Turakhia Lab
UC San Diego

Prof. Yatish Turakhia

I am an Assistant Professor in the Department of Electrical and Computer Engineering (ECE) at the University of California San Diego (UCSD) since July 2021. I am also affiliated with the Department of Computer Science and Engineering (CSE) and the Bioinformatics and Systems Biology (BISB) graduate program at UCSD. My lab is also affiliated with the Center of Machine-Integrated Computing and Security (MICS) and Center of Microbiome Innovation (CMI) at UCSD.

Previously, I was a postdoctoral scholar at the Genomics Institute at UC Santa Cruz. I obtained his Ph.D. in Electrical Engineering in 2019 from Stanford University and my bachelor’s and master’s degree in Electrical Engineering from the Indian Institute of Technology (IIT), Bombay in 2014.

Office: Jacobs Hall, Room 4408, Engineer Ln, University of California San Diego, CA 92093-0407

Email: yturakhia [at] eng [dot] ucsd [dot] edu

Phone: (858) 534-4493

Ongoing Research

Turakhia Lab works at the intersection of computer architecture and computational biology. Particularly, we work on developing algorithms and domain-specific hardware accelerators that enable faster and cheaper progress in biology and medicine.

Hardware acceleration of computational genomics

Genomic data is one of the fastest growing data types on the planet and is far outpacing Moore’s law. From personalized medicine to species conservation, genomic data has far-reaching applications, but computational costs are posing ever greater challenges to exploit the full potential of this data. We are exploring novel algorithms and hardware (GPU/FPGA/ASIC) acceleration approaches to speed up a wide range of computational genomics tasks, such as genome assembly, read alignment and whole-genome alignments, by orders of magnitude.

SARS-CoV-2 Phylogenetics

With over 5 million (and counting) whole SARS-CoV-2 genomes sequences already, the COVID-19 pathogen is the most sequenced pathogen in history. Phylogenetic analysis using these genomes has played a vital role in tracking the virus evolution and transmission, but is posing major computational challenges. Our lab is working closely with Prof. Corbett-Detig's lab at UC Santa Cruz in maintaining and refining a comprehensive phylogenetic tree consisting of all available SARS-CoV-2 genomes and further improving our tools for speed and accuracy. We are also working on studying the evolution of SARS-CoV-2, such as through recombination.

(Image: Taxonium.org)

News

  • [Jan, 2022] Cheng Ye et al. release a preprint on matOptimize: a parallel tree optimization tool capable of handling million-scale SARS-CoV-2 phylogenies

  • [Jan, 2022] Yatish starts teaching the graduate course ECE 284: Parallel Computing in Bioinformatics

  • [Jan, 2022] Alireza Mohammadidoost (PhD, ECE) joins the lab. Welcome, Alireza!

  • [Dec, 2021] Cheng Ye et al. release a preprint on pandemic-scale phylogenetics, which is covered by The Medical News.

  • [Nov, 2021] Yatish is quoted by The Guardian on the Omicron variant

  • [Nov, 2021] Yatish gives a talk on "Pandemic-scale Phylogenetics" in the CSE 290 class at UCSD

  • [Nov, 2021] Angie Hinrichs (UCSC) highlights UShER and matOptimize at the StaPH-B meeting

  • [Sep, 2021] Manuscript on matUtlils and the UCSC SARS-CoV-2 tree database published in Molecular Biology and Evolution (MBE)

  • [Sep, 2021] Sumit Walia (PhD, ECE) and Kyle Smith (UG, Bioinformatics) join the lab. Welcome, Sumit and Kyle

  • [Sep, 2021] RIPPLES and UShER are featured in an article in The Scientist

  • [Sep, 2021] Devika and Shoh wrap up their summer research internships. Congratulations!

  • [Aug, 2021] Yatish provides a tutorial on UShER at the Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME 2021)

  • [Aug, 2021] The Medical News features our work on SARS-CoV-2 recombination

  • [Aug, 2021] A preprint on RIPPLES, with contributions from Yatish (co-first author) and Cheng, is posted on bioRxiv

  • [Jul, 2021] Yatish interviews with The Wired on the Delta variant

  • [Jul, 2021] Yatish officially starts at UCSD as an Assistant Professor

MORE NEWS >>

Recent Publications

Journals:

  1. J. Schull*, Y. Turakhia*, J. Hemker, W. J. Dally, G. Bejerano, "Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference", Genome Biology and Evolution (GBE), February 2022. [paper, code]

  2. A. Kramer, Y. Turakhia, R. Corbett-Detig, "ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees", Journal of Open Source Software (JOSS), Oct 2021. [paper, code, web tool]

  3. J. McBroome, B. Thornlow, A. S. Hinrichs, A. Kramer, N. D. Maio, N. Goldman, D. Haussler, R. Corbett-Detig^, Y. Turakhia^, "A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees", Molecular Biology and Evolution (MBE), Sep 2021 [paper, code, wiki].

  4. Y. Turakhia^, B. Thornlow, A. S. Hinrichs, N. D. Maio, L. Gozashti, R. Lanfear, D. Haussler, and R. Corbett-Detig^, "Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic", Nature Genetics, May 2021 [paper, slides, code, wiki, video].

  5. N. D. Maio, C. R. Walker, Y. Turakhia, R. Lanfear, R. Corbett-Detig, N. Goldman, "Mutation rates and selection on synonymous mutations in SARS-CoV-2", Genome Biology and Evolution (GBE), April 2021 [paper, code]

Conference:

  1. S. D. Goenka*, Y. Turakhia*, B. Paten, M. Horowitz, "SegAlign: A Scalable GPU-Based Whole Genome Aligner", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2020. [paper, slides, code]

  2. Y. Turakhia*, S. D. Goenka*, G. Bejerano, W. Dally, “Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup” , International Symposium on High-Performance Computer Architecture (HPCA), 2019. [paper, slides, code]

  3. Y. Turakhia, G. Bejerano, W. Dally, “Darwin: A Genomic Co-processor Provides 15,000× Speedup on long read assembly”, Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2018 (Best paper award). [paper, slides, code]

More Publications >>