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https://doi.org/10.12688/f1000research.16516.1
Method Article metrics
Orchestrating a community-developed computational workshop and accompanying training materials
[version 1; peer review: 2 approved]
Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron
Peer Reviewers Ewy Mathe; Kevin Blighe
  • Funders
  • Horizon 2020
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 17 Oct 2018
https://doi.org/10.12688/f1000research.16290.1
Method Article metrics
A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens
[version 1; peer review: 2 approved with reservations]
Daniel E. Carlin, Forrest Kim, Trey Ideker, Jill P. Mesirov
Peer Reviewers Shouhong Guang; Xiaowei Wang
  • Funder
  • National Human Genome Research Institute
PUBLISHED 12 Oct 2018
https://doi.org/10.12688/f1000research.13197.2
Software Tool Article metrics
Revised
Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform
[version 2; peer review: 2 approved]
Ryan A. Miller, Peter Woollard, Egon L. Willighagen, Daniela Digles, Martina Kutmon, Antonis Loizou, Andra Waagmeester, Stefan Senger, Chris T. Evelo
Peer Reviewers Augustin Luna; Yi-An Chen
  • Funder
  • Innovative Medicines Initiative Joint Undertaking
LATEST VERSION PUBLISHED 12 Oct 2018
https://doi.org/10.12688/f1000research.14491.2
Method Article metrics
Revised
Computational assessment of stomach tumor volume from multi-slice computerized tomography images in presence of type 2 cancer
[version 2; peer review: 2 approved, 1 not approved]
Gerardo Chacón, Johel E. Rodríguez, Valmore Bermúdez, Miguel Vera, Juan Diego Hernández, Sandra Vargas, Aldo Pardo, Carlos Lameda, Delia Madriz, Antonio J. Bravo
Peer Reviewers Jorge Brieva; Fred Prior; Pablo Guillen-Rondon
  • Funder
  • Universidad Simón Bolívar
LATEST VERSION PUBLISHED 09 Oct 2018
https://doi.org/10.12688/f1000research.15789.2
Software Tool Article metrics
Revised
TRGAted: A web tool for survival analysis using protein data in the Cancer Genome Atlas.
[version 2; peer review: 2 approved]
Nicholas Borcherding, Nicholas L. Bormann, Andrew P. Voigt, Weizhou Zhang
Peer Reviewers Jean Claude Zenklusen; Austin Gillen
  • Funder
  • National Cancer Institute
LATEST VERSION PUBLISHED 01 Oct 2018
https://doi.org/10.12688/f1000research.16058.1
Research Article metrics
Computational genome-wide identification of heat shock protein genes in the bovine genome
[version 1; peer review: 2 approved, 1 approved with reservations]
Oyeyemi O. Ajayi, Sunday O. Peters, Marcos De Donato, Sunday O. Sowande, Fidalis D.N. Mujibi, Olanrewaju B. Morenikeji, Bolaji N. Thomas, Matthew A. Adeleke, Ikhide G. Imumorin
Peer Reviewers José Luis Martínez-Guitarte; Ankit K. Rochani; Anurag Sharma
  • Funders
  • U.S. Department of Agriculture
  • Cornell University Agricultural Experiment Station
  • United States Agency for International Development
  • National Institute of Food and Agriculture
  • Zoetis
PUBLISHED 20 Sep 2018
https://doi.org/10.12688/f1000research.15271.1
Review metrics
Regulatory network characterization in development: challenges and opportunities
[version 1; peer review: 2 approved]
Guangdun Peng, Jing-Dong J. Han
Peer Reviewers Volkhard Helms; GuoCheng Yuan
  • Funders
  • Chinese Academy of Sciences
  • National Natural Science Foundation of China
  • China Ministry of Science and Technology
PUBLISHED 17 Sep 2018
https://doi.org/10.12688/f1000research.16047.1
Software Tool Article metrics
methyvim: Targeted, robust, and model-free differential methylation analysis in R
[version 1; peer review: 1 approved with reservations, 2 not approved]
Nima S. Hejazi, Rachael V. Phillips, Alan E. Hubbard, Mark J. van der Laan
Peer Reviewers Peter F.  Hickey; Jimmy Breen and Nader Aryamanesh; Nandita Mitra and Ted Westling
  • Funders
  • National Institute of Environmental Health Sciences
  • U.S. National Library of Medicine
PUBLISHED 07 Sep 2018
https://doi.org/10.12688/f1000research.15704.1
Software Tool Article metrics
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
[version 1; peer review: 2 approved]
Adam R. Rivers, Kyle C. Weber, Terrence G. Gardner, Shuang Liu, Shalamar D. Armstrong
Peer Reviewers J. Gregory Caporaso; Johanna B. Holm
  • Funder
  • USDA Agricultural Research Service
PUBLISHED 06 Sep 2018
https://doi.org/10.12688/f1000research.8219.2
Data Note metrics
Revised
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis
[version 2; peer review: 2 approved]
Elise Ruark, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, Nazneen Rahman
Peer Reviewers Richard Bagnall; Brad Chapman and Oliver Hofmann
  • Funder
  • Institute of Cancer Research
LATEST VERSION PUBLISHED 05 Sep 2018
https://doi.org/10.12688/f1000research.15708.1
Software Tool Article metrics
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.
