Bioinformatics

Bioinformatics

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321-340 of 389 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.8290.2
Software Tool Article metrics
Revised
dbVar structural variant cluster set for data analysis and variant comparison
[version 2; peer review: 2 approved]
Lon Phan, Jeffrey Hsu, Le Quang Minh Tri, Michaela Willi, Tamer Mansour, Yan Kai, John Garner, John Lopez, Ben Busby
Peer Reviewers Lihua Julie Zhu; Justin M. Zook
LATEST VERSION PUBLISHED 28 Feb 2017
https://doi.org/10.12688/f1000research.10114.3
Research Note metrics
Revised
Optimal threshold estimation for binary classifiers using game theory
[version 3; peer review: 3 approved]
Ignacio Enrique Sanchez
Peer Reviewers Pieter Meysman; Luis Diambra; Marcel Brun and Arjen ten Have
LATEST VERSION PUBLISHED 08 Feb 2017
https://doi.org/10.12688/f1000research.10443.1
Method Article metrics
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
[version 1; peer review: 1 approved, 2 approved with reservations]
Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Peer Reviewers Marla I. Trindade and Leonardo van Zyl; Takashi Gojobori; Anders Blomberg
  • Funders
  • ELIXIR
  • EMBL-EBI
  • Universitetet i Tromsø
PUBLISHED 23 Jan 2017
https://doi.org/10.12688/f1000research.9909.1
Software Tool Article metrics
The PathLinker app: Connect the dots in protein interaction networks
[version 1; peer review: 1 approved, 2 approved with reservations]
Daniel P. Gil, Jeffrey N. Law, T. M. Murali
Peer Reviewers Barry Demchak; Tamás Korcsmáros and David Fazekas; Stefan Wuchty
  • Funders
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 20 Jan 2017
https://doi.org/10.12688/f1000research.8923.2
Software Tool Article metrics
Revised
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
[version 2; peer review: 1 approved, 2 approved with reservations]
Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Peer Reviewers Kyle Ellrott; Elena Papaleo; Charlotte Soneson
LATEST VERSION PUBLISHED 28 Dec 2016
https://doi.org/10.12688/f1000research.10420.1
Editorial metrics NOT PEER REVIEWED
ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016
[version 1; peer review: not peer reviewed]
Sayane Shome, Pieter Meysman, R. Gonzalo Parra, Alexander Miguel Monzon, Nicolas Palopoli, Benjamen White, Farzana Rahman, Mehedi Hassan, Zeynep Özkeserli, Efejiro Ashano, V. Keith Hughitt, Muhammad Uzair Khan, Denis J. Murphy
  • Funder
  • International Society for Computational Biology
PUBLISHED 20 Dec 2016
https://doi.org/10.12688/f1000research.10389.1
Editorial metrics NOT PEER REVIEWED
Highlights from the ISCB Student Council Symposia in 2016
[version 1; peer review: not peer reviewed]
Bart Cuypers, Annika Jacobsen, Ben Siranosian, Kevin Schwahn, Ashley Mae Conard, Nanne Aben, Mehedi Hassan, Nazeefa Fatima, Susanne M.A. Hermans, Melissa Woghiren, Pieter Meysman, Farzana Rahman, Anupama Jigisha
  • Funder
  • International Society for Computational Biology
PUBLISHED 15 Dec 2016
https://doi.org/10.12688/f1000research.9794.1
Software Tool Article metrics
The ISMARA client
[version 1; peer review: 2 approved]
Panu Artimo, Séverine Duvaud, Mikhail Pachkov, Vassilios Ioannidis, Erik van Nimwegen, Heinz Stockinger
Peer Reviewers Carsten O. Daub; Josep Lluís Gelpi
  • Funders
  • Swiss State Secretariat for Education, Research and Innovation
  • Universität Basel
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 15 Dec 2016
https://doi.org/10.12688/f1000research.9582.2
Software Tool Article metrics
Revised
Building pathway graphs from BioPAX data in R
[version 2; peer review: 3 approved, 1 approved with reservations]
Nirupama Benis, Dirkjan Schokker, Frank Kramer, Mari A. Smits, Maria Suarez-Diez
Peer Reviewers Lynn Fink; Stephen N. Floor; Hilary Ann Coller; Kyle Ellrott
LATEST VERSION PUBLISHED 12 Dec 2016
https://doi.org/10.12688/f1000research.10221.1
Software Tool Article metrics
Integration of EGA secure data access into Galaxy
[version 1; peer review: 2 approved]
Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln
Peer Reviewers Hervé Ménager; Anton Nekrutenko
  • Funders
  • ELIXIR
  • ELIXIR-EXCELERATE
  • CTMM-TraIT
  • European Molecular Biology Laboratory
PUBLISHED 12 Dec 2016
https://doi.org/10.12688/f1000research.10103.1
Method Article metrics
A data-driven approach to estimating the number of clusters in hierarchical clustering
[version 1; peer review: 2 approved, 1 approved with reservations]
Antoine E. Zambelli
