[Theory] 3/4 Talks at TTIC: Chirag Jain, NIH/NHGRI

[Mary Marre]

*When:*      Wednesday, March 4th at 11:00 am



*Where:*     TTIC, 6045 S. Kenwood Avenue, 5th Floor, Room 526



*Who: *       Chirag Jain, NIH/NHGRI



*Title:     *   Scalable Algorithms for Rapidly Advancing DNA Sequencing
Technologies

*Abstract:  *Genomics continues to have an immense impact in life sciences,
from elucidating fundamental genetic mechanisms to providing new keys to
understand diseases. Catalyzed by breakthroughs in genomic
technologies,high-throughput DNA sequencing has become a major generator of
data, catching up with the most prominent big-data applications such as
astronomy and social media. As a result, it has become challenging to
design scalable bioinformatics algorithms with suitable accuracy guarantees.

In the first part of my talk, I will formulate the problem of aligning a
biological sequence to a ‘pan-genome’ graph. The graph-based representation
has been touted as the new standard for human genome reference,as it can
succinctly capture human genetic variation across the globe. I will present
new complexity results and algorithms for computing an optimal sequence
alignment using such graphs. In the second part, I will present an approximate
sketch-based algorithm for mapping long noisy sequences. The proposed algorithm
is able to map sequences to the entire NCBI genome database (totaling ~1
Tbp) for the first time, enabling real-time genomic analysis. I will
also discuss
generalization of the proposed algorithms to a wider set of problems, and their
impact in tackling long-standing biological questions.

*Bio: *Dr. Jain is currently a postdoctoral fellow with Dr. Adam Phillippy
in the Genome Informatics Section at the National Institutes ofHealth
(NIH), USA. He got his doctorate in Computational Science at Georgia Tech
under the supervision of Prof. Srinivas Aluru, and bachelors in Computer
Science from IIT Delhi.  He is a recipient of the Best GPU Paper Award at
IEEE HiPC’14, Best Poster awards at RECOMB’19, CRIDC’19, IITD-Open
House’14, and Reproducibility-Initiative Award at ACM Supercomputing'16.

*Host:  *Jinbo Xu <j3xu at ttic.edu>



Mary C. Marre
Faculty Administrative Support
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 517*
*Chicago, IL  60637*
*p:(773) 834-1757*
*f: (773) 357-6970*
*mmarre at ttic.edu <mmarre at ttic.edu>*
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