title: A review of three different studies on hidden markov models for epigenetic problems: a computational perspective.
abstract: Recent technical advances, such as chromatin immunoprecipitation combined with DNA microarrays (ChIp-chip) and chromatin immunoprecipitation-sequencing (ChIP-seq), have generated large quantities of high-throughput data. Considering that epigenomic datasets are arranged over chromosomes, their analysis must account for spatial or temporal characteristics. In that sense, simple clustering or classification methodologies are inadequate for the analysis of multi-track ChIP-chip or ChIP-seq data. Approaches that are based on hidden Markov models (HMMs) can integrate dependencies between directly adjacent measurements in the genome. Here, we review three HMM-based studies that have contributed to epigenetic research, from a computational perspective. We also give a brief tutorial on HMM modelling-targeted at bioinformaticians who are new to the field.
authors.affiliation: Ewha Information and Telecommunication Institute, Ewha Womans University, Seoul 120-750, Korea. ; Bioinformatics Laboratory, School of Engineering, Ewha Womans University, Seoul 120-750, Korea.
authors.forename: Kyung-Eun
authors.initials: KE
authors.lastname: Lee
authors.affiliation: Ewha Information and Telecommunication Institute, Ewha Womans University, Seoul 120-750, Korea. ; Bioinformatics Laboratory, School of Engineering, Ewha Womans University, Seoul 120-750, Korea. ; Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul 120-750, Korea.
authors.forename: Hyun-Seok
authors.initials: HS
authors.lastname: Park
keywords: chromatin states; epigenomics; hidden Markov models; noncoding DNA