| Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, ... Molecular biology and evolution 37 (2), 599-603, 2020 | 368 | 2020 |
| ANGES: reconstructing ANcestral GEnomeS maps BR Jones, A Rajaraman, E Tannier, C Chauve Bioinformatics 28 (18), 2388-2390, 2012 | 81 | 2012 |
| Phylogenetic approach to recover integration dates of latent HIV sequences within-host BR Jones, NN Kinloch, J Horacsek, B Ganase, M Harris, PR Harrigan, ... Proceedings of the National Academy of Sciences 115 (38), E8958-E8967, 2018 | 52 | 2018 |
| HIV-1 variants are archived throughout infection and persist in the reservoir K Brooks, BR Jones, DA Dilernia, DJ Wilkins, DT Claiborne, S McInally, ... PLoS pathogens 16 (6), e1008378, 2020 | 41 | 2020 |
| HIV diversity and genetic compartmentalization in blood and testes during suppressive antiretroviral therapy RL Miller, R Ponte, BR Jones, NN Kinloch, FH Omondi, MA Jenabian, ... Journal of virology 93 (17), 10.1128/jvi. 00755-19, 2019 | 40 | 2019 |
| Aquaculture mediates global transmission of a viral pathogen to wild salmon GJ Mordecai, KM Miller, AL Bass, AW Bateman, AK Teffer, JM Caleta, ... Science Advances 7 (22), eabe2592, 2021 | 35 | 2021 |
| Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4+ T Cell Subsets during Long-Term Combination Antiretroviral Therapy BR Jones, RL Miller, NN Kinloch, O Tsai, H Rigsby, H Sudderuddin, ... Journal of virology 94 (5), 10.1128/jvi. 01786-19, 2020 | 23 | 2020 |
| Tree shape‐based approaches for the comparative study of cophylogeny M Avino, GT Ng, Y He, MS Renaud, BR Jones, AFY Poon Ecology and evolution 9 (12), 6756-6771, 2019 | 18 | 2019 |
| Genetic complexity in the replication-competent latent HIV reservoir increases with untreated infection duration in infected youth ZL Brumme, H Sudderuddin, C Ziemniak, K Luzuriaga, BR Jones, JB Joy, ... Aids 33 (2), 211-218, 2019 | 17 | 2019 |
| node.dating: dating ancestors in phylogenetic trees in R BR Jones, AFY Poon Bioinformatics 33 (6), 932-934, 2017 | 17 | 2017 |
| Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study H Sudderuddin, NN Kinloch, SW Jin, RL Miller, BR Jones, CJ Brumme, ... Retrovirology 17 (1), 3, 2020 | 13 | 2020 |
| HIV proviral burden, genetic diversity, and dynamics in viremic controllers who subsequently initiated suppressive antiretroviral therapy FH Omondi, H Sudderuddin, A Shahid, NN Kinloch, BR Jones, RL Miller, ... MBio 12 (6), e02490-21, 2021 | 11 | 2021 |
| The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus BR Jones, AYM Howe, PR Harrigan, JB Joy Virus Evolution 4 (1), vex041, 2018 | 10 | 2018 |
| The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically … A Shahid, S MacLennan, BR Jones, H Sudderuddin, Z Dang, ... Journal of virology, e01655-23, 2024 | 6 | 2024 |
| HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy A Shahid, BR Jones, JSW Yang, W Dong, T Shaipanich, K Donohoe, ... PLoS Pathogens 18 (11), e1010613, 2022 | 6 | 2022 |
| Proviral turnover during untreated HIV infection is dynamic and variable between hosts, impacting reservoir composition on ART K Brooks, FH Omondi, RH Liang, H Sudderuddin, BR Jones, JB Joy, ... Frontiers in microbiology 12, 719153, 2021 | 6 | 2021 |
| Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir BR Jones, JB Joy Virus evolution 6 (2), veaa089, 2020 | 5 | 2020 |
| Tree hook length formulae, Feynman rules and B-series BR Jones, K Yeats Annales de l’Institut Henri Poincaré D 2 (4), 413-430, 2015 | 3 | 2015 |
| HIV reservoirs are dominated by genetically younger and clonally enriched proviruses NN Kinloch, A Shahid, W Dong, D Kirkby, BR Jones, CJ Beelen, ... Mbio 14 (6), e02417-23, 2023 | 2 | 2023 |
| Inferring human immunodeficiency virus 1 proviral integration dates with Bayesian inference BR Jones, JB Joy Molecular Biology and Evolution 40 (8), msad156, 2023 | 2 | 2023 |
Jeffrey B JoyCentre for Excellence in HIV/AIDS, Department of Medicine, University of British ColumbiaVerified email at cfenet.ubc.ca
