We present a formalism for unifying the inference of population size from genetic sequences
and mathematical models of infectious disease in populations. Virus phylogenies have been …

The HIV epidemic in higher-income nations is driven by receptive anal intercourse, injection
drug use through needle/syringe sharing, and, less efficiently, vaginal intercourse. Alcohol …

Epidemic modeling of infectious diseases has a long history in both theoretical and
empirical research. However the recent explosion of genetic data has revealed the rapid …

The extreme variability of human immunodeficiency virus type 1 (HIV-1) makes it possible to
conduct transmission studies on the basis of genetic analysis and to trace global and local …

Genomic data are increasingly being used to understand infectious disease epidemiology.
Isolates from a given outbreak are sequenced, and the patterns of shared variation are used …

The control, prediction, and understanding of epidemiological processes require insight into
how infectious pathogens transmit in a population. The chain of transmission can in principle …

Information on the dynamics of the effective population size over time can be obtained from
the analysis of phylogenies, through the application of time-varying coalescent models. This …

The HIV epidemic has spawned a scientific effort unprecedented in the history of infectious
disease research. This effort has merged aspects of clinical research, basic molecular …

Quantifying epidemiological dynamics is crucial for understanding and forecasting the
spread of an epidemic. The coalescent and the birth-death model are used interchangeably …

Much of the existing theory for the evolutionary biology of infectious diseases uses an
invasion analysis approach. In this Ideas and Perspectives article, we suggest that …