Prof. Yatish Turakhia

I am an Assistant Professor in the Department of Electrical and Computer Engineering (ECE) at the University of California San Diego, with joint appointments in Computer Science and Engineering (CSE), Bioengineering, and the Bioinformatics and Systems Biology (BISB) graduate program.

My lab also collaborates closely with the Center for Machine-Integrated Computing and Security (MICS), the Center for Microbiome Innovation (CMI), and the Institute for Genomic Medicine (IGM) at UC San Diego.

You can find my most recent CV.

Email: yturakhia@ucsd.edu

Contact: +1 (858) 534-4493

Office: Room 4304, Franklin Antonio Hall, UC San Diego

Latest News

Sep 2025: Wen-Chieh Lo joins Turakhia Lab as a PhD student in ECE. Welcome, Wen-Chieh!
Sep 2025: Pranav passes his PhD qualifying exam. Congratulations, Pranav!
Aug 2025: Sumit passes his PhD qualifying exam. Congratulations, Sumit!
Aug 2025: Yatish presents a talk at the University of Chicago on "GPU-Accelerated Construction of Ultra-Large Pangenomes via Alignment-Phylogeny Co-Estimation."
Aug 2025: Allen Yan and Alan Wang present at the UC San Diego Summer Research Conference.
Aug 2025: Sumit Walia and Zexing Chen et al. release a preprint on DIPPER.
Aug 2025: Yu-Hsiang passes his PhD prelims exam. Congratulations, Yu-Hsiang!
July 2025: Yu-Hsiang attends ISMB/ECCB 2025 to present TWILIGHT.
July 2025: Sumit attends ISMB/ECCB 2025 to present PanMAN.
July 2025: TWILIGHT is published in Bioinformatics. Congratulations, Yu-Hsiang and Sumit!
June 2025: Yatish presents a talk at the Barcelona Supercomputing Center on "Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data."
June 2025: Yatish presents a talk at ETH Zurich on "Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data."
June 2025: Yatish presents a talk at the Biozentrum, University of Basel on "Compressive Pangenomics and Applications to Global Pathogen Surveillance."
June 2025: Yatish presents a talk at the PASC 2025 Minisymposium on "Building Ultra-large Pangenomes."
June 2025: Yu-Hsiang presents TWILIGHT at Evolution 2025.
June 2025: Pranav Gangwar et al. release a preprint on WEPP.
June 2025: Pranav presents WEPP at the Wastewater Disease Surveillance Summit 2025.
May 2025: Yatish presents a talk at Fred Hutch Cancer Center on "Compressive Pangenomics and Applications to Global Pathogen Surveillance."
May 2025: Jaden and Qiwen present their research projects at the UC San Diego Undergraduate Engineering Research Symposium.
May 2025: ROADIES is highlighted as the cover feature in PNAS.
May 2025: ROADIES is published in PNAS. Congratulations, Anshu!
Apr 2025: Yatish authors a Technical Perspective for a Research Highlight in Communications of the ACM.
Apr 2025: Turakhia Lab welcomes new members Anika Agarwal and Allen Yan to the team.
Mar 2025: Yatish presents a talk at the UC Santa Cruz BME Seminar on "Building Ultra-large Pangenomes."
Feb 2025: Yatish receives the Jacobs School Early Career Faculty Development Award to harness pangenomics for trait association studies in collaboration with Prof. Melissa Gymrek.
Jan 2025: Kyle Smith receives an Honorable Mention in the 2024-2025 CRA Outstanding Undergraduate Researcher Award. Congratulations, Kyle!
Jan 2025: Turakhia Lab welcomes new members Jaden Seangmany and Qiwen Xu to the team.
Nov 2024: Yatish gives a talk titled "Scaling Up Phylogenetics" at the ICERM Workshop 2024 at Brown University.
Nov 2024: Yingqi Cao and Anshu Gupta et al. release a preprint on DP-HLS.
Oct 2024: Yatish gives an HPC Sync talk at AMD.
Oct 2024: Yatish is selected as one of the "100 Young Scientists" worldwide at the 2024 WLA Forum in Shanghai, China.
Oct 2024: Turakhia Lab welcomes new members Jade Wang and Fahad Alkhazam to the team.
Sep 2024: Sunreet Khanna joins the lab as a co-advised student with Prof. Bill Lin. Welcome, Sunreet!

Affiliations

Sponsors and Collaborators

Our work is generously funded by the Centers for Disease Control and Prevention (CDC), California Department of Public Health (CDPH), Hellman Fellowship, National Institutes of Health (NIH), Advanced Micro Devices (AMD), Amazon Research Award (ARA), and the AMD AI & HPC Research Fund.

Research Mission

We are an interdisciplinary group tackling a broad set of problems at the leading edge of computer engineering and bioinformatics.

We focus on biological and medical applications where computational cost and turnaround time have become the bottleneck.

Our research mission is to develop parallel algorithms, software, and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.

Ongoing Research

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Pangenomics | study genetic variation across genomes

Low-cost, high-throughput sequencing has unlocked unprecedented cohorts and catalyzed pangenomics, the study of genetic variation within a species through collections of representative genomes. Realizing its potential demands moving beyond single-reference paradigms toward scalable, graph-aware methods.

Our team designs compressed data structures, novel algorithms, and hardware acceleration techniques that make pangenomic analysis more comprehensive and dramatically faster.

