About

I am a postdoctoral researcher in the department of Biomedical Informatics at Harvard Medical School. My research focuses on pathogen genomics, in particular in the context of viral or bacterial infections. I develop software for reconstruction of microbial genomes from sequencing data, also known as genome assembly, and apply these methods to characterize pathogen diversity in patient samples. Of particular interest are viral infections, which typically consist of many closely-related mutant strains: a viral quasispecies. Accurate reconstruction of each of these mutant strains (or haplotypes) is of medical importance, since mutations can affect drug resistance, thus causing treatment issues. Moreover, knowledge of individual haplotypes can help in reconstructing patterns of spread in disease outbreaks. The relevance of strain-aware genome assembly also applies to bacterial infections, where genomic variation can impact antibiotic resistance --- currently one of the biggest threats to human health.