E. Romero-Severson

The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees

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

Inferring viral transmission time from phylogenies for known transmission pairs

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.

Migration coupled with recombination explains disparate HIV-1 anatomical compartmentalization signals

This paper develops an evolutionary model incorporating migration and recombination to explain varying HIV-1 compartmentalization signals across tissues.

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

This paper develops a coalescent-based simulator of within-host HIV evolution that includes latency and recombination, showing how recombination recovers disrupted temporal signals caused by latency in phylogenetic trees.

Combining biomarker and virus phylogenetic models improves epidemiological source identification

This paper develops a method that combines HIV biomarkers with phylogenetic analysis to improve the accuracy of identifying transmission sources in HIV epidemics.