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https://doi.org/10.12688/f1000research.18676.1
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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.18458.2
Software Tool Article metrics
Revised
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
[version 2; peer review: 2 approved]
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Peer Reviewers Marta Szachniuk; Jerome Waldispühl and Roman Sarrazin-Gendron
  • Funder
  • Austrian Science Fund
LATEST VERSION 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.18139.1
Review metrics
Emerging novel agents for patients with advanced Ewing sarcoma: a report from the Children’s Oncology Group (COG) New Agents for Ewing Sarcoma Task Force
[version 1; peer review: 3 approved]
Kelly Bailey, Carrye Cost, Ian Davis, Julia Glade-Bender, Patrick Grohar, Peter Houghton, Michael Isakoff, Elizabeth Stewart, Nadia Laack, Jason Yustein, Damon Reed, Katherine Janeway, Richard Gorlick, Stephen Lessnick, Steven DuBois, Pooja Hingorani
Peer Reviewers Alan W Craft; Antonio Llombart-Bosch; David J Gordon
  • Funder
  • NCTN Operations Center Grant
PUBLISHED 15 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.18636.1
Method Article metrics
A Bioconductor workflow for the Bayesian analysis of spatial proteomics
[version 1; peer review: 1 approved, 2 approved with reservations]
Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Paul D.W. Kirk, Laurent Gatto
Peer Reviewers Pierre M. Jean Beltran; Susan Holmes; Angus Lamond and Alejandro Brenes Murillo
  • Funders
  • Medical Research Council
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 11 Apr 2019
https://doi.org/10.12688/f1000research.17352.2
Research Note metrics
Revised
A simple formula for enumerating comparisons in trials and network meta-analysis
[version 2; peer review: 2 approved]
Farhad Shokraneh, Clive E. Adams
Peer Reviewers Julie Broderick; G. Mustafa Soomro
  • Funder
  • None
LATEST VERSION PUBLISHED 03 Apr 2019
https://doi.org/10.12688/f1000research.16987.1
Review metrics
Recent technical advances in proteomics
[version 1; peer review: 2 approved]
John R. Yates, III
Peer Reviewers Albert J R. Heck; Ying Ge
  • Funder
  • National Institute of Health
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.17787.1
Review metrics
Advancing understanding, diagnosis, and therapies for cutaneous lupus erythematosus within the broader context of systemic lupus erythematosus
[version 1; peer review: 3 approved]
Kristen L. Chen, Rebecca L. Krain, Victoria P. Werth
Peer Reviewers Jan P. Dutz; Michelle Kahlenberg; Richard D. Sontheimer
  • Funder
  • National Institutes of Health
PUBLISHED 25 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.18300.1
Research Article metrics
Clinical trial
Using pens as an incentive for trial recruitment of older adults: An embedded randomised controlled trial
[version 1; peer review: 2 approved]
Katie Whiteside, Lydia Flett, Alex S. Mitchell, Caroline Fairhurst, Sarah Cockayne, Sara Rodgers, David J. Torgerson, OTIS Study Group
Peer Reviewers Daniel Hind; Nicola Mills
  • Funder
  • National Institute for Health Research
PUBLISHED 21 Mar 2019
https://doi.org/10.12688/f1000research.18541.1
Research Article metrics
In silico docking analysis of CCL28 (C-C motif chemokine ligand 28) and astragalin as the potential inhibitor of rheumatoid arthritis
[version 1; peer review: 1 approved, 1 approved with reservations]
Sadaf Noor, Syeda Tahira Qousain, Syed Aun Muhammad
Peer Reviewers Ihsan Ul Haq; Sagarika Biswas
PUBLISHED 20 Mar 2019
https://doi.org/10.12688/f1000research.15140.2
Opinion Article metrics
Revised
Recommendations for the packaging and containerizing of bioinformatics software
[version 2; peer review: 2 approved, 1 approved with reservations]
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol
Peer Reviewers Ka Yee Yeung and Daniel Kristiyanto; Monther Alhamdoosh; Evan Floden
  • Funders
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 20 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.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.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.17149.2
Research Article metrics
Revised
Hub genes in a pan-cancer co-expression network show potential for predicting drug responses
[version 2; peer review: 2 approved]
Francisco Azuaje, Tony Kaoma, Céline Jeanty, Petr V. Nazarov, Arnaud Muller, Sang-Yoon Kim, Gunnar Dittmar, Anna Golebiewska, Simone P. Niclou
Peer Reviewers Elizabeth A. Coker; Therese Commes
  • Funders
  • Fonds National de la Recherche Luxembourg
  • Ministère de l'Education Nationale, de l'Enseignement Superieur et de la Recherche
LATEST VERSION 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
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