Literature DB >> 20069535

Galaxy: a web-based genome analysis tool for experimentalists.

Daniel Blankenberg1, Gregory Von Kuster, Nathaniel Coraor, Guruprasad Ananda, Ross Lazarus, Mary Mangan, Anton Nekrutenko, James Taylor.   

Abstract

High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.

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Year:  2010        PMID: 20069535      PMCID: PMC4264107          DOI: 10.1002/0471142727.mb1910s89

Source DB:  PubMed          Journal:  Curr Protoc Mol Biol        ISSN: 1934-3647


  4 in total

1.  The UCSC Table Browser data retrieval tool.

Authors:  Donna Karolchik; Angela S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  A high-resolution map of active promoters in the human genome.

Authors:  Tae Hoon Kim; Leah O Barrera; Ming Zheng; Chunxu Qu; Michael A Singer; Todd A Richmond; Yingnian Wu; Roland D Green; Bing Ren
Journal:  Nature       Date:  2005-06-29       Impact factor: 49.962

3.  Using galaxy to perform large-scale interactive data analyses.

Authors:  James Taylor; Ian Schenck; Dan Blankenberg; Anton Nekrutenko
Journal:  Curr Protoc Bioinformatics       Date:  2007-09

4.  The UCSC Genome Browser Database: 2008 update.

Authors:  D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; J S Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2007-12-17       Impact factor: 16.971

  4 in total
  742 in total

1.  Polymorphic NumtS trace human population relationships.

Authors:  Martin Lang; Marco Sazzini; Francesco Maria Calabrese; Domenico Simone; Alessio Boattini; Giovanni Romeo; Donata Luiselli; Marcella Attimonelli; Giuseppe Gasparre
Journal:  Hum Genet       Date:  2011-12-08       Impact factor: 4.132

2.  Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.

Authors:  Mirco Fanelli; Stefano Amatori; Iros Barozzi; Saverio Minucci
Journal:  Nat Protoc       Date:  2011-11-10       Impact factor: 13.491

3.  msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Authors:  Berend Hoekman; Rainer Breitling; Frank Suits; Rainer Bischoff; Peter Horvatovich
Journal:  Mol Cell Proteomics       Date:  2012-02-07       Impact factor: 5.911

4.  The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales.

Authors:  Rahel Elevi Bardavid; Aharon Oren
Journal:  Extremophiles       Date:  2012-04-19       Impact factor: 2.395

5.  CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing.

Authors:  Guoguang Zhao; Dechao Bu; Changning Liu; Jing Li; Jian Yang; Zhiyong Liu; Yi Zhao; Runsheng Chen
Journal:  Protein Cell       Date:  2012-03-17       Impact factor: 14.870

Review 6.  OpenHelix: bioinformatics education outside of a different box.

Authors:  Jennifer M Williams; Mary E Mangan; Cynthia Perreault-Micale; Scott Lathe; Neeraj Sirohi; Warren C Lathe
Journal:  Brief Bioinform       Date:  2010-08-26       Impact factor: 11.622

7.  Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease.

Authors:  Tiffany M Lowe-Power; Connor G Hendrich; Edda von Roepenack-Lahaye; Bin Li; Dousheng Wu; Raka Mitra; Beth L Dalsing; Patrizia Ricca; Jacinth Naidoo; David Cook; Amy Jancewicz; Patrick Masson; Bart Thomma; Thomas Lahaye; Anthony J Michael; Caitilyn Allen
Journal:  Environ Microbiol       Date:  2017-12-22       Impact factor: 5.491

8.  Reduced infectivity of adenovirus type 5 particles and degradation of entering viral genomes associated with incomplete processing of the preterminal protein.

Authors:  Sayuri E Kato; Jasdave S Chahal; S J Flint
Journal:  J Virol       Date:  2012-10-03       Impact factor: 5.103

Review 9.  Identification and Quantification of Proteoforms by Mass Spectrometry.

Authors:  Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith
Journal:  Proteomics       Date:  2019-05       Impact factor: 3.984

10.  Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass.

Authors:  Trey K Sato; Tongjun Liu; Lucas S Parreiras; Daniel L Williams; Dana J Wohlbach; Benjamin D Bice; Irene M Ong; Rebecca J Breuer; Li Qin; Donald Busalacchi; Shweta Deshpande; Chris Daum; Audrey P Gasch; David B Hodge
Journal:  Appl Environ Microbiol       Date:  2013-11-08       Impact factor: 4.792

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