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https://doi.org/10.12688/f1000research.20510.1
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All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability in the pathogenesis of some chronic inflammatory diseases
[version 1; peer review: 3 approved]
Alessio Fasano
Peer Reviewers Xin M Luo; Michael Maes; Arul Jayaraman
  • Funder
  • National Institutes of Health
PUBLISHED 31 Jan 2020
https://doi.org/10.12688/f1000research.20928.1
Review metrics
Precision medicine in inflammatory bowel disease: concept, progress and challenges
[version 1; peer review: 2 approved]
Simon P. Borg-Bartolo, Ray Kiran Boyapati, Jack Satsangi, Rahul Kalla
Peer Reviewers Sunanda Kane; Claudio Fiocchi
PUBLISHED 28 Jan 2020
https://doi.org/10.12688/f1000research.20204.1
Review metrics
Recent advances in modulating the microbiome
[version 1; peer review: 2 approved]
Eamonn M.M Quigley, Prianka Gajula
Peer Reviewers Tom Van de Wiele; Francisco Guarner
  • Funder
  • Hughes Sterling Foundation
PUBLISHED 27 Jan 2020
https://doi.org/10.12688/f1000research.16804.4
Method Article metrics
Revised
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
[version 4; peer review: 2 approved, 2 not approved]
Federica Cattonaro, Alessandro Spadotto, Slobodanka Radovic, Fabio Marroni
Peer Reviewers Alejandro Sanchez-Flores; José F. Cobo Diaz; Francesco Dal Grande; Marcus Claesson and Shriram Patel
  • Funder
  • Coordinamento Regionale Veneto per la Libertà delle Vaccinazioni
LATEST VERSION PUBLISHED 22 Jan 2020
https://doi.org/10.12688/f1000research.17927.4
Software Tool Article metrics
Revised
Biobtree: A tool to search and map bioinformatics identifiers and special keywords
[version 4; peer review: 2 approved]
Tamer Gur
Peer Reviewers Maxim N. Shokhirev; Samuel Lampa
LATEST VERSION PUBLISHED 20 Jan 2020
https://doi.org/10.12688/f1000research.21508.1
Software Tool Article metrics
Identifying orthologs with OMA: A primer
[version 1; peer review: 2 approved]
Monique Zahn-Zabal, Christophe Dessimoz, Natasha M. Glover
Peer Reviewers Stephanie J. Spielman; Paula Ramos-Silva
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Swiss Institute of Bioinformatics
PUBLISHED 17 Jan 2020
https://doi.org/10.12688/f1000research.21773.1
Software Tool Article metrics
Pharmosome: an integrative and collective database for exploration and analysis of single nucleotide polymorphisms associated with disease
[version 1; peer review: 2 approved with reservations]
Peter T. Habib, Alsamman M. Alsamman, Sameh E. Hassanein, Kerolos M. Yousef, Aladdin Hamwieh
Peer Reviewers Fuyi Li; Mulin Jun Li
PUBLISHED 10 Jan 2020
https://doi.org/10.12688/f1000research.21797.1
Research Article metrics
Using synthetic datasets to bridge the gap between the promise and reality of basing health-related decisions on common single nucleotide polymorphisms
[version 1; peer review: 1 approved, 1 approved with reservations]
Thomas R. Wood, Nathan Owens
Peer Reviewers Yesim Aydin Son; Oliver Pain
  • Funder
  • Department of Pediatrics, University of Washington
PUBLISHED 30 Dec 2019
https://doi.org/10.12688/f1000research.21568.1
Editorial metrics NOT PEER REVIEWED
BOSC 2019, the 20th annual Bioinformatics Open Source Conference
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Peter J.A. Cock, Christopher J. Fields, Bastian Greshake Tzovaras, Michael Heuer, Karsten Hokamp, Monica Munoz-Torres, Alexander Peltzer, Bastian Rieck, Heather Wiencko, Yo Yehudi
PUBLISHED 20 Dec 2019
https://doi.org/10.12688/f1000research.11622.4
Method Article metrics
Revised
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
[version 4; peer review: 2 approved]
Malgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Peer Reviewers Aaron T. L. Lun and John C. Marioni; Greg Finak and Raphael Gottardo
  • Funders
  • Swiss National Science Foundation
  • Swiss Institute of Bioinformatics
  • University of Zurich
LATEST VERSION PUBLISHED 17 Dec 2019
https://doi.org/10.12688/f1000research.20575.1
Review metrics
Recent advances in understanding the phenotypes of osteoarthritis
[version 1; peer review: 2 approved]
Ali Mobasheri, Simo Saarakkala, Mikko Finnilä, Morten A. Karsdal, Anne-Christine Bay-Jensen, Willem Evert van Spil
Peer Reviewers Rik J U Lories; Charles J. Malemud
