Anshu Gupta

Anshu Gupta

PhD Candidate, Computer Science & Engineering
University of California San Diego

I am a 4th-year PhD candidate in Computer Science and Engineering at the University of California San Diego, advised by Prof. Yatish Turakhia.

My research stands at the unique intersection of computer architecture, hardware/software co-design, and computational genomics, with the broader goal of making large-scale genomic analysis fast, scalable, and accessible. I build tools that spans from FPGA-based accelerators for dynamic programming-based sequence alignment to a fully automated, GPU/CPU-parallelized workflow for evolutionary tree inference. These tools are open-sourced and being used by research groups worldwide, with publications at leading venues (PNAS, HPCA).

I collaborate with the Vertebrate Genomes Project (VGP) consortium led by Genomics Institute at University of California Santa Cruz, researchers at the Scripps Institution of Oceanography, UCSD, and the AMD Omics Group on accelerating bioinformatics workloads at scale.

Beyond research, I serve the community as a member of the Artifact Evaluation Committee for ISCA 2025 and ISCA 2024, as a reviewer for Bioinformatics, RECOMB 2026 and MBE, and as co-organizer of the BioSys Workshop at ASPLOS 2024.

I received my M.S. in Computer Engineering from UC San Diego and my B.Tech. from IIEST Shibpur, India. Before my PhD, I spent 3+ years as a Digital Design Engineer at Analog Devices, gaining ASIC design and chip tape-out experience. During my PhD, I interned at AMD Research. I was also a DAAD WISE Scholar at the University of Bremen, Germany.

Press & Media Coverage Full coverage →
PNAS Cover May 2025
PNAS
Journal Cover — Vol. 122, No. 19
UCSD Today
UCSD Today
A Fully Automated Tool for Species Tree Inference
Jacobs School of Engineering
A team of engineers at UC San Diego is making species tree inference fully automated
SciEnMag
New Breakthrough: Fully Automated Tool Revolutionizes Species Tree Inference
EurekAlert!
EurekAlert!
Automated Tool Enables Species Tree Inference from Raw Genome Assemblies
Service
Artifact Evaluation Committee, ISCA 2025, ISCA 2024.
Reviewer, Bioinformatics (Oxford Academic), RECOMB 2026 (Satellite Workshop).
Workshop Co-organizer, BioSys Workshop @ ASPLOS 2024 — San Diego, CA.
Collaborations and Affiliations
News All news →
Apr 2026 Defended my Ph.D. thesis proposal and advanced to candidacy. Committee: Prof. Siavash Mirarab, Prof. Melissa Gymrek, and Prof. Rob Knight.
Apr 2026 Presented DP-HLS poster at UC San Diego Research Expo 2026.
Mar 2026 Delivered a guest lecture for ECE 218 at UC San Diego.
Feb 2026 Presented and published DP-HLS at IEEE HPCA 2026, Sydney, Australia.
Jun 2025 Started research internship at AMD Research & Advanced Development (RAD), San Jose, CA.
May 2025 ROADIES published in PNAS and selected as the journal cover (Vol. 122, No. 19). Featured in UCSD Today.
Mar 2025 Served on Artifact Evaluation Committee for ISCA 2025.
Jul 2024 Presented talk on ROADIES at ISMB 2024, Montreal, Canada.
Apr 2024 Awarded ASPLOS 2024 Travel Grant. Co-organized the 1st BioSys workshop at ASPLOS 2024, San Diego.
Apr 2024 Presented poster on ROADIES at UC San Diego Research Expo 2024.
Mar 2024 Served on Artifact Evaluation Committee for ISCA 2024.
Sep 2023 Completed 3-month summer internship at Analog Devices, Inc., Wilmington, MA.
Nov 2022 Joined Turakhia Lab as a PhD student at UC San Diego.