Construction of genomic regulatory encyclopedias: Strategies and case studies

Jens Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus Ecker, Laura Elnitski, Susan Evans, Matt Geisler, Erich Grotewold, Dazhang Gu, Edwin Jacox, Kyle Kurz, Stephen S. Lee, Xiaoyu Liang, Pooja M. Majmudar, Paul Morris, Chase Nelson, Eric Stockinger, Joshua D. Welch, Sarah WyattAlper Yilmaz, Lonnie R. Welch

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Encyclopedias of regulatory genomic elements provide a foundation for research in areas such as disease diagnosis, disease treatment, and crop enhancement. The construction of complete encyclopedias of organism-specific genomic elements involved in gene regulation remains a significant challenge. To address this problem, the authors present novel bioinformatics strategies for exploring the word landscapes of putative regulatory regions of genomes. The methods are incorporated into the WordSeeker software tool, which is available at http://word-seeker.org. The effectiveness of these strategies is demonstrated through several case studies.

Original languageEnglish (US)
Title of host publicationOCCBIO'09
Subtitle of host publication2009 Ohio Collaborative Conference on Bioinformatics
Pages65-70
Number of pages6
DOIs
StatePublished - 2009
Externally publishedYes
Event2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009 - Cleveland, OH, United States
Duration: Jun 15 2009Jun 17 2009

Publication series

NameOCCBIO'09: 2009 Ohio Collaborative Conference on Bioinformatics

Conference

Conference2009 Ohio Collaborative Conference on Bioinformatics, OCCBIO 2009
Country/TerritoryUnited States
CityCleveland, OH
Period6/15/096/17/09

Keywords

  • Cis-regulatory element discovery
  • Gene regulation
  • Motif discovery
  • Regulatory elements
  • Regulatory genomics
  • Transcription factor binding site discovery

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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