[version 1; peer review: 1 approved, 1 not approved]
Friederike Ehrhart, Jonathan Melius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M.G. Curfs, Chris T. Evelo
Peer Reviewers Patrice Godard; Osman Ugur Sezerman
  • Funder
  • ELIXIR
PUBLISHED 03 Sep 2018
https://doi.org/10.12688/f1000research.15333.1
Review metrics
Recent Breakthroughs and Ongoing Limitations in Cryptosporidium Research
[version 1; peer review: 3 approved]
Seema Bhalchandra, Daviel Cardenas, Honorine D. Ward
Peer Reviewers Xian-Ming Chen; Boris Striepen and Elizabeth English; Robin Gasser
PUBLISHED 03 Sep 2018
https://doi.org/10.12688/f1000research.15599.1
Software Tool Article metrics
Quantification of cancer cell migration with an integrated experimental-computational pipeline
[version 1; peer review: 2 approved with reservations]
Edwin F Juarez, Carolina Garri, Ahmadreza Ghaffarizadeh, Paul Macklin, Kian Kani
Peer Reviewers Mohammed El-Kebir; Assaf Zaritsky
  • Funders
  • Breast Cancer Research Foundation
  • University of Southern California
  • National Institutes of Health
PUBLISHED 15 Aug 2018
https://doi.org/10.12688/f1000research.15845.1
Method Article metrics
Recursive module extraction using Louvain and PageRank
[version 1; peer review: 2 approved]
Dimitri Perrin, Guido Zuccon
Peer Reviewers Raghvendra Mall; Alina Sîrbu
PUBLISHED 14 Aug 2018
https://doi.org/10.12688/f1000research.15144.2
Software Tool Article metrics
Revised
Copycat Layout: Network layout alignment via Cytoscape Automation
[version 2; peer review: 2 approved]
Brett Settle, David Otasek, John H Morris, Barry Demchak
Peer Reviewers Bernhard Mlecnik; Katja Luck
  • Funders
  • National Resource for Network Biology
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 10 Aug 2018
https://doi.org/10.12688/f1000research.9973.2
Software Tool Article metrics
Revised
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
[version 2; peer review: 2 approved, 1 approved with reservations]
Andrea Komljenovic, Julien Roux, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian
Peer Reviewers Virag Sharma; Daniel S. Himmelstein; Leonardo Collado-Torres
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 07 Aug 2018
https://doi.org/10.12688/f1000research.14807.2
Software Tool Article metrics
Revised
Identifier Mapping in Cytoscape
[version 2; peer review: 3 approved]
Adam Treister, Alexander R. Pico
Peer Reviewers Ruth Isserlin; Augustin Luna; Nadezhda Doncheva
  • Funder
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 06 Aug 2018
https://doi.org/10.12688/f1000research.14116.1
Review metrics
Recent advances in the understanding and treatment of acute myeloid leukemia
[version 1; peer review: 3 approved]
Justin Watts, Stephen Nimer
Peer Reviewers Richard M. Stone; Christopher S. Hourigan; Bjorn T. Gjertsen
  • Funders
  • National Institutes of Health - National Cancer Institute
  • University of Miami Clinical and Translational Science Institute
  • Leukemia and Lymphoma Society
PUBLISHED 06 Aug 2018
https://doi.org/10.12688/f1000research.11146.2
Research Article metrics
Revised
De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
[version 2; peer review: 2 approved, 2 approved with reservations]
Michael Liem, Hans J. Jansen, Ron P. Dirks, Christiaan V. Henkel, G. Paul H. van Heusden, Richard J.L.F. Lemmers, Trifa Omer, Shuai Shao, Peter J. Punt, Herman P. Spaink
Peer Reviewers Mile Šikić; Jean-Marc Aury and Benjamin Istace; Christina A. Cuomo; Hayan Lee
LATEST VERSION PUBLISHED 03 Aug 2018
https://doi.org/10.12688/f1000research.14874.1
Review metrics
Tackling resistance: emerging antimalarials and new parasite targets in the era of elimination
[version 1; peer review: 2 approved]
Emily S. Mathews, Audrey R. Odom John
Peer Reviewers Kirsten Hanson; Emily Derbyshire
  • Funders
  • St. Louis Children's Hospital
  • Children's Discovery Institute of Washington University
  • Burroughs Wellcome Fund
  • National Institutes of Health
PUBLISHED 01 Aug 2018
161-180 of 380 ARTICLES
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