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Summary

Abstract: In this talk, I will introduce two new computational problems stemming from the analysis of next-generation sequencing data. In the first, I will describe the problem of determining the position of nucleosomes in a genome (nucleosomes are the basic elements of DNA chromatin structure). We solved this problem using a method based on a modified Gaussian mixture model. An expectation maximization (EM) algorithm is used to infer the parameters of the mixture of distributions.

In the second, I will briefly address the problem of obtaining the primary sequence for large, complex genomes. We propose a BAC-by-BAC sequencing protocol that leverages recent advances in combinatorial pooling design (group testing). I will show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case case gene-bearing BAC clones.

 

Bio: Stefano Lonardi is Professor and Vice Chair of the Department of Computer Science and Engineering at University of California, Riverside, CA. He is also a faculty member of the Graduate Program in Genetics, Genomics and Bioinformatics, the Center for Plant Cell Biology, the Institute for Integrative Genome Biology, and the Graduate Program in Cell, Molecular and Developmental Biology.

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). During the summer of 1999, he was intern at Celera Genomics, Department of Informatics Research, Rockville, MD.

Stefano's recent research interest includes design of algorithms, computational molecular biology, data compression and data mining. He has published over 40 papers in major theoretical computer science and computational biology journals and over 50 publications in refereed international conferences. In the year 2005, he received the CAREER award from National Science Foundation. He has received funding from NSF, NIH, DARPA, and USDA.

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