Pandemic-scale Phylogenetics

CSE 290 seminar, UC San Diego (Nov 2021)


UShER: the one-stop-shop SARS-CoV-2 phylogenetics package

Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) (virtual) (Aug 2021)


Real-Time SARS-CoV-2 Phylogenetics with UShER

BME281C: Genomic Science Seminar Series, UCSC (virtual) (Apr 2021)


Accelerating Biology and Medicine with Hardware Specialization

EE seminar (virtual), IIT Bombay (Oct 2020)

Computer Engineering Club seminar (virtual), Technion - Israel Institute of Technology (Nov 2020)

S21 seminar (virtual), New York University (Feb 2021)

ECE 290 seminar, UC San Diego (May 2021)


Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

COVID-19 Dynamics & Evolution Meeting, UCSD (virtual) (Oct 2020)

BME280B: Seminar on Bioinformatics & Bioengineering, UCSC (virtual) (Nov 2020)


Domain-specific acceleration of genomics to enable biological discoveries

Cornell Tech/Cornell, NYC and Ithaca, NY (Feb 2020)

Columbia University, New York City, NY (Feb 2020)

MIT, Boston, MA (Feb 2020)

UC San Diego, San Diego, CA (Mar 2020)

UT Austin, Austin, TX (virtual) (Apr 2020)

Rice University, Houston, TX (virtual) (Apr 2020)


GPU-acceleration of long read de novo assembly for pan-genome analysis

NVIDIA Workshop, American Society of Human Genetics (ASHG) 2019, Houston, TX (Oct 2019)


Darwin: A Genomics Co-processor provides up to 15,000x acceleration on long read assembly

The 18th International System-on-Chip (SoC) Conference, UC Irvine, CA (Oct 2019)


Darwin: A Genomics Co-processor provides up to 15,000x acceleration on long read assembly

USENIX Annual Technical Conference (ATC), Renton, WA (Jul 2019)

The 23rd International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Williamsburg, VA (Mar 2018)

Computer Science Faculty Lunch, Stanford, CA (Feb 2018)


Hardware-enabled biology: From hardware-acceleration to novel biological discoveries

University of California at Santa Cruz (UCSC), Santa Cruz, CA (Mar 2019)


All Gene Survey In Mammalian Genomes Reveals Surprising Genes Losses

Stanford Developmental Biology Retreat, Monterey, CA (Sep 2018)


Accelerating Bioinformatics Computations

Stanford Platform Lab Annual Review, Stanford, CA (Feb 2018)


Darwin: A Genomics Co-processor

Pacific Biosciences (PacBio), Menlo Park, CA (Jul 2017)


Accelerating Genomics Computations 1000x with Hardware

Stanford Platform Lab Retreat, Aptos, CA (Jun 2017)


Darwin: A Genomics Co-processor

Microsoft Research (MSR), Redmond, WA (May 2017)

NVIDIA GPU Technology Conference (GTC), San Jose, CA (May 2017)

Qualcomm Research, San Diego, CA (Aug 2016)


A Hardware-acceleration Framework for Genomic Sequence Alignment

Stanford Developmental Biology Data Discussion (3D) club, Stanford, CA (Mar 2017)