Yang Yang
Ph.D. Candidate, Carnegie Mellon University, Computational Biology
Research Website
Computational Methods for Multi-Species Comparison of 3D Genome Structure and Function
Thursday, January 23, 2 PM, RRI 101
Abstract: Recent development in chromatin interaction mapping technologies have greatly advanced the study of three-dimensional (3D) genome organization, which is closely related to vital genome functions such as DNA replication timing (RT) and transcription. However, the principles underlying 3D genome organization and the detailed patterns on how the 3D genome has changed in mammalian evolution remain largely unclear. In this talk, I will primarily introduce two probabilistic models that I have developed during my Ph.D. research: Phylo-HMGP and Phylo-HMRF, which provide the new generic frameworks for genome-wide comparison of continuous genomic features, including RT and Hi-C data for 3D genome structures. The methods incorporate the temporal dependencies of species in the context of evolution with the spatial dependencies of genomic loci, to identify genome-wide evolutionary patterns of continuous genomic features. Real data applications to the RT data and Hi-C data from multiple primate species demonstrated the effectiveness of the models and offered high resolution characterization of evolutionary patterns of 3D genome structure and function. Together, the methods have the potential to help reveal genomic regions with conserved or species-specific structural and regulatory roles, and provide key insights into nuclear organization and function through cross-species comparisons.
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