Abstract:

The landscape of computing has undergone a significant transformation with the death of Dennard scaling and the slowing of Moore’s law: applications now drive innovations in computer systems architecture. At the same time, the advent of high throughput, low cost sequencing technology has revolutionized genomics. The massive amount of data generated in genomics has uncovered acute compute challenges in biological inference due to limitations of software on traditional multi-core systems. To address this challenge, my research employs a hardware-software-algorithm co-design approach to significantly improve computational performance in key areas of comparative and clinical genomics.

In this talk, I will present systems that accelerate pipelines in both these domains of genomics. First, I will present Darwin-WGA (FPGA/ASIC) and SegAlign (GPU) for cross-species whole genome alignment where co-design has yielded orders of magnitude increase in speed. Additionally, there are gains in accuracy while modifying the algorithm to improve the underlying hardware implementation. Next, I will talk about the ultra-rapid nanopore whole genome sequencing pipeline that can deliver a genetic diagnosis in under 8 hours, making it the fastest pipeline to date. The scalable, cloud-based distributed infrastructure overcomes system bottlenecks to enable near real-time computation and improved variant identification. This pipeline has been deployed in critical care units in Stanford hospitals and applied to 13 patients. Finally, I will share my vision for continued advancements in computer systems applied to emerging fields such as pangenomics, single cell genomics, and long read clinical sequencing.

Bio:

Sneha Goenka is a Ph.D. candidate in the Electrical Engineering Department at Stanford University where she is advised by Prof. Mark Horowitz. Her research centers on designing efficient computer systems for advancing genomic pipelines for clinical and research applications, with a focus on improving speed and cost. She is a 2023 Forbes 30 Under 30 Honoree in the Science category, 2022 NVIDIA Graduate Fellow, and 2021 Cadence Women in Technology Scholar. She has a B.Tech. and M.Tech. (Microelectronics) in Electrical Engineering from the Indian Institute of Technology, Bombay where she received the Akshay Dhoke Memorial Award for the most outstanding student in the program.