Thomas Leitner

wavess 1.2 simulates within-host virus sequences with an HLA-aware CTL response and variable recombination rate to improve accuracy in immune-dominated regions.

The paper models SIV provirus divergence in CD4+ T cells, finding that short-lived cells harbor more diverged virus, while long-lived cells contain less diverged virus, explaining contradictory prior results on reservoir timing.

Hypermut 3 detects hypermutation patterns in sequences, handling multistate characters and gaps, and is available as a web and command-line tool.

This paper shows that reassortment events in segmented viruses cannot be reliably inferred from segment trees alone, even with perfect data.

This paper develops a Markov model to infer HIV transmission times from phylogenies and finds it provides accurate and narrower estimates compared to existing methods.

The paper develops a simulation tool to assess how contact tracing affects phylogenetic inferences from molecular epidemiology data.

This paper develops a deep learning method for real-time HIV outbreak detection using genomic data, achieving high specificity and sensitivity in identifying outbreaks.