Our Research Focus
We aim to identify principles underlying gene regulatory dynamics on a genome-wide scale.
Transcriptional dynamics of the bacterial cell cycle
Using new single cell microbial RNA sequencing technologies, we have found that the replication cycle is a major driver of transcriptional variation in bacterial populations. By modeling this effect, we can resolve individual bacteria based on their replication state. This reveals a widespread and complex relationship between DNA replication and transcriptional dynamics. We are applying single cell experimental techniques with computational analysis methods drawn from fields from deep learning to biophysical modeling to understand these transformative but challenging datasets.
Phenotypic heterogeneity in pathogenesis
A single pathogen species can have multiple modes of interaction with its host. The bacterium Staphylococcus aureus, for example, can express a wide array of toxic factors promoting invasion and tissue destruction, or it can adopt defensive postures that enable high stress tolerance and chronic infection. We aim to understand how these fate decisions are made in the context of an individual bacterium's environment and physiological state.