Department of Computer Science

Bhubaneswar (Bud) Mishra

Date: Sep 25, 2008

Time: 3:30pm

Location: 1213 Hoover Hall

Title :SMASH: Single Molecule Approach to Sequencing by Hybridization

Abstract: SMASH is a technology for sequencing a human size genome of 6 Gigabases (including both haplotypes) without using any prior sequence information. We have aimed the technology for eventually (e.g., in less than a decade) achieving a competitively low cost for each genome sequence produced (e.g.US$1000 or less), while assuring a high quality (e.g., standard of "high quality draft sequence" similar to the mouse genome sequence published in December 2002). This technology is hoped to play a significant disruptive role in the future predictive personal-ized biomedicine as well as other areas of biotech industries.

These goals require successful integration of three different component technologies: (1) Optical Mapping to create Ordered Restriction Maps with respect to an enzyme, (2) Hybridization of a pool of oligonucleotide probes (LNA probes) with Single Genomic dsDNAs, and (3) Algorithms to solve "localized versions" of PSBH (Positional Sequencing by Hybridization) problems over the whole genome.

Unlike many of its competitors, the technology works with small amount of genomic materials, operates top-down, employs a Bayesian algorithm to create haplotypic sequence assembly without an auxiliary shotgun assem-bler, tolerates noise in the data well and is cost-effective at multiple scales. By construction, it avoids errors due to hompolymeric runs, haplotypic ambiguities and large-scale rearrangement errors. Its scientific feasibility has been demonstrated through many important algorithmic, chemical, and mathematical innovations over the last two years, further reassuring the soundness of the principles, science, and strategy for technology development.

About the Speaker:

Dr. Bhubaneswar (Bud) Mishra

Professor of Computer Science, Mathematics, Human Genetics, & Cell Biology Courant Institute, NYU School of Medicine, & Mt. Sinai School of Medicine

Prof. Bud Mishra is a professor of computer science and mathematics at NYU's Courant Institute of Mathematical Sciences, professor of human genetics at Mt. Sinai School of Medicine, and a professor of cell biology at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, a multi-disciplinary group working on re-search at the interface of computer science, applied mathematics, biology, biomedicine and bio/nano-technologies. Prof. Mishra has a degree in Physics from Utkal University, in Electronics and Communication Engi-neering from IIT, Kharagpur, and MS and PhD degrees in Computer Science from Carnegie Mellon University. He has industrial experience in Computer Science (Tartan Laboratories, and ATTAP), Finance (Tudor Investment and PRF, LLC), Robotics and Bio- and Nanotechnologies (OpGen, and Bioarrays). He is editor of Molecular Cancer Therapeutics, AMRX (Applied Mathematics Research Exchange), Nanotechnology, Science and Applications, and Transactions on Systems Biology, and author of a textbook on algorithmic algebra and more than two hundred archived publications. He is an inventor of Optical Mapping and Sequencing (SMASH), Array Mapping, Copy-Number Variation Mapping, Model Checker for circuit verification, Robot Grasping and Fixturing devices and algo-rithms, Reactive Robotics, and Nanotechnology for DNA profiling. He has been keynote and distinguished speak-ers at many symposia and colloquia and has chaired workshop and conference program committees: most re-cently, Algebraic Biology 2008 and Hybrid Systems: Computation and Control 2008. He is an ACM fellow and a NYSTAR Distinguished Professor (2001). He also holds adjunct professorship at Tata Institute of Fundamental Re-search in Mumbai, India. From 2001-04, he was a professor at the Watson School of Biological Sciences, Cold Spring Harbor Lab.