  • Funders
  • Innovative Medicines Initiative
  • FP7 People: Marie-Curie Actions
  • Lietuvos Mokslo Taryba
  • Seventh Framework Programme
PUBLISHED 12 Dec 2019
https://doi.org/10.12688/f1000research.20633.2
Research Article metrics
Revised
Epitope mapping of an uncertain endogenous antigen implies secretogranin II peptide splicing
[version 2; peer review: 1 approved, 2 approved with reservations]
David R. Howlett, Iain J. Clarke, Russell P. Newton, John E. Hart
Peer Reviewers Michael O. Glocker; Steven D. Shnyder; Alice Sijts
LATEST VERSION PUBLISHED 05 Dec 2019
https://doi.org/10.12688/f1000research.20210.2
Software Tool Article metrics
Revised
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
[version 2; peer review: 2 approved]
Lukas M. Weber, Charlotte Soneson
Peer Reviewers Shila Ghazanfar; Laurent Gatto
  • Funder
  • Universität Zürich
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.20887.3
Software Tool Article metrics
Revised
RCy3: Network biology using Cytoscape from within R
[version 3; peer review: 3 approved]
Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Peer Reviewers James Denvir; Krithika Bhuvaneshwar; Ludwig Geistlinger
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.19481.1
Review metrics
Metabolic phenotyping of the human microbiome
[version 1; peer review: 2 approved]
Wiley Barton, Orla O'Sullivan, Paul D. Cotter
Peer Reviewers Robert E Brown; Jack A Gilbert
  • Funders
  • Department of Agriculture, Food and the Marine
  • Science Foundation Ireland
PUBLISHED 22 Nov 2019
https://doi.org/10.12688/f1000research.20002.1
Review metrics
Past, present, and future efforts to enhance the efficacy of cord blood hematopoietic cell transplantation
[version 1; peer review: 3 approved]
Xinxin Huang, Bin Guo, Maegan Capitano, Hal E. Broxmeyer
Peer Reviewers Jonathan Hoggatt; Mariusz Ratajczak; Elizabeth J Shpall
  • Funders
  • NIH/NHLBI
  • NIH/NIDDK
PUBLISHED 31 Oct 2019
https://doi.org/10.12688/f1000research.20415.1
Software Tool Article metrics
SNPnotes: high-throughput tissue-specific functional annotation of single nucleotide variants
[version 1; peer review: 2 approved with reservations]
Shraddha Pai, Michael J. Apostolides, Andrew Jung, Matthew A. Moss
Peer Reviewers Deepti Jain; Pavel P. Kuksa
PUBLISHED 22 Oct 2019
https://doi.org/10.12688/f1000research.18866.2
Software Tool Article metrics
Revised
MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
[version 2; peer review: 2 approved]
Mike W.C. Thang, Xin-Yi Chua, Gareth Price, Dominique Gorse, Matt A. Field
Peer Reviewers Saskia Hiltemann; Leo Lahti
  • Funder
  • Australian Institute of Tropical Health and Medicine
LATEST VERSION PUBLISHED 18 Oct 2019
https://doi.org/10.12688/f1000research.20136.1
Opinion Article metrics
An intrinsically disordered proteins community for ELIXIR
[version 1; peer review: 2 approved]
Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas, John M. Hancock, Jen Harrow, Desmond Higgins, Cy M. Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A. Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J. Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C. Shields, Joel L. Sussman, Jonathan A. Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F. Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C. E. Tosatto
Peer Reviewers Iva Pritisanac and Julie Forman-Kay; Osman Ugur Sezerman
  • Funders
  • Vetenskapsrådet
  • BBSRC
  • European Molecular Biology Laboratory
  • Carlsberg Foundation Distinguished Fellowship
  • National Institutes of Health
  • Israel I-CORE Project
  • ELIXIR
  • Danmarks Grundforskningsfond
  • Instruct-ERIC
  • Swiss Federal Government
  • Marie Skłodowska-Curie
  • COST Action BM1405 NGP-net
  • Wellcome Trust
PUBLISHED 15 Oct 2019
https://doi.org/10.12688/f1000research.18490.3
Research Article metrics
Revised
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data
[version 3; peer review: 2 approved, 1 approved with reservations]
J. Javier Diaz-Mejia, Elaine C. Meng, Alexander R. Pico, Sonya A. MacParland, Troy Ketela, Trevor J. Pugh, Gary D. Bader, John H. Morris
Peer Reviewers Saskia Freytag; Jimmy Tsz Hang Lee and Tallulah Andrews; Lindsay Cowell
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 14 Oct 2019
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