The Combinatorics of Sequencing the Corn Genome

  Speaker 

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Srinivas Aluru is the Stanley Chair in Interdisciplinary Engineering and Professor of Electrical and Computer Engineering at Iowa State University. He recently served as Chair of Iowa State's Bioinformatics and Computational Biology program. He conducts research in high performance computing, algorithms and systems for large-scale applications, bioinformatics and systems biology, combinatorial scientific computing, and applied algorithms. Aluru is a recipient of the NSF Career award, IBM faculty award, Iowa State University Foundation award for mid-career achievement in research, two best paper awards (IPDPS 2006 and CSB 2005), and two best paper finalist recognitions (SC 2007 and SC 2002). He co-chairs an annual workshop in High Performance Computational Biology and edited a comprehensive handbook on computational molecular biology.

 Abstract

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The scientific community has recently finished the first draft sequence of the corn (also known as maize) genome. This genome is approximately 2.5 billion nucleotides long with an estimated 65-80% repeat content. A team of university and private laboratory researchers under the auspices of  NSF/USDA/DOE is working towards deciphering the majority of the sequence information including all genes, determining their order and orientation, and anchoring them to genetic/physical maps. In this talk, I will present some of the combinatorial problems that arise in this context and outline the role of graph, string and parallel algorithms in solving them.

http://www.ee.iastate.edu/~aluru/