The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

1986, The Vancouver Lymphadenopathy-AIDS Study: 6. HIV seroconversion in a cohort of homosexual men, CMAJ, 135, 1355

1997, Modelling the impact of HIV disease on mortality in gay and bisexual men, Int J Epidemiol, 26, 657, 10.1093/ije/26.3.657

2003, Intensive injection cocaine use as the primary risk factor in the Vancouver HIV-1 epidemic, AIDS, 17, 887, 10.1097/00002030-200304110-00014

2012, Needle exchange and the HIV epidemic in Vancouver: lessons learned from 15 years of research, Int J Drug Policy, 23, 261, 10.1016/j.drugpo.2012.03.006

2009, HIV/AIDS in Vancouver, British Columbia: a growing epidemic, Harm Reduct J, 6, 5, 10.1186/1477-7517-6-5

1995, Revealing the history of infectious disease epidemics through phylogenetic trees, Philos Trans R Soc Lond B Biol Sci, 349, 33, 10.1098/rstb.1995.0088

1996, Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis, Proc Natl Acad Sci U S A, 93, 10864, 10.1073/pnas.93.20.10864

2013, Viral phylodynamics, PLoS Comput Biol, 9, e1002947, 10.1371/journal.pcbi.1002947

2005, Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups, Proc Natl Acad Sci U S A, 102, 4425, 10.1073/pnas.0407534102

2008, Episodic sexual transmission of HIV revealed by molecular phylodynamics, PLoS Med, 5, e50, 10.1371/journal.pmed.0050050

2011, Transmission clustering drives the onward spread of the HIV epidemic among men who have sex with men in Quebec, J Infect Dis, 204, 1115, 10.1093/infdis/jir468

1999, Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial, Lancet, 353, 2195, 10.1016/S0140-6736(98)12291-2

2002, Clinical utility of HIV-1 genotyping and expert advice: the Havana trial, AIDS, 16, 209, 10.1097/00002030-200201250-00010

2004, Prospects for inferring very large phylogenies by using the neighbor-joining method, Proc Natl Acad Sci U S A, 101, 11030, 10.1073/pnas.0404206101

2011, Transmission network parameters estimated from HIV sequences for a nationwide epidemic, J Infect Dis, 204, 1463, 10.1093/infdis/jir550

2012, Inferring epidemic contact structure from phylogenetic trees, PLoS Comput Biol, 8, e1002413, 10.1371/journal.pcbi.1002413

2013, Modelling tree shape and structure in viral phylodynamics, Philos Trans R Soc Lond B Biol Sci, 368

BC Centre for Disease Control, 2012, HIV in British Columbia: annual surveillance report 2011

2007, Prediction of HIV-1 drug susceptibility phenotype from the viral genotype using linear regression modeling, J Virol Methods, 145, 47, 10.1016/j.jviromet.2007.05.009

2009, An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1, PLoS Comput Biol, 5, e1000581, 10.1371/journal.pcbi.1000581

2007, HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance, AIDS, 21, 215, 10.1097/QAD.0b013e328011e691

2010, FastTree 2–approximately maximum-likelihood trees for large alignments, PLoS One, 5, e9490, 10.1371/journal.pone.0009490

1987, Multiple imputation for nonresponse in surveys. Wiley series in probability and statistics

2008, qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis, Bioinformatics, 24, 1549, 10.1093/bioinformatics/btn227

2006, Evidence of differential selection of HIV-1 variants carrying drug-resistant mutations in seroconverters, Antivir Ther, 11, 329, 10.1177/135965350601100304

2012, Global epidemiology of HIV infection in men who have sex with men, Lancet, 380, 367, 10.1016/S0140-6736(12)60821-6

2004, HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy, AIDS, 18, 719, 10.1097/00002030-200403260-00002

2013, The global transmission network of HIV-1, J Infect Dis, 209, 304

1996, Among-site rate variation and its impact on phylogenetic analyses, Trends Ecol Evol, 11, 367, 10.1016/0169-5347(96)10041-0

2012, “Criminalization creep”: a brief discussion of the criminalization of HIV/AIDS nondisclosure in Canada, Can J Law Soc, 27, 55, 10.3138/cjls.27.1.055

2013, Nondisclosure prosecutions and population health outcomes: examining HIV testing, HIV diagnoses, and the attitudes of men who have sex with men following nondisclosure prosecution media releases in Ottawa, Canada, BMC Public Health, 13, 94, 10.1186/1471-2458-13-94

2007, HIV forensics: pitfalls and acceptable standards in the use of phylogenetic analysis as evidence in criminal investigations of HIV transmission, HIV Med, 8, 382, 10.1111/j.1468-1293.2007.00486.x

2006, Service uptake and characteristics of injection drug users utilizing North America's first medically supervised safer injecting facility, Am J Public Health, 96, 770, 10.2105/AJPH.2004.057828