The human immunodeficiency virus (HIV) evolves rapidly owing to the combined activity of
error-prone reverse transcriptase, recombination, and short generation times, leading to …

Two-locus sampling probabilities have played a central role in devising an efficient
composite-likelihood method for estimating fine-scale recombination rates. Due to …

Within-host genetic diversity and large transmission bottlenecks confound phylodynamic
inference of epidemiological dynamics. Conventional phylodynamic approaches assume …

The first deep sequencing method was announced in 2005. Due to an increasing number of
sequencing data and a reduction in the costs of each sequencing dataset, this innovative …

The treatment of HCV infection has seen significant progress, particularly since the approval
of new direct-acting antiviral drugs. However these clinical achievements have been made …

Modern phylogeography aims at reconstructing the geographic movement of organisms
based on their genomic sequences and spatial information. Phylogeographic approaches …

Archeogenetics has been revolutionary, revealing insights into demographic history and
recent positive selection. However, most studies to date have ignored the nonrandom …

Bacillus anthracis, the etiological agent of anthrax, is a well-established model organism.
For B. anthracis and most other infectious diseases, knowledge regarding transmission and …

The dynamics of a population exhibiting exponential growth can be modelled as a birth–
death process, which naturally captures the stochastic variation in population size over time …

Modern phylogeography aims at reconstructing the geographic diffusion of organisms based
on their genomic sequences and spatial information. Phylogeographic approaches usually …