The School of Informatics, Computing, and Engineering Center for Bioinformatics Research Talk
Speaker: Jian Ma, Associate Professor, Computational Biology
Where: Indiana Memorial Union (IMU), Dogwood Room
When: Thursday, January 18, 2018, 3:00 pm
Topic: New algorithms to decode nuclear genome organization
Abstract:: The chromosomes of the human genome are organized in three-dimensions by interacting with each other and also compartmentalizing the cell nucleus. Such organization plays important roles in gene regulation. However, the principles underlying chromatin interaction and nuclear compartmentalization remain largely unclear.
In this talk, I will first introduce an algorithm to elucidate whether the sequence-based features in the DNA alone are sufficient to predict enhancer-promoter chromatin interactions, as compared to the state-of-the-art methods that use numerous non-sequence based functional genomic signals. Next, I will describe an ongoing project to develop a probabilistic model to effectively integrate TSA-seq (which estimates mean chromosomal microscopic distances from specific nuclear compartments) and DamID (which estimates molecular contact frequency of chromosomal regions with the same specific nuclear
compartments) as well as Hi-C data to model the spatial organization of chromosomes relative to different nuclear compartments. We found that the spatial position states from the model strongly correlate with different genomic and epigenomic features. Collectively, we hope our new computational methods will provide new insights into nuclear genome organization.
Biography: Jian Ma has been an Associate Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University since January 2016. He is also Affiliate Faculty of the Machine Learning Department at CMU. He was previously on the faculty of the University of Illinois at Urbana-Champaign. The research in his group has been focused on algorithm development to help better understand the basic functions of the human genome and the molecular mechanisms of human diseases such as cancer.