Computer Science Faculty Recruiting Colloquium
Dr. Yatish Turakhia (UC Santa Cruz)

ABSTRACT:
Genome sequencing data continues to rise exponentially at a rate (125%/year) that far outpaces transistor performance scaling (currently 3%/year). New medical and comparative genomics applications have emerged that ensure that the demand for more sequencing will continue to rise. As genomics data overwhelms our current compute capacity, domain-specific acceleration (DSA), i.e. using specialized hardware for accelerating a narrow domain of algorithms, will enable us to tap the vast potential of this data. In this talk, I will present the design of two co-processors (Darwin and Darwin-WGA) for the applications of long-read genome assembly and cross-species whole-genome alignments. I will demonstrate how specialized hardware can provide massive speedup (1,000-10,000x) for genomic computations using a hardware-software co-design approach and how hardware can sometimes also facilitate new discoveries by enabling computations that are otherwise prohibitive in software. In the second half of my talk, I will show how we used whole genome alignments in our research to make fascinating biological discoveries, including finding the molecular basis of convergent evolution and hundreds of gene losses in mammals. In the end, I will highlight how hardware-acceleration would be indispensable to solve the emerging problems in genomics.

BIO:
Dr. Yatish Turakhia is a postdoctoral research at Genomics Institute, UC Santa Cruz, where he is jointly advised by Prof. David Haussler and Prof. Benedict Paten. His research interests are in developing hardware accelerators and algorithms for faster and cheaper genomic analysis. Dr. Turakhia obtained his PhD from Stanford University in 2019, where he was jointly advised by Prof. Bill Dally and Prof. Gill Bejerano. His work has won the best paper award at ASPLOS 2018 and IEEE Micro Top Picks award 2018. He is also a recipient of the NVIDIA Graduate Fellowship (2016).