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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
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
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