|
| 37229349 | Model design for nonparametric phylodynamic inference and applications to pathogen surveillance. | | 2023 |
| 37283544 | Use of Next-Generation Sequencing in a State-Wide Strategy of HIV-1 Surveillance: Impact of the SARS-COV-2 Pandemic on HIV-1 Diagnosis and Transmission. | J Infect Dis | 2023 |
| 35317349 | Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa. | Virus Evol | 2022 |
| 36216891 | Pneumococcal within-host diversity during colonization, transmission and treatment. | Nat Microbiol | 2022 |
| 35915480 | Differences in epidemiology of enteropathogens in children pre- and post-rotavirus vaccine introduction in Kilifi, coastal Kenya. | Gut Pathogens | 2022 |
| 34528099 | Molecular epidemiology of dengue in a setting of low reported endemicity: Kupang, East Nusa Tenggara province, Indonesia. | Transactions of the Royal Society of Tropical Medicine and Hygiene | 2021 |
| 34195581 | HIV-1 Transmission linkages among persons with incident infection to inform public health surveillance. | eClinicalMedicine | 2021 |
| 32663847 | Near Real-Time Identification of Recent Human Immunodeficiency Virus Transmissions, Transmitted Drug Resistance Mutations, and Transmission Networks by Multiplexed Primer ID-Next-Generation Sequencing in North Carolina. | J Infect Dis | 2021 |
| 31504749 | HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. | Mol Biol Evol | 2020 |
| 32082287 | Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China. | Frontiers in Microbiology | 2020 |
| 32054488 | Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia. | Virology Journal | 2020 |
| 32049340 | Identification of Hidden Population Structure in Time-Scaled Phylogenies. | Syst Biol | 2020 |
| 32698896 | Producing polished prokaryotic pangenomes with the Panaroo pipeline. | Genome Biol | 2020 |
| 33347450 | An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia. | PLoS Neglected Tropical Diseases | 2020 |
| 33292095 | Disease control across urban-rural gradients. | Journal of the Royal Society Interface | 2020 |
| 33335904 | Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017-2019. | Frontiers in Medicine | 2020 |
| 31106820 | Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection. | Genome Biology and Evolution | 2019 |
| 29680827 | HIV seroprevalence, self-reported STIs and associated risk factors among men who have sex with men: a cross-sectional study in Rwanda, 2015. | Sexually Transmitted Infections | 2019 |
| 31076776 | Fast hierarchical Bayesian analysis of population structure. | Nucleic Acids Research | 2019 |
| 29415690 | The role of venues in structuring HIV, sexually transmitted infections, and risk networks among men who have sex with men. | BMC Public Health | 2018 |
| 30345380 | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. | Wellcome Open Research | 2018 |
| 29688481 | Neutral Theory and Rapidly Evolving Viral Pathogens. | Molecular Biology and Evolution | 2018 |
| 28053012 | Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. | Molecular Biology and Evolution | 2017 |
| 28602726 | The changing molecular epidemiology of HIV in the Philippines. | International Journal of Infectious Diseases | 2017 |
| 28458917 | Adaptation of avian influenza virus to a swine host. | Virus Evolution | 2017 |
| 28852573 | Biased phylodynamic inferences from analysing clusters of viral sequences. | Virus Evolution | 2017 |
| 28540766 | HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. | AIDS Res Hum Retroviruses | 2017 |
| 28257143 | Modeling and analyzing respondent-driven sampling as a counting process. | Biometrics | 2017 |
| 28202767 | Genotype-Specific Evolution of Hepatitis E Virus. | Journal of Virology | 2017 |
| 26768255 | Surveys, Serologies, and Sequences Reveal History of Iatrogenic Transmission of HIV-1. | Journal of Infectious Diseases | 2016 |
| 27281020 | Assessing Commitment and Reporting Fidelity to a Text Message-Based Participatory Surveillance in Rural Western Uganda. | PLoS ONE | 2016 |
| 26147205 | Measuring Asymmetry in Time-Stamped Phylogenies. | PLoS Computational Biology | 2015 |
| 25886745 | Assessing the use of hospital staff influenza-like absence (ILA) for enhancing hospital preparedness and national surveillance. | BMC Infectious Diseases | 2015 |
| 25843391 | Eight challenges in phylodynamic inference. | Epidemics | 2015 |
| 25843388 | Six challenges in measuring contact networks for use in modelling. | Epidemics | 2015 |
| 25495675 | Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China. | AIDS Research and Human Retroviruses | 2015 |
| 25312038 | Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV. | Journal of Infectious Diseases | 2015 |
| 25766240 | Modeling infectious disease dynamics in the complex landscape of global health. | Science | 2015 |
| 26058342 | Genomic characterization of two novel HIV-1 unique (CRF01_AE/B) recombinant forms among men who have sex with men in Beijing, China. | AIDS Research and Human Retroviruses | 2015 |
| 26194754 | Assigning and visualizing germline genes in antibody repertoires. | Philosophical Transactions of the Royal Society B: Biological Sciences | 2015 |
| 24928667 | OutbreakTools: a new platform for disease outbreak analysis using the R software. | Epidemics | 2014 |
| 25401173 | Sampling through time and phylodynamic inference with coalescent and birth-death models. | Journal of the Royal Society Interface | 2014 |
| 24471866 | Stability of immunophenotypic lymphoid markers in fixed canine peripheral blood for flow cytometric analysis. | Veterinary Clinical Pathology | 2014 |
| 24845574 | Beyond bushmeat: animal contact, injury, and zoonotic disease risk in Western Uganda. | | 2014 |
| 24752791 | HIV prevalence and demographic determinants of unprotected anal sex and HIV testing among men who have sex with men in Beirut, Lebanon. | Archives of Sexual Behavior | 2014 |
| 23382430 | Modelling tree shape and structure in viral phylodynamics. | Philosophical Transactions of the Royal Society B: Biological Sciences | 2013 |
| 24205221 | Respondent driven sampling: determinants of recruitment and a method to improve point estimation. | PLoS ONE | 2013 |
| 24244151 | Can non-lytic CD8+ T cells drive HIV-1 escape? | PLoS Pathogens | 2013 |
| 23967111 | Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. | PLoS ONE | 2013 |
| 24367249 | Inferring the source of transmission with phylogenetic data. | PLoS Computational Biology | 2013 |