Epidemics of HIV in men who have sex with men (MSM) continue to expand in most
countries. We sought to understand the epidemiological drivers of the global epidemic in …

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention
strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based …

Background As sequence data sets used for the investigation of pathogen transmission
patterns increase in size, automated tools and standardized methods for cluster analysis …

Background Sexually transmitted infections spread across contact networks. Partner
elicitation and notification are commonly used public health tools to identify, notify, and offer …

Clustering homologous sequences based on their similarity is a problem that appears in
many bioinformatics applications. The fact that sequences cluster is ultimately the result of …

Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global
transmission network has not been characterized. A better understanding of the properties …

Objective To reconstruct the local HIV-1 transmission network from 1996 to 2011 and use
network data to evaluate and guide efforts to interrupt transmission. Design HIV-1 pol …

Background: Studying HIV transmission networks provides insight into the spread of HIV and
opportunities for intervention. We identified transmission dynamics among risk groups and …

HIV-1 genetic variability within individuals and populations plays a central role in the HIV
pandemic. Multiple zoonotic transmissions of SIV to humans have resulted in distinct HIV …

Background. Many studies of sexual behavior have shown that individuals vary greatly in
their number of sexual partners over time, but it has proved difficult to obtain parameter …