|ANGES: reconstructing ANcestral GEnomeS maps|
BR Jones, A Rajaraman, E Tannier, C Chauve
Bioinformatics 28 (18), 2388-2390, 2012
|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
|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
|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), 2019
|node.dating: dating ancestors in phylogenetic trees in R|
BR Jones, AFY Poon
Bioinformatics 33 (6), 932-934, 2017
|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
|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
|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
|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
|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
|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), 2020
|Tree hook length formulae, Feynman rules and B-series|
BR Jones, K Yeats
arXiv preprint arXiv:1412.6053, 2014
|Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir|
BR Jones, JB Joy
Virus Evolution, 2020
|The latent reservoir as a genetically diverse archive recapitulating within-host HIV evolutionary history|
B Jones, N Kinloch, J Horacsek, B Ganase, M Harris, R Harrigan, ...
Journal of Virus Eradication 3, 27, 2017
|22 The HIV reservoir as a genetically heterogeneous archive of within-host viral evolution: implications for immunotherapeutic cure strategies|
BR Jones, NN Kinloch, J Horacsek, P Mwimanzi, B Baraki, K Cobarrubias, ...
Journal of Virus Eradication 3, 14, 2017
|GENERATING TREES: COMPUTING AND GENERATING FUNCTIONS|
MATH 821-Final Projects December 2010, 91, 2010