Lab News
2025
DP-HLS: A High-Level Synthesis Framework for Accelerating Dynamic Programming Algorithms in Bioinformatics
accepted to
HPCA 2026.
Congratulations to Anshu Gupta, Yingqi Cao, and Jason Liang!
Kyle Smith and Pranav Gangwar et al. release a preprint on
Genetic Diversity Drives the Rate and Fitness Jumps of Detectable SARS-CoV-2 Recombination
. Congratulations, Kyle and Pranav!
Turakhia Lab welcomes new undergraduate researcher, Anya Wang!
Wen-Chieh Lo joins Turakhia Lab as a PhD student in ECE. Welcome, Wen-Chieh!
Pranav Gangwar passes his PhD qualifying exam. Congratulations, Pranav!
Sumit Walia passes his PhD qualifying exam. Congratulations, Sumit!
Yatish presents a talk at an IMSI workshop on
“GPU-Accelerated Construction of Ultra-Large Pangenomes via Alignment-Phylogeny Co-Estimation”
at University of Chicago.
Allen Yan and Alan Wang present at the UCSD Summer Research Conference.
Sumit Walia and Zexing Chen et al. release a preprint on
Ultrafast and Ultralarge Distance-Based Phylogenetics Using DIPPER
Yu-Hsiang Tseng passes his PhD preliminary exam. Congratulations, Yu-Hsiang!
Ultrafast and ultralarge multiple sequence alignments using TWILIGHT
is published in Bioinformatics. Congratulations, Yu-Hsiang and Sumit!
Yatish presents a talk at Barcelona Supercomputing Center on
“Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data”.
Yatish presents a talk at ETH Zurich on
“Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data”.
Yatish presents a talk at Biozentrum, University of Basel on “Compressive Pangenomics and Applications to Global Pathogen Surveillance”
Pranav Gangwar et al. release a preprint on
WEPP: Phylogenetic Placement Achieves Near-Haplotype Resolution in Wastewater-Based Epidemiology.
Yatish presents a talk at Fred Hutch Cancer Center on “Compressive Pangenomics and Applications to Global Pathogen Surveillance”
Jaden and Qiwen present their research project on Metagenomic Classification of Wastewater Data at UCSD Undergraduate Engineering Research Symposium.
ROADIES is highlighted as the cover feature in
PNAS.
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES
is published in Proceedings of the National Academy of Sciences. Congratulations, Anshu!
Yatish wrote a
Technical Perspective
for a Research Highlight in the
Communications of the ACM.
Turakhia Lab welcomes new members Anika Agarwal and Allen Yan to the lab.
Yatish presents a talk at BME Seminar, UC Santa Cruz on “Building Ultra-large Pangenomes”
Yatish receives the
Jacobs School Early Career Faculty Development Award
to harness Pangenomics for trait association studies in collaboration with
Prof. Melissa Gymrek.
Kyle Smith gets an Honorable Mention in the 2024-2025
CRA Outstanding Undergraduate Researcher Award.
Congratulations, Kyle!
Turakhia Lab welcomes new members Jaden Seangmany and Qiwen Xu to the lab.
2024
Yingqi Cao and Anshu Gupta et al. release a preprint on
DP-HLS: A High-Level Synthesis Framework for Accelerating Dynamic Programming Algorithms in Bioinformatics.
Yatish gives HPC Sync talk at
AMD
on “Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data”
Yatish selected as one of 100 ‘Young Scientists’ worldwide to attend and present at the
2024 WLA Forum in Shanghai, China,
an event that featured several Nobel Prize laureates and leading academics from around the world.
Turakhia Lab welcomes new members Jade Wang and Fahad Alkhazam to the lab.
Sunreet Khanna joins lab co-advised with
Prof. Bill Lin.
Welcome, Sunreet!
Sumit Walia begins summer internship at AMD.
Sumit Walia and Harsh Motwani et al. release a preprint on
Compressive Pangenomics Using Mutation-Annotated Networks.
Pranav Gangwar passes his PhD preliminary exam. Congratulations, Pranav!
Anshu Gupta passes her PhD preliminary exam. Congratulations, Anshu!
Yingqi Cao wins ECE best undergraduate research award 2024! Congratulations, Yingqi!
Anshu Gupta et al. release a preprint on
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.
Turakhia Lab organizes
BioSys Workshop on Emerging Computer Systems Challenges and Applications in Biomedicine
in Conjuction with
ASPLOS 2024
in San Diego.
Harsh Motwani completes his masters thesis on
Compressive Microbial Pangenomics.
Congratulations Harsh!
Sumit Walia passes his PhD preliminary exam. Congratulations, Sumit!
Turakhia Lab wins AMD HPC fund.
Turakhia Lab welcomes new members Zexing Chen, Manu Bhat, Haochen Jiang and Arnav Saxena to the lab.
Yatish presents at SAS innovate conference.
Yatish presents an invited talk on “Building Ultra-Large Pangenomes” at the
UCSD Genetics, Bioinformatics, & Systems Biology Colloquium.
2023
Yatish invited to interview at TR35 Festival.
Yatish starts teaching ECE 108 Digital Circuits.
Tracking and curating putative SARS-CoV-2 recombinants with RIVET
is published in Bioinformatics. Congratulations, Kyle Smith and Cheng Ye for contributing to this study!
