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: Franklin Antonio Hall, Room 0104, 3180 Voigt Dr, University of California San Diego, CA 92093-0407
Email: yturakhia [at] 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
[Oct, 2022] Yatish gives a keynote talk at the NGS 2022 conference organized by the American Society for Microbiology.
[Sep, 2022] Yatish gives a talk at the Massachusetts General Hospital and a chalk talk at the UCSD Undergraduate Bioinformatics Club (UBIC).
[Sep, 2022] Turakhia Lab welcomes new members Arkid Bera, Yingqi Cao, Debabrata Chaudhury, Dhruvi Lodhavia and Harsh Motwani to the lab.
[Sep, 2022] Turakhia Lab joins the SEARCH team which is tracking the spread of SARS-CoV-2 in San Diego.
[Aug, 2022] RIPPLES manuscript on SARS-CoV-2 recombination is published in Nature. Read press release. Congratulations, Cheng Ye and Kyle Smith, for contributing to this study!
[Jul, 2022] Yatish presents at phyloseminar. Watch recording.
[Jun, 2022] matOptimize is published in Bioinformatics! Read press coverage. Congratulations, Cheng et al.!
[Jun, 2022] High school interns Vidhi Kulkarnia and Ronnie Volman join the lab for Summer 2022. Welcome, Vidhi and Ronnie!
[Jun, 2022] Alireza presents his work at AACBB 2022, held in conjunction with ISCA 2022.
[Jun, 2022] Undergraduate researchers Arthur Lu, Crystal Zou and Kevin Lie join the lab. Welcome, Arthur, Crystal and Kevin!
[May, 2022] Cheng Ye wins ECE best undergraduate research award 2022! Read Cheng's story here. Congratulations, Cheng!
[May, 2022] Yatish presents an invited talk on "Pandemic-scale Phylogenetics" at the HiCOMB 2022 workshop
[Apr, 2022] Undergraduate researchers Carol Bao and Xuan Wang join the lab for Spring and Summer internships
[Apr, 2022] Yatish starts teaching ECE 111: Advanced Digital Design Project
[Mar 2022] Turakhia Lab has a fun outing in Catalina Island during the Spring break!
Recent Publications
Journals:
Y. Turakhia*,^, B. Thornlow*, A. S. Hinrichs, J. McBroome, N.Ayala, C. Ye, K. Smith, N. D. Maio, D. Haussler, R. Lanfear, R. Corbett-Detig^, "Pandemic-Scale Phylogenomics Reveals The SARS-CoV-2 Recombination Landscape", Nature, August2022. [paper, code]
J. McBroome, Y. Turakhia, R. Corbett-Detig, "BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees", Journal of Open Source Software (JOSS), Aug 2022. [paper, code]
C. Ye, B. Thornlow, A. Hinrichs, A. Kramer, C. Mirchandani, D. Torvi, R. Lanfear, Russell Corbett-Detig, Y. Turakhia^, "matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2", Bioinformatics, June 2022. [paper, code]
N. D. Maio, L. Weilguny, C. R. Walker, Y. Turakhia, R. Corbett-Detig, N. Goldman, "phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets", PLOS Computational Biology, April 2022 [paper, code]
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]
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]
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].
Conference:
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]
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]
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]