Computational Epigenetics and the Human Malaria Parasite

ABSTRACT: In this talk I will discuss a few computational problems associated with the analysis of next-generation sequencing data. In the first, I will describe the problem of determining the position of nucleosomes in the genome of the human malaria parasite (nucleosomes are the basic elements of DNA chromatin structure). The problem is first modeled using a parametric probabilistic model (modified Gaussian mixture). An expectation maximization (EM) algorithm is then used to infer the parameters of the mixture of distributions. I will describe next the challenges of detecting DNA methylation in bisulfite treated reads. I will conclude discussing the findings on the genome of P. falciparum.

 

BIO: Stefano Lonardi is Professor and Vice Chair of the Department of Computer Science and Engineering at University of California, Riverside, CA. Stefano received his Laurea cum laude from University of Pisa in 1994 and his Ph.D. in the summer of 2001 from the Department of Computer Sciences, Purdue University, West Lafayette, IN.  He also holds a doctorate degree in Electrical and Information Engineering from University of Padua (1999).

 

Stefano's recent research interest includes design of algorithms, computational molecular biology, data compression and data mining. He has published over 100 peer-reviewed papers in major theoretical computer science and computational biology journal and conferences. In the year 2005, he received the CAREER award from National Science Foundation. He has received funding from NSF, US-AID, NIH, DARPA, and USDA. He is currently serving on the Steering Committee of IEEE Transactions on Computational Biology and Bioinformatics.