research-article

Discovering geometric patterns in genomic data

Authors:

Christopher Brown,

Matthew Slattery,

Robert L. Grossman,

Kevin P. WhiteAuthors Info & Claims

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

Pages 147 - 154

https://doi.org/10.1145/2382936.2382955

Published: 07 October 2012 Publication History

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.

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Cited By

Matkarimov OPolivoda DPoptsova M(2018)Searching for patterns of association between functional genomic elementsProceedings of the International Conference "Mathematical Biology and Bioinformatics"10.17537/icmbb18.82Online publication date: 7-Nov-2018
https://doi.org/10.17537/icmbb18.82

Index Terms

Discovering geometric patterns in genomic data
1. Applied computing
  1. Life and medical sciences
2. Information systems
  1. Information systems applications
    1. Data mining

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Published In

cover image ACM Conferences

BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine

October 2012

725 pages

ISBN:9781450316705

DOI:10.1145/2382936

General Chair:
Sanjay Ranka
University of Florida
,
Program Chairs:
Tamer Kahveci
University of Florida
,
Mona Singh
Princeton University

Copyright © 2012 ACM.

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SIGBio: ACM Special Interest Group on Bioinformatics

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Association for Computing Machinery

New York, NY, United States

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Published: 07 October 2012

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BCB' 12: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine

October 7 - 10, 2012

Florida, Orlando

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BCB '12 Paper Acceptance Rate 33 of 159 submissions, 21%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

Matkarimov OPolivoda DPoptsova M(2018)Searching for patterns of association between functional genomic elementsProceedings of the International Conference "Mathematical Biology and Bioinformatics"10.17537/icmbb18.82Online publication date: 7-Nov-2018
https://doi.org/10.17537/icmbb18.82

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