| Q37264576 | A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland |
| Q34634310 | A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes |
| Q36119466 | Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia |
| Q34561395 | An epidemiological view of microbial genomic data |
| Q36254975 | Analysis of the history and spread of HIV-1 in Uganda using phylodynamics |
| Q64058710 | Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada |
| Q35919781 | Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1. |
| Q34658101 | Assessment of a new web-based sexual concurrency measurement tool for men who have sex with men. |
| Q34493132 | Automated analysis of phylogenetic clusters |
| Q40065668 | Biased phylodynamic inferences from analysing clusters of viral sequences |
| Q35132985 | Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe |
| Q35795095 | CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba |
| Q36299332 | Centralized HIV Program Oversight: An Investigation of a Case Series of New HIV Infections among US Army Soldiers, 2012 to 2013. |
| Q36486845 | Characterizing HIV transmission networks across the United States |
| Q47625016 | Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases. |
| Q47564118 | Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population |
| Q37605946 | Coreceptor usage of Chinese HIV-1 and impact of X4/DM transmission clusters among recently infected men who have sex with men. |
| Q57157111 | DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference |
| Q33829130 | Defining HIV-1 transmission clusters based on sequence data |
| Q30593892 | Detectable signals of episodic risk effects on acute HIV transmission: strategies for analyzing transmission systems using genetic data |
| Q95371858 | Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction |
| Q31161547 | Effects of contact network structure on epidemic transmission trees: implications for data required to estimate network structure |
| Q39507516 | Emergence of clusters of CRF02_AG and B human immunodeficiency viral strains among men having sex with men exhibiting HIV primary infection in southeastern France |
| Q28655331 | Ensuring privacy in the study of pathogen genetics |
| Q92844297 | Ethical issues in HIV phylogenetics and molecular epidemiology |
| Q36289722 | Expanding HIV-1 subtype B transmission networks among men who have sex with men in Poland |
| Q64104794 | Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach |
| Q36945699 | Future of phylogeny in HIV prevention |
| Q47560008 | Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in "Real-World" Settings |
| Q57176056 | Growth of HIV-1 Molecular Transmission Clusters in New York City |
| Q40049433 | HIV Transmission Dynamics among Foreign-born Persons in the United States |
| Q37729475 | HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania |
| Q28542528 | HIV-1 diversity, transmission dynamics and primary drug resistance in Angola |
| Q60915581 | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
| Q40215127 | HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters |
| Q37186690 | HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries |
| Q28536682 | HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis |
| Q42773999 | HIV-1 transmission networks in a small world |
| Q46209757 | High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach |
| Q34789253 | How the dynamics and structure of sexual contact networks shape pathogen phylogenies |
| Q36267935 | Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain. |
| Q38852280 | Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. |
| Q40794836 | Impact of sampling density on the extent of HIV clustering. |
| Q40501110 | Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering. |
| Q64268868 | In-depth Sampling of High-risk Populations to Characterize HIV Transmission Epidemics Among Young MSM Using PrEP in France and Quebec |
| Q37470109 | Integrating molecular epidemiology and social network analysis to study infectious diseases: Towards a socio-molecular era for public health. |
| Q57092078 | Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions |
| Q34059636 | Intercontinental dispersal of HIV-1 subtype B associated with transmission among men who have sex with men in Japan |
| Q92043397 | Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model |
| Q38596317 | Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management |
| Q35868716 | Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering |
| Q28550140 | Molecular Epidemiology and Transmission Dynamics of Recent and Long-Term HIV-1 Infections in Rural Western Kenya |
| Q30235142 | Molecular Epidemiology of Human Immunodeficiency Virus. |
| Q36887582 | Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States |
| Q31062029 | Molecular epidemiology of HIV-1 transmission in a cohort of HIV-1 concordant heterosexual couples from Dakar, Senegal |
| Q89395082 | Molecular evolution methods to study HIV-1 epidemics |
| Q64094788 | National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort |
| Q92132388 | Natural selection favoring more transmissible HIV detected in United States molecular transmission network |
| Q64452225 | Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data |
| Q28606881 | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| Q28727841 | Phylodynamic analysis of a viral infection network |
| Q28540757 | Phylodynamic analysis reveals CRF01_AE dissemination between Japan and neighboring Asian countries and the role of intravenous drug use in transmission |
| Q28354115 | Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain |
| Q35152000 | Phylodynamic inference for structured epidemiological models |
| Q36325542 | Phylodynamics on local sexual contact networks |
| Q35840881 | Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011 |
| Q30670919 | Phylogenetic Investigation of a Statewide HIV-1 Epidemic Reveals Ongoing and Active Transmission Networks Among Men Who Have Sex With Men. |
| Q90524457 | Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda |
| Q37206422 | Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions |
| Q62487956 | Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort |
| Q35069391 | Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana |
| Q35006672 | Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? |
| Q92670545 | Phylogenetics in HIV transmission: taking within-host diversity into account |
| Q61805645 | Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations |
| Q93034324 | Prediction of HIV Transmission Cluster Growth With Statewide Surveillance Data |
| Q91833121 | Pretreatment HIV drug resistance spread within transmission clusters in Mexico City |
| Q47205333 | QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. |
| Q52692658 | Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. |
| Q46190520 | Racial disparities in HIV prevalence and risk behaviors among injection drug users and members of their risk networks |
| Q37391336 | Reconstructing contact network parameters from viral phylogenies. |
| Q28652568 | Sampling through time and phylodynamic inference with coalescent and birth-death models |
| Q30388886 | Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic |
| Q34285912 | Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection |
| Q28468363 | Social and Genetic Networks of HIV-1 Transmission in New York City |
| Q37620368 | Social networks, sexual networks and HIV risk in men who have sex with men. |
| Q37661745 | Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies |
| Q40372881 | Stochastic epidemic dynamics on extremely heterogeneous networks |
| Q36141239 | Targeting HIV Prevention Based on Molecular Epidemiology Among Deeply Sampled Subnetworks of Men Who Have Sex With Men |
| Q39546435 | Testing the hypothesis of preferential attachment in social network formation. |
| Q35902684 | The HIV Epidemic: High-Income Countries. |
| Q40517781 | The Interaction of Risk Network Structures and Virus Natural History in the Non-spreading of HIV Among People Who Inject Drugs in the Early Stages of the Epidemic |
| Q40702989 | The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States |
| Q33553778 | The contribution of viral genotype to plasma viral set-point in HIV infection |
| Q30354847 | The global transmission network of HIV-1 |
| Q35152768 | The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada |
| Q40040029 | The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters. |
| Q46415816 | The role of individual and neighborhood factors: HIV acquisition risk among high-risk populations in San Francisco |
| Q40115582 | Transmission network characteristics based on env and gag sequences from MSM during acute HIV-1 infection in Beijing, China |
| Q36745253 | Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters |
| Q36922133 | Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada |
| Q92772801 | TreeCluster: Clustering biological sequences using phylogenetic trees |
| Q28540490 | Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic |
| Q33717011 | Using HIV networks to inform real time prevention interventions |
| Q30989440 | Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States |
| Q31150908 | Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic |
| Q35753695 | Viral Genetic Linkage Analysis in the Presence of Missing Data. |