2024

DP-HLS: A High-Level Synthesis Framework for Accelerating Dynamic Programming Algorithms in Bioinformatics

Yingqi Cao*, Anshu Gupta*, Jason Liang, and Yatish Turakhia

arXiv

DOI | Github | Slides | Video

Compressive Pangenomics Using Mutation-Annotated Networks

Sumit Walia, Harsh Motwani, Kyle Smith, Russell Corbett-Detig, and Yatish Turakhia

bioRxiv

DOI | Github | Slides

TALCO: Tiling Genome Sequence Alignment using Convergence of Traceback Pointers

Sumit Walia, Cheng Ye, Arkid Bera, Dhruvi Lodhavia and Yatish Turakhia

IEEE International Symposium on High Performance Computer Architecture (HPCA)

A framework for automated scalable designation of viral pathogen lineages from genomic data

Jakob McBroome, Adriano de Bernardi Schneider, Cornelius Roemer, Michael T. Wolfinger, Angie S. Hinrichs, Aine Niamh O’Toole, Christopher Ruis, Yatish Turakhia, Andrew Rambaut, and Russell Corbett-Detig

Nature Microbiology

DOI | Paper | Github

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Anshu Gupta, Siavash Mirarab, and Yatish Turakhia

bioRxiv

DOI | Github | Slides | Video

The ongoing evolution of UShER during the SARS-CoV-2 pandemic

Angie Hinrichs, Cheng Ye, Yatish Turakhia, and Russell Corbett-Detig

Nature Genetics

DOI | Paper

2023

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method

Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine O’Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola De Maio, Scott Hughes, and Russ Corbett-Detig

Virus Evolution

DOI | Paper | Github

Tracking and curating putative SARS-CoV-2 recombinants with RIVET

Kyle Smith, Cheng Ye, Yatish Turakhia

Bioinformatics

Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages

Heidi I Chen, Yatish Turakhia, Gill Bejerano, and David M Kingsley

Molecular Biology and Evolution

DOI | Paper | Github | Featured on cover page

DecentTree: scalable Neighbour-Joining for the genomic era

Wang, Weiwen, James Barbetti, Thomas Wong, Bryan Thornlow, Russ Corbett-Detig, Yatish Turakhia, Robert Lanfear, and Bui Quang Minh

Bioinformatics

DOI | Paper | Github

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations

Kramer, Alexander M., Bryan Thornlow, Cheng Ye, Nicola De Maio, Jakob McBroome, Angie S. Hinrichs, Robert Lanfear, Yatish Turakhia, and Russell Corbett-Detig

Systematic Biology

DOI | Paper | Github

Maximum likelihood pandemic-scale phylogenetics

De Maio, Nicola, Kalaghatgi, Prabhav, Turakhia, Yatish, Corbett-Detig, Russell, Minh, Bui Quang, and Goldman, Nick

Nature Genetics

DOI | Paper | Github

A lung-specific mutational signature enables inference of viral and bacterial respiratory niche

Christopher Ruis, Thomas P. Peacock, Luis M. Polo, Diego Masone, Maria Soledad Alvarez, Angie S. Hinrichs, Yatish Turakhia, Ye Cheng, Jakob McBroome, Russell Corbett-Detig, Julian Parkhill and R. Andres Floto

Microbial Genomics

DOI | Paper | Github

2022

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

Yatish Turakhia, Bryan Thornlow, Angie Hinrichs, Jakob McBroome, Nicolas Ayala, Cheng Ye, Kyle Smith, Nicola De Maio, David Haussler, Robert Lanfear, and Russell Corbett-Detig

Nature

BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees

Jakob McBroome, Yatish Turakhia, and Russell Corbett-Detig

Journal of Open Source Software

DOI | Paper | Github

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Cheng Ye, Bryan Thornlow, Angie Hinrichs, Alexander Kramer, Cade Mirchandani, Devika Torvi, Robert Lanfear, Russell Corbett-Detig, and Yatish Turakhia

Bioinformatics

phastSim: efficient simulation of sequence evolution for pandemic-scale datasets

Nicola De Maio, William Boulton, Lukas Weilguny, Conor R. Walker, Yatish Turakhia, Russell Corbett-Detig, and Nick Goldman

PLOS Computational Biology

DOI | Paper | Github

Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference

James K Schull, Yatish Turakhia, James A Hemker, William J Dally, and Gill Bejerano

Genome Biology and Evolution

DOI | Paper | Github

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

Jakob McBroome, Jennifer Martin, Adriano de Bernardi Schneider, Yatish Turakhia, and Russell Corbett-Detig

Virus Evolution

DOI | Paper | Github | MedicalXPress, EurekAlert, Scienmag, News Medical, The Academic Times

2021

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

Nicola De Maio, Conor R Walker, Yatish Turakhia, Robert Lanfear, Russell Corbett-Detig, and Nick Goldman

Genome Biology and Evolution

DOI | PAPER | Github

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Yatish Turakhia, Bryan Thornlow, Angie S. Hinrichs, Nicola De Maio, Landen Gozashti, Robert Lanfear, David Haussler, and Russell Corbett-Detig

Nature Genetics

ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees

Alexander Kramer, Yatish Turakhia, and Russell Corbett-Detig

Journal of Open Source Software

DOI | Paper | Github

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Jakob McBroome, Bryan Thornlow, Angie S Hinrichs, Alexander Kramer, Nicola De Maio, Nick Goldman, David Haussler, Russell Corbett-Detig, and Yatish Turakhia

Molecular Biology and Evolution

DOI | Paper | Github | Slides | Video

Pandemic-scale phylogenetics

Cheng Ye, Bryan Thornlow, Alexander Kramer, Jakob McBroome, Angie Hinrichs, Russell Corbett-Detig, Yatish Turakhia

bioRxiv

DOI | Paper

2020 and earlier

Domain-specific hardware accelerators

William J. Dally, Yatish Turakhia, and Song Han

Communications of the ACM

DOI | Paper | Video | Featured on cover page

A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals

Yatish Turakhia, Heidi I Chen, Amir Marcovitz, and Gill Bejerano

Nucleic acids research

DOI | Paper | Github | Video

SegAlign: A scalable GPU-based whole genome aligner

Sneha D. Goenka, Yatish Turakhia, Benedict Paten, Mark Horowitz

International Conference for High Performance Computing, Networking, Storage and Analysis

DOI | Paper | Github | Slides | Video

Stability of SARS-CoV-2 phylogenies

Yatish Turakhia, Nicola De Maio, Bryan Thornlow, Landen Gozashti, Robert Lanfear, Conor R. Walker, Angie S. Hinrichs, Jason D. Fernandes, Rui Borges, Greg Slodkowicz, Lukas Weilguny, David Haussler, Nick Goldman, and Russell Corbett-Detig

PLoS Genetics

DOI | Paper | Github