| Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic Y Turakhia, B Thornlow, AS Hinrichs, N De Maio, L Gozashti, R Lanfear, ... Nature genetics 53 (6), 809-816, 2021 | 273 | 2021 |
| Stability of SARS-CoV-2 phylogenies Y Turakhia, N De Maio, B Thornlow, L Gozashti, R Lanfear, CR Walker, ... PLoS genetics 16 (11), e1009175, 2020 | 96 | 2020 |
| Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape Y Turakhia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, K Smith, ... Nature 609 (7929), 994-997, 2022 | 72 | 2022 |
| A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees J McBroome, B Thornlow, AS Hinrichs, A Kramer, N De Maio, N Goldman, ... Molecular biology and evolution 38 (12), 5819-5824, 2021 | 69 | 2021 |
| Transfer RNA genes experience exceptionally elevated mutation rates BP Thornlow, J Hough, JM Roger, H Gong, TM Lowe, RB Corbett-Detig Proceedings of the National Academy of Sciences 115 (36), 8996-9001, 2018 | 49 | 2018 |
| Pandemic-scale phylogenomics reveals elevated recombination rates in the SARS-CoV-2 spike region Y Turkahia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, ... BioRxiv, 2021 | 41 | 2021 |
| Estimating the timing of multiple admixture pulses during local ancestry inference P Medina, B Thornlow, R Nielsen, R Corbett-Detig Genetics 210 (3), 1089-1107, 2018 | 39 | 2018 |
| Predicting transfer RNA gene activity from sequence and genome context BP Thornlow, J Armstrong, AD Holmes, JM Howard, RB Corbett-Detig, ... Genome research 30 (1), 85-94, 2020 | 25 | 2020 |
| Transposable elements drive intron gain in diverse eukaryotes L Gozashti, SW Roy, B Thornlow, A Kramer, M Ares Jr, R Corbett-Detig Proceedings of the National Academy of Sciences 119 (48), e2209766119, 2022 | 20 | 2022 |
| matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 C Ye, B Thornlow, A Hinrichs, A Kramer, C Mirchandani, D Torvi, ... Bioinformatics 38 (15), 3734-3740, 2022 | 16 | 2022 |
| Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures E Westhof, B Thornlow, PP Chan, TM Lowe Nucleic Acids Research 50 (7), 4100-4112, 2022 | 11 | 2022 |
| 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 … B Thornlow, A Kramer, C Ye, N De Maio, J McBroome, AS Hinrichs, ... BioRxiv, 2021 | 9 | 2021 |
| A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control B Thornlow, AS Hinrichs, M Jain, N Dhillon, S La, JD Kapp, I Anigbogu, ... biorxiv, 2021 | 7 | 2021 |
| Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region. bioRxiv. 2021 Y Turkahia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, ... Google Scholar, 0 | 6 | |
| Pandemic-scale phylogenetics C Ye, B Thornlow, A Kramer, J McBroome, A Hinrichs, R Corbett-Detig, ... bioRxiv, 2021 | 5 | 2021 |
| Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and … AM Kramer, B Thornlow, C Ye, N De Maio, J McBroome, AS Hinrichs, ... Systematic Biology 72 (5), 1039-1051, 2023 | 4 | 2023 |
| DecentTree: scalable Neighbour-Joining for the genomic era W Wang, J Barbetti, T Wong, B Thornlow, R Corbett-Detig, Y Turakhia, ... Bioinformatics 39 (9), btad536, 2023 | 2 | 2023 |
| matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 (preprint) C Ye, B Thornlow, AS Hinrichs, D Torvi, R Lanfear, R Corbett-Detig, ... | | 2022 |
| DecentTree: Scalable Neighbour-Joining for the Genomic Era (preprint) W Wang, J Barbetti, T Wong, B Thornlow, R Corbett-Detig, Y Turakhia, ... | | 2022 |
| Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region (preprint) Y Turakhia, B Thornlow, AS Hinrichs, J Mcbroome, N Ayala, C Ye, ... | | 2021 |
