background I am an evolutionary biologist and infectious disease epidemiologist with a focus on using genomic data to better understand the dynamics of human pathogens. Broadly speaking, I am interested in identifying novel data signatures in pathogen genomic data and developing quantitative analytical methods to generate epidemiological and evolutionary insights from those signals. My work spans biological scales, from within-host pathogen evolution to pathogen dynamics on the host population scale. I have a particular interest in analyses that link these scales, e.g. through the transmission bottleneck.

I am currently a post-doctoral research fellow as a part of the Infectious Disease Dynamics group at the Johns Hopkins Bloomberg School of Public Health. My primary appointment is in the Department of Epidemiology, working with Dr. Derek Cummings although I also work closely with Dr. M. Kate Grabowski in the Department of Pathology at the School of Medicine. I am focused on a number of infectious disease-genomes related research projects including the evolution and transmission of HIV antiretroviral therapy (ART) resistance, the genomic epidemiology of Neisseria gonorrhoeae in Uganda, and inter-and intra-strain dynamics of dengue virus. Much of my work is rooted in the development of new analytical methods, particularly those that are scalable to large data sets.

I completed my doctoral training in Dr. Katia Koelle’s group in the Population Biology, Ecology, and Evolution graduate program. My work there was funded in part by an NIH NIAID F31 fellowship to study the evolution of influenza defective viral genomes within- and between-hosts. I also spent significant time researching SARS-CoV-2 during my doctoral training including estimating the transmission bottleneck and phylodynamic epidemiological modeling.

Prior to my doctoral training I earned a master’s in epidemiology at the Harvard T.H. Chan School of Public Health where I did research in the Center for Communicable Disease Dynamics with Dr. Bill Hanage. Here I mainly focused on the within-host genomic diversity of M. tuberculosis.

News

2025

  • We recently made a pre-print available on the dynamics of HIV viral load suppression and resistance during the dolutegravir transition. We estimate suppresison to be at 90% among all people with HIV and 95% among those on treatment. We observe minimal DTG resistance overall but do identify the recent emergence of the inS153Y mutation, which confers about two-fold DTG resistance, with putative evidence for transmission. One of my favorite results from this work is that pre-existing NNRTI/NRTI resistance is not associated with individual-level probabilities of achieving viral load suppression in recent years, highlighting important programmatic efforts to increase suppression in this population. I had the opportunity to present this work in an oral at the International Workshop on HIV Drug Resistance and Treatment Strategies. PDF.
  • Our work on HIV multiple infections in the Rakai Community Cohort Study is now published in PLOS Pathogens. The main results are similar to the pre-print (see below), however, we now incorporate Bayesian post-stratification to account for potential sampling biases in our sequence data. We therefore are able to estimate that ~4% of viremic PLHIV in the population (as opposed to ~6% in the sample) harbor MIs at the time of sampling. Further, we incorporated direct comparison to what I call “synthetic amplicon” data to show that using whole-genome data increases sensitivity of the method more than two-fold. PDF.

    2024

  • Our preprint on HIV multiple infections in the Rakai Community Cohort Study is now available. We develop a Bayesian model to identify MIs in whole genome deep-sequence data. We use the model to show that ~6% of viremic PLHIV harbor MIs at time of sampling and that the risk of MI is ~two-fold higher in high prevalence fishing communities. PDF.
  • We have considerably revised our work on the dynamics of HIV drug resistance in Rakai, Uganda in response to reviewer comments. Hopefully the revised version is more digestible for readers. PDF.
  • Our work on the within- and between-host dynamics of influenza A virus defective viral genomes is now out in Virus Evolution [PDF]. This work was (mostly) completed during my doctoral research in Dr. Katia Koelle’s group.
  • I finally found the motivation to make a professional website. Thank you Clif McKee for the nudge.