Discovering geometric patterns in genomic data

Wenxuan Gao, Christopher Brown, Robert L. Grossman, Lijia Ma, Matthew Slattery, Kevin P. White, Philip S. Yu

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

Abstract

ChIP-chip and ChIP-seq are techniques for the isolation and identification of the binding sites of DNA-associated proteins along the genome. Both techniques produce genome-wide location data. The geometric arrangements of these binding sites can provide valuable information about biological function, such as the activation or repression of genes. In this paper, we formalize this problem and propose a novel graph based algorithm called Patterns of Marks (PoM) to discover efficiently these types of geometric patterns in genomic data. We also describe how we validate the algorithm using experimental data.

Original languageEnglish (US)
Title of host publication2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012
Pages147-154
Number of pages8
DOIs
StatePublished - Nov 26 2012
Event2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012 - Orlando, FL, United States
Duration: Oct 7 2012Oct 10 2012

Publication series

Name2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012

Other

Other2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012
CountryUnited States
CityOrlando, FL
Period10/7/1210/10/12

Keywords

  • DNA binding sites
  • Geometric pattern
  • Graph mining

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