Peer Reviewers Xin Zou; Alok Sharma; Dylan M. Owen
PUBLISHED 01 Dec 2016
https://doi.org/10.12688/f1000research.9434.1
Method Article metrics
DWCox: A density-weighted Cox model for outlier-robust prediction of prostate cancer survival
[version 1; peer review: 1 approved, 2 approved with reservations]
Jinfeng Xiao, Sheng Wang, Jingbo Shang, Henry Lin, Doris Xin, Xiang Ren, Jiawei Han, Jian Peng
Peer Reviewers Motoki Shiga; Sebastian Pölsterl; Riku Klen and Mehrad Mahmoudian
  • Funders
  • National Institutes of Health
  • National Science Foundation
PUBLISHED 01 Dec 2016
https://doi.org/10.12688/f1000research.10116.1
Research Article metrics
Dynamics of tRNA fragments and their targets in aging mammalian brain
[version 1; peer review: 2 approved]
Spyros Karaiskos, Andrey Grigoriev
Peer Reviewers Tatiana V. Tatarinova; Laura Kamenetzky and Natalia Macchiaroli
PUBLISHED 24 Nov 2016
https://doi.org/10.12688/f1000research.8201.1
Method Article metrics
Two-step feature selection for predicting survival time of patients with metastatic castrate resistant prostate cancer
[version 1; peer review: 2 approved]
Motoki Shiga
Peer Reviewers Niels Richard Hansen and Søren Wengel Mogensen; Ka Yee Yeung
PUBLISHED 16 Nov 2016
https://doi.org/10.12688/f1000research.9357.2
Software Tool Article metrics
Revised
Genomic variant annotation workflow for clinical applications
[version 2; peer review: 2 approved]
Thomas Thurnherr, Franziska Singer, Daniel J. Stekhoven, Niko Beerenwinkel
Peer Reviewers Christopher Southan; Ankush Sharma and Md. Sahidul Islam
LATEST VERSION PUBLISHED 24 Oct 2016
https://doi.org/10.12688/f1000research.9663.1
Editorial metrics NOT PEER REVIEWED
The 2016 Bioinformatics Open Source Conference (BOSC)
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Peter J.A. Cock, Brad Chapman, Christopher J. Fields, Karsten Hokamp, Hilmar Lapp, Monica Muñoz-Torres, Heather Wiencko
PUBLISHED 06 Oct 2016
https://doi.org/10.12688/f1000research.3-53.v3
Software Tool Article metrics
Revised
wigExplorer, a BioJS component to visualise wig data
[version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Anil S. Thanki, Rafael C. Jimenez, Gemy G. Kaithakottil, Manuel Corpas, Robert P. Davey
Peer Reviewers Robert Buels; Phil Lord; Stefan Thomas Lang; Chunlei Wu and Jiwen Xin
LATEST VERSION PUBLISHED 09 Aug 2016
https://doi.org/10.12688/f1000research.9093.1
Research Article metrics
Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements
[version 1; peer review: 1 approved, 2 approved with reservations]
Efejiro Ashano, Itunuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
Peer Reviewers Manuel Corpas; Hilary Ann Coller; Thomas D. Otto and Gavin Rutledge
PUBLISHED 08 Aug 2016
https://doi.org/10.12688/f1000research.9090.1
Software Tool Article metrics
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
[version 1; peer review: 2 approved]
Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D. Bader
Peer Reviewers Pablo Porras Millán; Harm Nijveen
PUBLISHED 15 Jul 2016
https://doi.org/10.12688/f1000research.9158.1
Editorial metrics NOT PEER REVIEWED
2016 ISCB Overton Prize awarded to Debora Marks
[version 1; peer review: not peer reviewed]
Christiana N. Fogg, Diane E. Kovats
PUBLISHED 05 Jul 2016
321-340 of 389 ARTICLES
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  • Methods and Tools
    The Methods and Tools Gateway Area will allow researchers to publish outputs concerning both the application and research into the use of various computational methods to analyse quantities of biological data for a range of different results, including predictions and discoveries. Read more keyboard_arrow_right
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    The Genetics & Genomics Gateway Area will enable researchers to publish content related to the analysis, storage and accessibility of DNA, RNA and protein sequences. This analysis can be conducted in a variety of ways, including comparison of sequences and relationships, identification of functions, and recognition of patterns across the samples. Read more keyboard_arrow_right
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    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
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    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
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    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
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