TUTORIAL 2: T-2 9:00am-12:30pm

Title: An introduction to molecular biology and bioinformatics for information theorists

Presenters: Sharon Aviran, University of California and Olgica Milenkovic, University of Illinois

Abstract:

The tutorial will consist of three parts. In the first part, we will cover the basics of cellular and molecular biological function as well as basic concepts in genome research. We will then review the state-of-the-art technology for genomic and proteomic data acquisition, including the new nextgeneration high-throughput DNA sequencing technologies, ChIP-based technology for determining protein-nucleic acid interactions, and protein tandem mass spectrometry. The second part will focus on mathematical problems arising in the study of genomic and proteomic sequences, such as DNA and RNA-transcript assembly and the quantification and folding of RNAs and proteins. We will devote the third part to mathematical modeling and analysis of gene regulatory and protein-protein interaction networks. No prior knowledge in bioinformatics or molecular biology is needed.

Biography:

Sharon Aviran is a researcher at the Center for Computational Biology at UC Berkeley and is affiliated with the departments of Mathematics and Molecular and Cell Biology. Her current research is at the intersection of genomics, statistics, and signals processing, and focuses on developing computational methods for high-throughput analysis of RNA molecular dynamics. She received her Ph.D. in Electrical Engineering from the University of California, San Diego (UCSD) in 2006, specializing in the areas of information theory and signal processing for communications, and was awarded the 2006 Sheldon Schultz Prize for Excellence in Graduate Student Research. Dr. Aviran was a Calit2 Fellow at UCSD and a Celera/TCS Postdoctoral Innovation Fellow at UC Berkeley. She also served as a Lecturer for UCSD in 2007 and has several years of industrial R&D experience.

Olgica Milenkovic received an MSc degree in mathematics and PhD degree in electrical engineering from the University of Michigan, Ann Arbor, in 2001 and 2002, respectively. From 2002 until 2006 she was with the faculty of University of Colorado, Boulder. In 2006, she was a visiting professor at the University of California, San Diego Center for Information Theory and Application. In 2007, she joined University of Illinois, Urbana-Champaign were she currently holds the position of associate professor. Her research interests are in algorithmic analysis, bioinformatics, coding theory, combinatorics and signal processing. Prof. Milenkovic is a UIUC Center for Advanced Studies (CAS) Associate, recipient of the NSF Career Award, the DARPA Young Faculty Award and a number of best conference paper awards. She served as Associate editor of the Transactions on Communications, Transactions on Signal Processing and the Transactions on Information Theory.