The New Era in Genomics: Opportunities and Challenges for High Performance Computing

Srinivas Aluru

Ross Martin and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State University

Bajaj Chair Professor of Computer Science and Engineering at Indian Institute of Technology Bombay

Abstract:

The advent of second and third generation sequencing technologies is revolutionizing biosciences research by enabling high-throughput sampling of genomes and transcriptomes. With these technologies, it is now possible to sequence a few billion DNA fragments in a single experiment. This quantum leap in throughput creates many technical challenges: 1) instrumentation-specific challenges such as error correction; 2) reinventing methodologies for classic applications such as genome assembly; 3) challenges due to rapid scale up in scope and number of research projects driven by lower economic costs; and 4) expanding the repertoire of applications – e.g., personalized genome sequencing, and digital expression analysis for systems biology. The rapid development of next generation technologies, and the richness and diversity of their applications, has created a pressing need for new bioinformatics tools and computational methods capable of dealing with large volumes of data. This talk will outline the computational challenges in exploiting high-throughput sequencing technologies, and the role of high performance computing as we transition to this new era.

Bio:

Srinivas Aluru is the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State University, and the Bajaj Chair Professor of Computer Science and Engineering at Indian Institute of Technology Bombay. He leads the Dean's Research Initiative in high-throughput computational biology, a multi-disciplinary and multi-investigator initiative at the interface of high performance computing and computational biology. Earlier, he served as Chair of Iowa State's Bioinformatics and Computational Biology program, and has held faculty positions at New Mexico State University and Syracuse University. Aluru conducts research in parallel algorithms and applications, bioinformatics and systems biology, combinatorial scientific computing, and applied algorithms. He pioneered the development of parallel methods in computational biology, and contributed to the assembly and analysis of plant genomes. His contributions in scientific computing lie in the development of parallel Fast Multipo

le Method, spatial data structures, and applications to computational electromagnetics and materials science. He serves on the editorial boards of IEEE Transactions on Parallel and Distributed Systems, Journal of Parallel and Distributed Computing, International Journal of Data Mining and Bioinformatics, and Journal of Computing from the Computer Society of India. He is a recipient of the NSF career award, IBM faculty award, Swarnajayanti Fellowship from the Government of India, and the mid-career (2006) and outstanding (2011) research achievement awards from Iowa State University. He is a Fellow of the IEEE and AAAS.