Jointly characterizing epigenetic dynamics across multiple human cell types

Yu Zhang*, Lin An, Feng Yue, Ross C. Hardison

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

52 Scopus citations


Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an integrative and discriminative epigenome annotation system, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.

Original languageEnglish (US)
Pages (from-to)6721-6731
Number of pages11
JournalNucleic acids research
Issue number14
StatePublished - Aug 19 2016

ASJC Scopus subject areas

  • Genetics


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