Title:
Computational algorithm development for epigenomic analysis

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dc.contributor.advisor Jordan, I. King
dc.contributor.author Wang, Jianrong
dc.contributor.committeeMember Borodovsky, Mark
dc.contributor.committeeMember Fan, Yuhong
dc.contributor.committeeMember McDonald, John
dc.contributor.committeeMember Yi, Soojin
dc.contributor.department Biology
dc.date.accessioned 2013-09-19T13:03:31Z
dc.date.available 2013-09-19T13:03:31Z
dc.date.issued 2012-07-03
dc.description.abstract Multiple computational algorithms were developed for analyzing ChIP-seq datasets of histone modifications. For basic ChIP-seq data processing, the problems of ambiguous short sequence read mapping and broad peak calling of diffuse ChIP-seq signals were solved by novel statistical methods. Their performance was systematically evaluated compared with existing approaches. The potential utility of finding meaningful biological information was demonstrated by the applications on real datasets. For biological question driven data mining, several important topics were selected for algorithm developments, including hypothesis-driven insulator prediction, unbiased chromatin boundary element discovery and combinatorial histone modification signature inference. The integrative computational pipeline for insulator prediction not only produced a list of putative insulators but also recovered specific associated chromatin and functional features. Selected predictions have been experimentally validated. The unbiased chromatin boundary element prediction algorithm was feature-free and had the capability to discover novel types of boundary elements. The predictions found a set of chromatin features and provided the first report of tRNA-derived boundary elements in the human genome. The combinatorial chromatin signature algorithm employed chromatin profile alignments for unsupervised inferences of histone modification patterns. The signatures were associated with various regulatory elements and functional activities. Both the computational advantages and the biological discoveries were discussed.
dc.description.degree Ph.D.
dc.identifier.uri http://hdl.handle.net/1853/48984
dc.language.iso en_US
dc.publisher Georgia Institute of Technology
dc.subject ChIP-seq
dc.subject Histone modifications
dc.subject Bioinformatics
dc.subject Epigenetics
dc.subject Insulators
dc.subject.lcsh Algorithms
dc.subject.lcsh Bioinformatics
dc.subject.lcsh Genetics Data processing
dc.subject.lcsh Epigenesis
dc.title Computational algorithm development for epigenomic analysis
dc.type Text
dc.type.genre Dissertation
dspace.entity.type Publication
local.contributor.advisor Jordan, I. King
local.contributor.corporatename College of Sciences
local.contributor.corporatename School of Biological Sciences
relation.isAdvisorOfPublication 1c155699-6f2d-418d-83cd-9e1424896d4f
relation.isOrgUnitOfPublication 85042be6-2d68-4e07-b384-e1f908fae48a
relation.isOrgUnitOfPublication c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5
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