Lab News

2025

Yatish wins 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

Yatish gives a talk on “Scaling Up Phylogenetics” at The Institute for Computational and Experimental Research in Mathematics (ICERM) at Brown University.

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!

Anshu Gupta presents ROADIES at ISMB 2024 in Montreal, Québec Canada.

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.

Sumit Walia presents TALCO at HPCA 2024 and receives Best Paper Nominee.

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 in HPCA’24. 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.

Kyle Smith attends  ISMB 2023 in Lyon, France to present work on RIVET.

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!

Yatish won the Amazon Research Award. Congratulations, Yatish!

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 joins the SEARCH team which is tracking the spread of SARS-CoV-2 in San Diego.

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!

Alireza presents his work at AACBB 2022 in conjunction with ISCA 2022.

High school interns Vidhi Kulkarnia and Ronnie Volman join the lab for Summer 2022. Welcome, Vidhi and Ronnie!

matOptimize is published in Bioinformatics! Congratulations, Cheng et al.! Read the press coverage.

Yatish presents an invited talk on “Pandemic-scale Phylogenetics” at the HiCOMB 2022 workshop.

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.

Yatish is quoted by The Guardian on the Omicron variant.

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.

Yatish interviews with The Wired on the Delta variant.

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!