Publications

2023

  • Hinrichs, Angie, Cheng Ye, Yatish Turakhia, and Russell Corbett-Detig. “The ongoing evolution of UShER during the SARS-CoV-2 pandemic.”, Nature Genetics (2023).

  • Wang, Weiwen, James Barbetti, Thomas Wong, Bryan Thornlow, Russ Corbett-Detig, Yatish Turakhia, Robert Lanfear, and Bui Quang Minh. “DecentTree: scalable Neighbour-Joining for the genomic era.”, Bioinformatics (2023)

  • Kramer, Alexander M., Bryan Thornlow, Cheng Ye, Nicola De Maio, Jakob McBroome, Angie S. Hinrichs, Robert Lanfear, Yatish Turakhia, and Russell Corbett-Detig. “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.Systematic Biology (2023)

  • Wang, Weiwen, Barbetti, James, Wong, Thomas, Thornlow, Bryan, Corbett-Detig, Russ, Turakhia, Yatish, Lanfear, Robert, and Minh, Bui Quang, “DecentTree: scalable Neighbour-Joining for the genomic era”, Bioinformatics 2023

  • De Maio, Nicola, Kalaghatgi, Prabhav, Turakhia, Yatish, Corbett-Detig, Russell, Minh, Bui Quang, and Goldman, Nick, “Maximum likelihood pandemic-scale phylogenetics”, Nature Genetics 2023

  • Chen, Heidi I, Turakhia, Yatish, Bejerano, Gill, and Kingsley, David M, “Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages”, bioRxiv 2023

  • Bernardi Schneider, Adriano, Su, Michelle, Hinrichs, Angie S, Wang, Jade, Amin, Helly, Bell, John, Wadford, Debra A, O’Toole, Áine, Scher, Emily, Perry, Marc D, Turakhia, Yatish, and others, “SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method”, bioRxiv 2023

  • Ruis, Christopher, Peacock, Thomas P, Polo, Luis M, Masone, Diego, Alvarez, Maria Soledad, Hinrichs, Angie S, Turakhia, Yatish, Cheng, Ye, McBroome, Jakob, Corbett-Detig, Russell, and others, “A lung-specific mutational signature enables inference of viral and bacterial respiratory niche”,Microbial Genomics 2023

  • Smith, Kyle, Ye, Cheng, and Turakhia, Yatish, “Tracking and curating putative SARS-CoV-2 recombinants with RIVET”, Bioinformatics 2023

  • McBroome, Jakob, Bernardi Schneider, Adriano, Roemer, Cornelius, Wolfinger, Michael T, Hinrichs, Angie S, O’Toole, Aine N, Ruis, Chris, Turakhia, Yatish, Rambaut, Andrew, and Corbett-Detig, Russell, “Automated Agnostic Designation of Pathogen Lineages”, bioRxiv 2023

2022

  • Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie, McBroome, Jakob, Ayala, Nicolas, Ye, Cheng, Smith, Kyle, De Maio, Nicola, Haussler, David, Lanfear, Robert, and others, “Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape”, Nature 2022

  • Ruis, Christopher, Peacock, Thomas P, Polo, Luis Mariano, Masone, Diego, Alvarez, Maria Soledad, Hinrichs, Angie S, Turakhia, Yatish, Cheng, Ye, McBroome, Jakob, Corbett-Detig, Russell, and others, “Mutational spectra distinguish SARS-CoV-2 replication nichesBioRxiv 2022

  • McBroome, Jakob, Turakhia, Yatish, and Corbett-Detig, Russell, “BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees”, Journal of Open Source Software 2022

  • Ye, Cheng, Thornlow, Bryan, Hinrichs, Angie, Kramer, Alexander, Mirchandani, Cade, Torvi, Devika, Lanfear, Robert, Corbett-Detig, Russell, and Turakhia, Yatish, “matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2Bioinformatics 2022

  • De Maio, Nicola, Boulton, William, Weilguny, Lukas, Walker, Conor R, Turakhia, Yatish, Corbett-Detig, Russell, and Goldman, Nick, “phastSim: efficient simulation of sequence evolution for pandemic-scale datasetsPLoS computational biology 2022

  • Schull, James K, Turakhia, Yatish, Hemker, James A, Dally, William J, and Bejerano, Gill, “Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free InferenceGenome Biology and Evolution 2022

  • McBroome, Jakob, Martin, Jennifer, Bernardi Schneider, Adriano, Turakhia, Yatish, and Corbett-Detig, Russell, “Identifying SARS-CoV-2 regional introductions and transmission clusters in real time”, Virus Evolution 2022

2021

  • De Maio, Nicola, Walker, Conor R, Turakhia, Yatish, Lanfear, Robert, Corbett-Detig, Russell, and Goldman, Nick, “Mutation rates and selection on synonymous mutations in SARS-CoV-2”, Genome Biology and Evolution 2021

  • Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie S, De Maio, Nicola, Gozashti, Landen, Lanfear, Robert, Haussler, David, and Corbett-Detig, Russell, “Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic”, Nature Genetics 2021

  • Kramer, Alexander, Turakhia, Yatish, and Corbett-Detig, Russell, “ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees”, Journal of Open Source Software 2021

  • McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, Kramer, Alexander, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, and Turakhia, Yatish, “A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees”, Molecular biology and evolution 2021

  • Ye, Cheng, Thornlow, Bryan, Kramer, Alexander, McBroome, Jakob, Hinrichs, Angie, Corbett-Detig, Russell, and Turakhia, Yatish, “Pandemic-scale phylogenetics”, bioRxiv 2021

2020

  • Dally, William J, Turakhia, Yatish, and Han, Song, “Domain-specific hardware accelerators”, Communications of the ACM 2020

  • Turakhia, Yatish, Chen, Heidi I, Marcovitz, Amir, and Bejerano, Gill, “A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammalsNucleic acids research 2020

  • Goenka, Sneha D, Turakhia, Yatish, Paten, Benedict, and Horowitz, Mark, “SegAlign: A scalable GPU-based whole genome alignerInSC20: International Conference for High Performance Computing, Networking, Storage and Analysis 2020

  • Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R, Hinrichs, Angie S, Fernandes, Jason D, Borges, Rui, Slodkowicz, Greg, and others, “Stability of SARS-CoV-2 phylogeniesPLoS genetics 2020

2019

  • Schull, James Kusik, Turakhia, Yatish, Dally, William J, and Bejerano, Gill, “Champagne: whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia”, bioRxiv 2019

  • Turakhia, Yatish, Goenka, Sneha D, Bejerano, Gill, and Dally, William J, “Darwin-WGA: A co-processor provides increased sensitivity in whole genome alignments with high speedupIn 2019 IEEE International Symposium on High Performance Computer Architecture (HPCA) 2019

  • Marcovitz, Amir, Turakhia, Yatish, Chen, Heidi I, Gloudemans, Michael, Braun, Benjamin A, Wang, Haoqing, and Bejerano, Gill, “A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whalesProceedings of the National Academy of Sciences 2019

  • Snytsar, Roman, and Turakhia, Yatish, “</i>Parallel approach to sliding window sums</i>”, In International Conference on Algorithms and Architectures for Parallel Processing 2019

2018

  • Turakhia, Yatish, Bejerano, Gill, and Dally, William J, “Darwin: A genomics co-processor provides up to 15,000 x acceleration on long read assemblyACM SIGPLAN Notices 2018