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Authors: Jieun Jeong 1 ; Mudit Gupta 2 ; Andrey Poleshko 2 and Jonathan A. Epstein 2

Affiliations: 1 Massachusetts General Hospital and Harvard Medical School, United States ; 2 Perelman School of Medicine at the University of Pennsylvania, United States

Keyword(s): ChIP-seq Data, Regions of Protein Binding, Global Optimization.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Next Generation Sequencing

Abstract: Motivation: Differentiation of cells into different cell types involves many types of chromatin modifications, and mapping these modifications is a key computational task as researchers uncover different aspects of that process. Modifications associated with heterochromatin formation pose new challenges in this context because we must define very broad regions that have only a moderately stronger signal than the rest of the chromatin. Lamin-associated domains (LADs) are a prime example of such regions. Results: We present Combinatorial Identification of Broad Association Regions (CIBAR), a new method to identify these types of broad regions. CIBAR is based on an efficient solution to a natural combinatorial problem, which adapts to widely variable yields of reads from ChIP-seq data and the associated controls and performs competitively with previous methods, including DamID, which has been used in many publications on LADs but cannot be applied in most in vivo situations.

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Paper citation in several formats:
Jeong, J.; Gupta, M.; Poleshko, A. and Epstein, J. (2016). Combinatorial Identification of Broad Association Regions with ChIP-seq Data. In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS; ISBN 978-989-758-170-0; ISSN 2184-4305, SciTePress, pages 27-34. DOI: 10.5220/0005663400270034

@conference{bioinformatics16,
author={Jieun Jeong. and Mudit Gupta. and Andrey Poleshko. and Jonathan A. Epstein.},
title={Combinatorial Identification of Broad Association Regions with ChIP-seq Data},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS},
year={2016},
pages={27-34},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005663400270034},
isbn={978-989-758-170-0},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS
TI - Combinatorial Identification of Broad Association Regions with ChIP-seq Data
SN - 978-989-758-170-0
IS - 2184-4305
AU - Jeong, J.
AU - Gupta, M.
AU - Poleshko, A.
AU - Epstein, J.
PY - 2016
SP - 27
EP - 34
DO - 10.5220/0005663400270034
PB - SciTePress