| 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 | 313 | 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 | 104 | 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 | 90 | 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 | 76 | 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 | 51 | 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 | 42 | 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 | 32 | 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 | 28 | 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 | 22 | 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 | 17 | 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 | 10 | 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 |
| 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 | 6 | 2023 |
| 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 | 5 | 2023 |
| Pandemic-scale phylogenetics C Ye, B Thornlow, A Kramer, J McBroome, A Hinrichs, R Corbett-Detig, ... bioRxiv, 2021 | 5 | 2021 |
| matutils: Tools to interpret and manipulate mutation annotated trees J McBroome, B Thornlow, AS Hinrichs, N De Maio, N Goldman, ... life sciences 15, 475-476, 2021 | 5 | 2021 |
| Ultrafast sample placement on existing trees (UShER) empowers real-time phylogenetics for the SARS-CoV-2 pandemic. bioRxiv preprint Server Biol Y Turakhia, B Thornlow, AS Hinrichs, N De Maio, L Gozashti, R Lanfear, ... | 2 | 2020 |
| LINE1 Reverse Transcriptase Inhibitors Abrogate Type 1 Interferon Responses D Rios, N Hafeez, B Desrosiers, S Rao, J Floro, J Baddour, N Perez, ... ARTHRITIS & RHEUMATOLOGY 74, 3376-3377, 2022 | 1 | 2022 |
| DecentTree: Scalable Neighbour-Joining for the Genomic Era (preprint) W Wang, J Barbetti, T Wong, B Thornlow, R Corbett-Detig, Y Turakhia, ... | | 2022 |
