I am a scientist in the Design group at Ginkgo Bioworks, where I help engineer microbes to produce useful chemicals by doing enzyme discovery and quantitative genetics.
My CV has more details on my research and publications.
Metagenomic enzyme discovery and screening
Synthetically designed metabolic pathways use parts from across the tree of life, but the existing "codebase" of enzymes is often limited to a few model examples. Using modern sequence databases and DNA synthesis technology, it is now possible to systematically evaluate many members of an enzyme family for fine-tuned functional diversity. At Ginkgo, I am developing computational tools to identify enzymes in metagenomic data and support functional screens. We hope to not only establish a useful codebase for synthetic biology, but also better understand how sequences encode the biochemical properties of enzymes.
Natural variation and tradeoffs in nutrient decisions
Microbes growing in mixtures of nutrients have to decide which nutrient(s) to consume first. This decision is made by gene regulatory circuits which can diversify and adapt to different environments. In a paper from my PhD, we studied yeast strains from different geographic and ecological niches and found that the strains make different nutrient decisions, corresponding to whether they "prepare" for impending depletion of a preferred nutrient. Because this preparation requires costly gene expression, it leads to a fitness tradeoff, perhaps explaining why we see such diverse decision-making across extant yeast strains.
Natural Genetic Variation Can Independently Tune the Induced Fraction and Induction Level of a Bimodal Signaling Response
Polymorphisms in the Yeast Galactose Sensor Underlie a Natural Continuum of Nutrient-Decision Phenotypes
Natural Variation in Preparation for Nutrient Depletion Reveals a Cost-Benefit Tradeoff
Large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium
Agashe, D., Sane, M., Phalnikar, K., Diwan, G. D., Habibullah, A., Cecilia Martinez-Gomez, N., Sahasrabuddhe V., Polachek W., Wang J., Chubiz L. M., Marx C. J. (2016) Molecular Biology and Evolution, 33(6), 1542–1553. 10.1093/molbev/msw035
Galactose metabolic genes in yeast respond to a ratio of galactose and glucose