Related Publications

  • Sumit Walia, Harsh Motwani, Kyle Smith, Russell Corbett-Detig, Yatish Turakhia, "Compressive Pangenomics Using Mutation-Annotated Networks" bioRxiv (2024) | DOI | Talk | PDF

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Phylogenetics | study evolutionary relationships of species

Phylogenetics examines the evolutionary relationships among biological sequences, organisms, or species, underpinning evolutionary biology, outbreak analysis, and comparative genomics. Large-scale consortia such as the Vertebrate Genomes Project (VGP) and the Earth Biogenome Project (EBP) generate vast genomic data sets, yet constructing and analyzing the resulting phylogenies remains computationally demanding.

In collaboration with Prof. Siavash Mirarab's lab at UC San Diego, we are developing automated, scalable, and hardware-software co-designed methods that address these challenges end to end.

Related Publications

  • Anshu Gupta, Siavash Mirarab, Yatish Turakhia, "Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES", PNAS (2025) | DOI | Talk | PDF

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Hardware Acceleration | make computational genomics faster

Genomic data is among the fastest-growing data types on the planet and already outpaces Moore’s law. From personalized medicine to species conservation, realizing its value demands far more efficient computation.

We design novel algorithms and GPU/FPGA/ASIC acceleration strategies that speed up genome assembly, read alignment, multiple sequence alignment, and whole-genome alignment workflows by orders of magnitude.

Related Publications

  • Sumit Walia, Zexing Chen, Yu-Hsiang Tseng, Yatish Turakhia, "Ultrafast and Ultralarge Distance-Based Phylogenetics Using DIPPER", bioRxiv (2025) | DOI | PDF

  • Yu-Hsiang Tseng, Sumit Walia, Yatish Turakhia, "Ultrafast and ultralarge multiple sequence alignments using TWILIGHT", Bioinformatics (2025) | DOI | Talk

  • Yingqi Cao, Anshu Gupta, Jason Liang, Yatish Turakhia, "DP-HLS: A High-Level Synthesis Framework for Accelerating Dynamic Programming Algorithms in Bioinformatics", arXiv (2024) | DOI | Talk | PDF

  • Sumit Walia, Cheng Ye, Arkid Bera, Dhruvi Lodhavia, Yatish Turakhia, "TALCO: Tiling Genome Sequence Alignment using Convergence of Traceback Pointers", HPCA (2024) | DOI | Talk | PDF

  • Sneha D. Goenka, Yatish Turakhia, Benedict Paten, Mark Horowitz, "SegAlign: A scalable GPU-based whole genome aligner", SC20 (2020) | DOI | Talk | PDF

  • Yatish Turakhia, Sneha D. Goenka, Gill Bejerano, William J. Dally, "Darwin-WGA: A co-processor provides increased sensitivity in whole genome alignments with high speedup", HPCA (2019) | DOI | Talk | PDF

  • Yatish Turakhia, Gill Bejerano, William J. Dally, "Darwin: A Genomic Co-processor Provides 15,000× Speedup on long read assembly", ASPLOS (2018) | DOI | Talk | PDF

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Outbreak Analysis | real-time phylogenetics for pandemic analysis

With more than 16 million complete SARS-CoV-2 genomes already sequenced, COVID-19 is the most comprehensively characterized pathogen in history. Phylogenetic analysis of these data is essential for tracking viral evolution and transmission, yet keeping pace with the deluge of sequences is a formidable computational challenge.

Our lab partners with Prof. Russell Corbett-Detig’s group at UC Santa Cruz to maintain and refine a comprehensive phylogenetic tree that incorporates every available SARS-CoV-2 genome.

Related Publications

  • Kyle Smith, Cheng Ye, Yatish Turakhia, "Tracking and curating putative SARS-CoV-2 recombinants with RIVET", Bioinformatics (2023) | DOI | Talk

  • Yatish Turakhia, Bryan Thornlow, Angie Hinrichs, Jakob McBroome, Nicolas Ayala, Cheng Ye, Kyle Smith, Nicola De Maio, David Haussler, Robert Lanfear, and Russell Corbett-Detig, "Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape", Nature (2022) | DOI | Talk

  • Cheng Ye, Bryan Thornlow, Angie Hinrichs, Alexander Kramer, Cade Mirchandani, Devika Torvi, Robert Lanfear, Russell Corbett-Detig, and Yatish Turakhia, "matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2", Bioinformatics (2022) | DOI | Talk

  • Yatish Turakhia, Bryan Thornlow, Angie S. Hinrichs, Nicola De Maio, Landen Gozashti, Robert Lanfear, David Haussler, and Russell Corbett-Detig, "Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic", Nature Genetics (2021) | DOI | Talk

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Wastewater-based Epidemiology | tracking pathogen evolution and transmission

Wastewater-based epidemiology (WBE) analyzes community sewage to recover genome sequences of circulating pathogens. A UC San Diego team showed that WBE can detect emerging variants up to two weeks earlier than traditional clinical genomic surveillance.

Today, WBE is being rapidly adopted worldwide to monitor pathogens such as SARS-CoV-2, RSV, mpox, influenza, and polio, yet the resulting torrent of data poses significant computational and algorithmic challenges.

We are developing algorithms and software that enhance the accuracy, resolution, and timeliness of wastewater genomics.

Related Publications

  • Pranav Gangwar, Pratik Katte, Manu Bhat, and Yatish Turakhia, "WEPP: Phylogenetic Placement Achieves Near-Haplotype Resolution in Wastewater-Based Epidemiology" medRxiv (2025) | DOI | Talk | PDF