthony T. Bogetti; Eric C. Dybeck
  • Funders
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
  • National Science Foundation
LATEST VERSION PUBLISHED 04 Jan 2019
https://doi.org/10.12688/f1000research.17315.1
Method Article metrics
Rapid identification of novel protein families using similarity searches
[version 1; peer review: 2 approved]
Matt Jeffryes, Alex Bateman
Peer Reviewers Daniel J. Rigden; Desmond G Higgins
  • Funder
  • European Molecular Biology Laboratory
PUBLISHED 24 Dec 2018
https://doi.org/10.12688/f1000research.15274.1
Review metrics
Recent advances in functional genome analysis
[version 1; peer review: 2 approved]
Roderic Guigo, Michiel de Hoon
Peer Reviewers Feng Zhang; Kerstin Lindblad-Toh
  • Funder
  • Program “Salvador de Madariaga”, Spanish Ministry of Education, Culture and Sports.
PUBLISHED 21 Dec 2018
https://doi.org/10.12688/f1000research.15895.2
Software Tool Article metrics
Revised
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
[version 2; peer review: 2 approved]
Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey
Peer Reviewers Bjarni V. Halldorsson; Korbinian Schneeberger and Manish Goel
  • Funders
  • U.S. National Library of Medicine
  • Jürgen Manchot Stiftung
  • National Institutes of Health
  • National Human Genome Research Institute
LATEST VERSION PUBLISHED 10 Dec 2018
https://doi.org/10.12688/f1000research.16338.1
Software Tool Article metrics
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
[version 1; peer review: 2 approved]
Clarence K. Mah, Jill P. Mesirov, Lukas Chavez
Peer Reviewers Robert  Ivanek; Aris Floratos
  • Funder
  • National Institutes of Health
PUBLISHED 05 Dec 2018
https://doi.org/10.12688/f1000research.16146.1
Review metrics
RNA interactomics: recent advances and remaining challenges
[version 1; peer review: 2 approved]
Brigitte Schönberger, Christoph Schaal, Richard Schäfer, Björn Voß
Peer Reviewers Roland Hartmann; Lennart Randau
  • Funder
  • Bundesministerium für Bildung und Forschung
PUBLISHED 20 Nov 2018
https://doi.org/10.12688/f1000research.16404.1
Review metrics
Transcripts and tumors: regulatory and metabolic programming during biotrophic phytopathogenesis
[version 1; peer review: 3 approved]
Lara Schmitz, Sean McCotter, Matthias Kretschmer, James W. Kronstad, Kai Heimel
Peer Reviewers Armin Djamei; Barry Saville; José Ruiz-Herrera
  • Funders
  • Natural Sciences and Engineering Research Council of Canada
  • Deutsche Forschungsgemeinschaft
PUBLISHED 19 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.16498.1
Method Article metrics
Evaluation of broad-spectrum antiviral compounds against chikungunya infection using a phenotypic screening strategy
[version 1; peer review: 2 approved with reservations, 1 not approved]
Rafaela M. Bonotto, Glaucia Souza-Almeida, Soraya Jabur Badra, Luiz Tadeu Figueiredo, Carolina B. Moraes, Lucio H. Freitas-Junior
Peer Reviewers Rana Abdelnabi; Mukesh Kumar; Paban Kumar Dash and Amrita Saha
  • Funder
  • Fundação de Amparo à Pesquisa do Estado de São Paulo
PUBLISHED 31 Oct 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
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