Yatish named
MIT Technology Review Innovator Under 35
in computing for vital contributions to SARS-CoV-2 phylogenetics during the COVID-19 pandemic. Read press coverage by
UC San Diego Today.
Yu-Hsiang Tseng wins the J. Yang Scholarship! Congratulations Yu-Hsiang!
Yu-Hsiang Tseng (PhD, ECE) joins the lab. Welcome Yu-Hsiang!
Anshu and Pranav wraps their summer internship at Analog Devices and Intel, respectively.
Max wraps up his summer research internship with the lab. Congratulations Max!
TALCO: Tiling Genome Sequence Alignment Using Convergence of Traceback Pointers
accepted to
HPCA 2024.
Congratulations to Sumit, Cheng, Arkid, and Dhruvi!
Max Doblas, from the Barcelona Supercomputing Center (BSC) joins the lab as a visiting summer research intern. Welcome Max!
Carolyn Zhang and Girish Krishnan present their summer research project on wastewater-based epidemiology at the ECE Summer Research Internship Program (SRIP) conference.
Turakhia Lab has fun day trip whale watching off the coast of San Diego!
Kyle Smith attends the
Undergraduate Architecture Mentoring Workshop (uArch)
in Orlando Florida, in conjunction with
ISCA 2023.
Yatish organised the
5th workshop on Accelerator Architecure in computational Biology and Bioinformatics (AACBB)’23
, held in conjunction with
ISCA 2023.
Yatish won the Hellman Fellowship, Congratulations, Yatish!
Carolyn Zhang and Girish Krishnan join the lab. Welcome Carolyn and Girish!
Pranav Gangwar (PhD, ECE) and Jason Liang (UG, ECE) join the lab. Welcome, Pranav and Jason!
2022
FA’22 End of Quarter Lab Dinner
Anshu Gupta (PhD, CSE) joins the lab. Welcome, Anshu!
Yatish gives a keynote talk at the NGS 2022 conference organized by the American Society for Microbiology.
Turakhia Lab welcomes new members Arkid Bera, Yingqi Cao, Debabrata Chaudhury, Dhruvi Lodhavia and Harsh Motwani to the lab.
Yatish gives a talk at the Massachusetts General Hospital and a chalk talk at the
UCSD Undergraduate Bioinformatics Club (UBIC).
RIPPLES manuscript,
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
, published in Nature. Congratulations, Cheng Ye and Kyle Smith, for contributing to this study!
Read the press release.
Yatish presents at
phyloseminar.
Undergraduate researchers Arthur Lu, Crystal Zou and Kevin Lie join the lab. Welcome, Arthur, Crystal and Kevin!
High school interns Vidhi Kulkarnia and Ronnie Volman join the lab for Summer 2022. Welcome, Vidhi and Ronnie!
Cheng Ye wins ECE best undergraduate research award 2022! Congratulations, Cheng!
Read about Cheng’s story.
Yatish starts teaching ECE 111 Advanced Digital Design Project.
Undergraduate researchers Carol Bao and Xuan Wang join the lab for Spring and Summer internships.
Turakhia Lab has a fun outing in Catalina Island during the Spring break!
Alireza Mohammadidoost (PhD, ECE) joins the lab. Welcome, Alireza!
Yatish starts teaching the graduate course ECE 284 Parallel Computing in Bioinformatics.
Cheng Ye et al. release a preprint on
matOptimize: a parallel tree optimization tool capable of handling million-scale SARS-CoV-2 phylogenies.
2021
Cheng Ye et al. release a preprint on
Pandemic-scale Phylogenetics
, which is covered by
The Medical News.
Angie Hinrichs (UCSC) highlights UShER and matOptimize at the
StaPH-B meeting.
Yatish gives a talk on “Pandemic-scale Phylogenetics” in the CSE 290 class at UCSD.
Devika and Shoh wrap up their summer research internships. Congratulations!
RIPPLES and UShER are featured in an article in
The Scientist.
Sumit Walia (PhD, ECE) and Kyle Smith (UG, Bioinformatics) join the lab. Welcome, Sumit and Kyle!
Manuscript on matUtils and the UCSC SARS-CoV-2 tree database published in
Molecular Biology and Evolution (MBE).
The Medical News
features our work on SARS-CoV-2 recombination.
A preprint on RIPPLES, with contributions from Yatish (co-first author) and Cheng, is posted on bioRxiv.
Yatish provides a tutorial on UShER at the Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME 2021).
Yatish officially starts at UCSD as an Assistant Professor.
Manuscript on UShER published in
Nature Genetics.
UShER is featured by
GenomeWeb,
UCSC NewsCenter,
MedicalXPress
, and several other media outlets.
Yatish contributes to a manuscript published in
Genome Biology and Evoution (GBE).
UCSC makes an announcement about the UShER-based SARS-CoV-2 tree that just surpassed 1M genomes.
Read the press release.
Yatish gives a seminar talk on UShER for the BME 281C class at UCSC.
Zihao Kong joins the lab for research.
Devika Torvi and Shoh Mollenkamp join the lab for Spring and Summer internships.
Cheng Ye (UG, ECE) joined the lab. Welcome Cheng!