Andrew Pountain

My lab uses experimental and computational techniques to understand the systems biology of gene regulation in microbes and microbial pathogens. We use advanced transcriptional technologies, particularly bacterial single cell RNA sequencing, to dissect the factors shaping transcriptional dynamics, and how genes interact with each other to produce a particular behavior or phenotype. There are two major directions for this. Firstly, we are establishing the bacterial replication cycle as a model system for modeling gene regulatory changes. As my recent work has shown, reconstructing transcriptional dynamics from single cells allows us to infer huge amounts of information about a system, from global replication patterns to the regulatory states of individual genes. I am looking to build on this framework as well as to explore the effects of environmental shifts or genetic perturbations. A second direction is to understand how variation in gene expression and physiology results in key fate decisions in how pathogenic microbes interact with their host – for example whether they adopt an aggressive, cytotoxic phenotype or enter a non-replicating, antibiotic tolerant state. A central theme of my lab is the combination of molecular microbiology, emerging transcriptional technologies, and quantitative, computational analysis. My goal is to provide students with transdisciplinary training across these areas. Therefore, projects could involve experimental investigation of microbial growth or pathogenesis, applying and developing new computational methods, and optimizing transcriptomics pipelines, with opportunities for students to learn skills in each of these areas. Interested students can learn more by viewing my publication history.