Publications

2024

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Compressive Pangenomics Using Mutation-Annotated Networks

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

bioRxiv

DOI | Github | Slides

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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

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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

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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

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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

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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

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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

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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

DOI | Paper | Github | Slides | Video | N Phys.org, EurekAlert, Scienmag, News Medical, Verve Times

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

DOI | Paper | Github | Slides | Video | N MedicalXPress, UK Today News, UCSD Newscenter

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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

2021

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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

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

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Pandemic-scale phylogenetics

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

bioRxiv

DOI | Paper

2020 and earlier

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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