Literature DB >> 18388141

GeneTrack--a genomic data processing and visualization framework.

Istvan Albert1, Shinichiro Wachi, Cizhong Jiang, B Franklin Pugh.   

Abstract

MOTIVATION: High-throughput 'ChIP-chip' and 'ChIP-seq' methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com

Mesh:

Year:  2008        PMID: 18388141      PMCID: PMC7058423          DOI: 10.1093/bioinformatics/btn119

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  4 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

Authors:  Istvan Albert; Travis N Mavrich; Lynn P Tomsho; Ji Qi; Sara J Zanton; Stephan C Schuster; B Franklin Pugh
Journal:  Nature       Date:  2007-03-29       Impact factor: 49.962

4.  A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Authors:  Daniel Blankenberg; James Taylor; Ian Schenck; Jianbin He; Yi Zhang; Matthew Ghent; Narayanan Veeraraghavan; Istvan Albert; Webb Miller; Kateryna D Makova; Ross C Hardison; Anton Nekrutenko
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

  4 in total
  68 in total

1.  A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

Authors:  Judith B Zaugg; Nicholas M Luscombe
Journal:  Genome Res       Date:  2011-09-19       Impact factor: 9.043

2.  Genome-wide function of H2B ubiquitylation in promoter and genic regions.

Authors:  Kiran Batta; Zhenhai Zhang; Kuangyu Yen; David B Goffman; B Franklin Pugh
Journal:  Genes Dev       Date:  2011-11-01       Impact factor: 11.361

3.  Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.

Authors:  Jung-Shin Lee; Alexander S Garrett; Kuangyu Yen; Yoh-Hei Takahashi; Deqing Hu; Jessica Jackson; Christopher Seidel; B Franklin Pugh; Ali Shilatifard
Journal:  Genes Dev       Date:  2012-05-01       Impact factor: 11.361

4.  Genome-wide nucleosome specificity and directionality of chromatin remodelers.

Authors:  Kuangyu Yen; Vinesh Vinayachandran; Kiran Batta; R Thomas Koerber; B Franklin Pugh
Journal:  Cell       Date:  2012-06-22       Impact factor: 41.582

5.  A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

Authors:  Chongzhi Zang; Dustin E Schones; Chen Zeng; Kairong Cui; Keji Zhao; Weiqun Peng
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  Stable and dynamic nucleosome states during a meiotic developmental process.

Authors:  Liye Zhang; Hong Ma; B Franklin Pugh
Journal:  Genome Res       Date:  2011-04-22       Impact factor: 9.043

Review 7.  Genomic location analysis by ChIP-Seq.

Authors:  Artem Barski; Keji Zhao
Journal:  J Cell Biochem       Date:  2009-05-01       Impact factor: 4.429

8.  HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.

Authors:  Zhaohui S Qin; Jianjun Yu; Jincheng Shen; Christopher A Maher; Ming Hu; Shanker Kalyana-Sundaram; Jindan Yu; Arul M Chinnaiyan
Journal:  BMC Bioinformatics       Date:  2010-07-02       Impact factor: 3.169

9.  A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.

Authors:  Cizhong Jiang; B Franklin Pugh
Journal:  Genome Biol       Date:  2009-10-08       Impact factor: 13.583

10.  A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.

Authors:  Teemu D Laajala; Sunil Raghav; Soile Tuomela; Riitta Lahesmaa; Tero Aittokallio; Laura L Elo
Journal:  BMC Genomics       Date:  2009-12-18       Impact factor: 3.969

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