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 …

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being
published on a daily basis, including a regularly updated phylogeny on nextstrain. org. Here …

Genomic sequencing has significant potential to inform public health management for SARS-
CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of …

Abstract The development of High-Throughput Sequencing (HTS) technologies is having a
major impact on the genomic analysis of viral populations. Current HTS platforms can …

We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly
identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering …

Background The incidence of HIV infection in young women in Africa is very high. We did a
large-scale community-wide phylogenetic study to examine the underlying HIV transmission …

Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing
a remarkable economic impact because of direct losses and indirect costs for its control. As …

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

The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has
exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of …

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 …