Jeremy Gunawardena, Ph.D.
Department of Systems Biology
Harvard Medical School
“Beyond the bacterial paradigm in gene regulation”
There are striking differences between bacterial and eukaryotic genomes. Bacterial genes typically have one or two transcription factors (TFs) binding at a few promoter-proximal sites with strong motifs and regulation takes place in the absence of energy expenditure. In contrast, eukaryotic genes often have multiple TFs binding with weak motifs at numerous, widely-distributed sites and regulation takes place while energy is being expended to restructure chromatin, move nucleosomes, post-translationally modify co-regulators and methylate DNA. Despite this remarkable complexity, much of our quantitative understanding of how genes work is still based on a bacterial perspective. I will discuss the linear framework, a graph-based approach to time-scale separation in biochemical systems, which allows us to extend the classical bacterial paradigm and to analyze the information integration and energy expenditure that are the hallmarks of eukaryotic gene regulation.
I received my PhD in pure mathematics from the University of Cambridge. I spent some years at Hewlett-Packard Research, leading HP's “blue skies” research program. I returned to academic life as a faculty member in the Department of Systems Biology at Harvard Medical School, where my lab studies cellular information processing using a combination of experimental, mathematical and computational methods.