ECE Seminar Series

Joint Electrical and Computer Engineering Department and Computer Science Department Seminar Series

Title: Compressed Genome Sequencing and de novo Assembly for Sparse Microbial Communities
Speaker: Zeinab Taghavi
Affiliation: Colorado State University
Day: Monday, September 8, 2014
Time: 11:00 am - 12:00 pm
Location: CSB 130

Abstract: Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly (i.e., sensing and reconstruction) of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue is that deep sequencing of every cell should not be necessary to capture all distinct genomes, as the majority of cells are biological replicates. Biologically important samples are often sparse in that sense. As opposed to general understanding of sparsity in the field of compressed sensing in which the number of distinct events is often constant and sparsity is equivalent to rarity of an event, sparsity in our case means scarcity of distinct events in comparison to the data size. In this talk, we propose compressed methods to capture all distinct genomes in a sparse microbial community with reduced sequencing effort.

Bio: Zeinab Taghavi has recently joined the Computer Science Department at CSU, as a special assistant professor in Sep 2014. Her broad research interests include information theory, bioinformatics, communications, and signal processing. Her current research focus is compressive sensing and mathematical modeling of nonlinear systems. She received her PhD from the University of California, San Diego in Electrical Engineering - Communications and Information Theory in 2011. Her doctoral research was on modulation coding for magnetic recording and mitigation of the linear and nonlinear interferences in long-haul fiber optic communications. Dr. Taghavi added application of information theory in bioinformatics to her portfolio while she did her postdoctoral training at Wayne State University (WSU). She proposed and simulated the first mathematical model for the biochemical process of DNA multiple displacement amplification (MDA), which is widely used in single-cell genomic studies. In collaboration with the Algorithmic Biology Laboratory at Wayne State University, she worked on single-cell and compressive genome sequencing and de novo assembly of (diversity-) sparse microbial communities. During her bachelor's and master's studies at Sharif University of Technology, Dr. Taghavi worked on video processing and spread spectrum communications.