Presenter: Dr. Yatish Turakhia, Assistant Professor in the Department of Electrical and Computer Engineering, University of California San Diego

Description: The continued exponential growth of genomic data presents a tremendous opportunity to deepen our understanding of biological processes, but it also introduces significant computational and storage challenges that must be addressed to fully harness its potential. The new wave of genomic data is driven by dense sampling—sequencing large populations within and across closely related species—leading to a growing interest in pangenomics. While existing pangenome formats can capture genetic variation across a collection of genomes, they do not preserve shared evolutionary and mutational histories—an important missed opportunity—and are unlikely to scale with the growing volume of genome sequencing data. 

In this talk, I will present a new pangenomics data representation developed in my lab, called PanMAN, which significantly improves the representative power of pangenomes while also providing astonishing lossless compression compared to existing formats. PanMAN is the first to unify phylogenetic networks, mutational histories, genomic variation, and multiple whole-genome alignments within a single, cohesive file format. This advancement would empower new applications and also allow us to compress, construct, analyze, and share pangenomes at an unprecedented scale. I will also discuss how my lab is leveraging hardware-software co-design techniques to develop new GPU-accelerated tools for multiple-sequence alignment (MSA) and phylogenetic inference that scale to millions of whole-genome sequences under dense sampling scenarios, paving the way for the construction of ultra-large pangenomes.

Bio: Dr. Yatish Turakhia is an Assistant Professor in the Department of Electrical and Computer Engineering at the University of California San Diego (UCSD), with affiliations in the Department of Computer Science and Engineering (CSE) and the Bioinformatics and Systems Biology (BISB) graduate program. Prior to joining UCSD, he was a postdoctoral scholar at the Genomics Institute, UC Santa Cruz. Dr. Turakhia earned his Ph.D. in Electrical Engineering from Stanford University in 2019 and his bachelor’s and master’s degrees in Electrical Engineering from the Indian Institute of Technology (IIT) Bombay in 2014. He is a recipient of the MIT Technology Review’s Innovators Under 35 award, Hellman Fellowship, Jacobs Early Career Award, Amazon Research Award, NVIDIA Graduate Fellowship, and multiple paper awards.

Hosted by: Professor Russ Corbett-Detig, BME Department