The Chinese University of Hong Kong
Department of Computer Science and Engineering


Title: Algorithms to decode genome structure
Date: May 9, 2017 (Tuesday)
Time: 10:00 a.m. - 11:30 a.m.
Venue: Room 1009, William M. W. Mong Engineering Building (ERB 1009),
The Chinese University of Hong Kong,
Shatin, N.T.
Speaker: Prof. Jian MA
Associate Professor
Computational Biology Department
School of Computer Science
Carnegie Mellon University



Our understanding on how the human genome is organized and how it regulates complex cellular functions is still primitive. One of the hallmarks of cancer genome is aneuploidy and structural variations (SVs). In this talk, I will first introduce a new algorithm we developed recently, called Weaver, to achieve a more complete view of cancer genome structure. Weaver utilizes a probabilistic graphical model to estimate joint probabilities of allele-specific copy numbers of SVs and their inter-connectivity based on whole-genome sequencing data. I will discuss new results that have the potential to provide a more complete assessment of the complex genomic architectures inherent to many cancer genomes. In the second part of the talk, I will introduce another new algorithm to decode instructions encoded in the genome sequence for determining long-range chromatin interactions in higher order genome organization. The machine learning method, named PEP, predicts enhancer-promoter interactions based on sequence-based features only using two different but complementary feature extraction strategies. Collectively, we hope our methods will contribute to accelerating our understanding of genome structure and function and their variations that result in phenotypic diversity and abnormality.



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 (Assistant Professor (2009-2015) and Associate Professor (2015)). 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.


Enquiries: Ms Ricola Lo at tel 3943 8439

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