CSE Distinguished Lecture: Bud Mishra

Talk Title:

Genomics Algorithms: Try Again! Fail Again!! Fail Better!!!

Abstract:

We will describe a new approach to genomics problems based on a new technology: Nano Mapping, which is ultra-cheap, fast (low latency/high throughput), accurate and potentially highly disruptive. As the genomic analyses of humans have continued to gain momentum (ancestry.com, 23andMe, etc.), we are frustrated by the problem of not being able to accurately create and interpret data that reflect the genome’s true complexity: in tumor analysis (single cell/single molecule), microbiomics, liquid biopsy (circulating tumor cells and cell free DNA), epigenetics, etc. The new technology addresses these issues. The talk will focus on various computational and complexity theoretic questions related to data analyses and their applications: Solving instances of NP-hard problems associated with Variant Detection, Haplotype Phasing, Whole Genome Off-target analysis (e.g., with CRISPR assays), Sequence Assembly, etc. And doing so in Polynomial time (so-called NP-easy problems) or even in Polylog/Constant time (using hashing and hardware acceleration). Additional topics may be discussed upon request.

Bio:

Professor Bud Mishra is an educator, an inventor as well as a mentor to technologists, entrepreneurs and scientists. Prof. Mishra founded the NYU/Courant Bioinformatics Group, a multidisciplinary group working on research at the interface of computer science, applied mathematics, biology, biomedicine and bio/nano-technologies as well as Tandon-Online program on Bioinformatics Engineering.

Mishra has industrial experience in Computer and Data Science (aiNexusLab, ATTAP, behold.ai, brainiad, Genesis Media, Pypestream, and Tartan Laboratories), Finance (Instadat, Pat- tern Recognition Fund and Tudor Investment), Robotics and Bio- and Nanotechnologies (Abraxis, Bioarrays, InSilico, MRTech, OpGen and Seqster). He is the author of a textbook on algorithmic algebra and more than two hundred archived publications. He has advised and mentored more than 35 graduate students and post-docs in the areas of computer science, robotics and control engineering, applied mathematics, finance, biology and medicine. He holds 21 issued and 23 pending patents in areas ranging over robotics, model checking, intrusion detection, cyber security, emergency response, disaster management, data analysis, biotechnology, nanotechnology, genome mapping and sequencing, mutation calling, cancer biology, fintech, adtech, internet architecture and linguistics.

Mishra’s pioneering work includes: first application of model checking to hardware verifica- tion; first robotics technologies for grasping, reactive grippers and work holding; first single molecule genotype/haplotype mapping technology (Optical Mapping); first analysis of copy number variants with a segmentation algorithm, first whole-genome haplotype assembly technology (SUTTA), first clinical-genomic variant/base calling technology (TotalRecaller), first single molecule single cell nanomapping technology, etc.

Mishra’s current work in progress continues in the areas of single-molecule nano-mapping (with Reed, Payton, Picco et al.), clinical genomics (with Bannon, Cantor, Menges, Narzisi, Reed et al.), liquid biopsies (with Jee, Nudler et al.), cancer data (with Antoniotti, Bannon, Burakoff, Cantor, Khianbian, Korsunsky, Rabadan, Ramazzotti, Zhavoronkov et al.), cyber security (with Cai, Casey, Morales, Moore, Novak et al.), cryptography (with Gvili, Janwa, Kahrobaei et al.), linguistics (with Chakraborty, Rinberg, Tamaskar, Young et al.) financial engineering (with Deboneuill, Qi, Subramaniam, et al.) and internet of the future (with Rudolph, Savas, Weill et al.).

Mishra is currently a professor of computer science and mathematics at NYU’s Courant Institute of Mathematical Sciences, professor of engineering at NYUs Tandon School of engineering, professor of human genetics at MSSM Mt. Sinai School of Medicine, visiting scholar in quantitative biology at CSHL Cold Spring Harbor Laboratory and a professor of cell biology at NYU SoMSchool of Medicine.

Mishra has a degree in Science from Utkal University, in Electronics and Communication Engineering from IIT, Kharagpur, and MS and Ph.D. degrees in Computer Science from Carnegie Mellon University. He is a fellow of IEEE, ACM and AAAS, a fellow of National Academy of Inventors (NAI), a Distinguished Alumnus of IIT (Kharagpur), and a NYSTAR Distinguished Professor.