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

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Estimating the Timing of Multiple Admixture Pulses During Local Ancestry Inference von Medina, Paloma, Thornlow, Bryan, Nielsen, Rasmus, Corbett-Detig, Russell

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Stability of SARS-CoV-2 phylogenies von Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R., Hinrichs, Angie S., Fernandes, Jason D., Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell

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Predicting transfer RNA gene activity from sequence and genome context von Thornlow, Bryan P., Armstrong, Joel, Holmes, Andrew D., Howard, Jonathan M., Corbett-Detig, Russell B., Lowe, Todd M.

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Transfer RNA genes experience exceptionally elevated mutation rates von Thornlow, Bryan P., Hough, Josh, Roger, Jacquelyn M., Gong, Henry, Lowe, Todd M., Corbett-Detig, Russell B.

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Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape von Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie, McBroome, Jakob, Ayala, Nicolas, Ye, Cheng, Smith, Kyle, De Maio, Nicola, Haussler, David, Lanfear, Robert, Corbett-Detig, Russell

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A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees von McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, Kramer, Alexander, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish

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Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures von Westhof, Eric, Thornlow, Bryan, Chan, Patricia P, Lowe, Todd M

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Transposable elements drive intron gain in diverse eukaryotes von Gozashti, Landen, Roy, Scott W, Thornlow, Bryan, Kramer, Alexander, Ares, Jr, Manuel, Corbett-Detig, Russell

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

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

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

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Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approach... von Thornlow, Bryan

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Stability of SARS-CoV-2 phylogenies von Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R, Hinrichs, Angie S, Fernandes, Jason D, Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell

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Online phylogenetics with matOptimize for SARS-CoV-2 von Thornlow, Bryan, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie, Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell, Kramer, Alexander

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Mt_africanum_GCF_000195955.2.final.vcf.genozip von Ye, Cheng, Thornlow, Bryan, Hinrichs, Angie S., Kramer, Alexander, Mirchandani, Cade, Tori, Devika, Lanfear, Robert, Corbett-Detig, Russell, Turakhia, Yatish

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Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination von Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie S., McBroome, Jakob, Ayala, Nicolas, Ye, Cheng, Smith, Kyle, De Maio, Nicola, Haussler, David, Lanfear, Robert, Corbett-Detig, Russell

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