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https://doi.org/10.12688/f1000research.18424.1
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Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress
[version 1; peer review: 2 approved]
Khurram Bashir, Akihiro Matsui, Sultana Rasheed, Motoaki Seki
Peer Reviewers Byeong-ha Lee; Hikmet Budak
  • Funders
  • Japan Science and Technology Agency (CREST)
  • Ministry of Education, Culture, Sports, Science and Technology, Japan
PUBLISHED 14 May 2019
https://doi.org/10.12688/f1000research.14012.3
Software Tool Article metrics
Revised
Gene Annotation Easy Viewer (GAEV): Integrating KEGG’s Gene Function Annotations and Associated Molecular Pathways
[version 3; peer review: 3 approved]
Trung Huynh, Sen Xu
Peer Reviewers Fragiskos N Kolisis and Efthymios Ladoukakis; Tonia S. Schwartz; Simo V. Zhang
  • Funder
  • University of Texas at Arlington
LATEST VERSION PUBLISHED 09 May 2019
https://doi.org/10.12688/f1000research.13204.3
Method Article metrics
Revised
META-pipe cloud setup and execution
[version 3; peer review: 2 approved, 1 approved with reservations]
Aleksandr Agafonov, Kimmo Mattila, Cuong Duong Tuan, Lars Tiede, Inge Alexander Raknes, Lars Ailo Bongo
Peer Reviewers Olivier Collin; Kang Ning; Chunlei Wu
  • Funders
  • Norges Forskningsråd
  • UiT The Arctic University of Norway
  • EGI-Engage
  • Horizon 2020
LATEST VERSION PUBLISHED 02 May 2019
https://doi.org/10.12688/f1000research.17956.1
Review metrics
Detection and analysis of RNA methylation
[version 1; peer review: 2 approved]
Nigel P. Mongan, Richard D. Emes, Nathan Archer
Peer Reviewers Thomas Preiss; Marco Biggiogera
  • Funder
  • University of Nottingham
PUBLISHED 26 Apr 2019
https://doi.org/10.12688/f1000research.18676.1
Software Tool Article metrics
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
[version 1; peer review: 2 approved]
Saket Choudhary
Peer Reviewers Simon Andrews; Ryan K. Dale
PUBLISHED 23 Apr 2019
https://doi.org/10.12688/f1000research.15091.2
Research Note metrics
Revised
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach
[version 2; peer review: 2 approved with reservations]
Pedro Morell Miranda, Francesca Bertolini, Haja N. Kadarmideen
Peer Reviewers Yasir Suhail; Manikandan Narayanan
  • Funders
  • Technical University of Denmark, DTU Bioinformatics
  • The Danish Independent Research Council
LATEST VERSION PUBLISHED 17 Apr 2019
https://doi.org/10.12688/f1000research.16005.3
Software Tool Article metrics
Revised
MSF: Modulated Sub-graph Finder
[version 3; peer review: 3 approved]
Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
Peer Reviewers Guanming Wu; Stefanie Widder; Haibo Liu
  • Funder
  • Austrian Science Fund
LATEST VERSION PUBLISHED 14 Apr 2019
https://doi.org/10.12688/f1000research.17548.2
Software Tool Article metrics
Revised
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
[version 2; peer review: 2 approved]
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Peer Reviewers Bastian Greshake Tzovaras and Ngoc-Vinh Tran; Laurent Gatto
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • University College London
  • Swiss State Secretariat for Education
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 29 Mar 2019
https://doi.org/10.12688/f1000research.16252.3
Method Article metrics
Revised
Improved inference of chromosome conformation from images of labeled loci
[version 3; peer review: 2 approved]
Brian C. Ross, James C. Costello
Peer Reviewers Ewan Birney and Carl Barton; Marco Cosentino Lagomarsino and Vittore Scolari
  • Funders
  • Boettcher Foundation
  • Cancer League of Colorado
  • National Institutes of Health
LATEST VERSION PUBLISHED 28 Mar 2019
https://doi.org/10.12688/f1000research.18435.1
Research Article metrics
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
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