CAREER: Probabilistic Frameworks for Studying Gene Regulatory Sequences and their Evolution

University Of Illinois At Urbana-Champaign, Urbana IL

Investigators

Abstract

The University of Illinois at Urbana-Champaign is awarded a grant by the NSF Faculty Early Career Development (CAREER) Program for a promising young researcher to study gene regulatory sequences and their evolution, combined with an educational agenda directed towards training of graduate students and introducing middle-school girls to topics in bioinformatics. The research component will build probabilistic frameworks to discover cis-regulatory modules in metazoan genomes and elucidate how they have evolved across moderate to high divergence times. The computational methods will also explore what a well-studied regulatory system, e.g., fruitfly development, can teach us about the workings of an uncharted regulatory system, e.g., honeybee behavior. From a technical perspective, the novel thrusts will be on (1) multiple species comparison in the regime of poor sequence alignment, (2) adaptive motif discovery that exploits knowledge of binding sites in one species to predict sites in diverged species, and (3) compositional rules of cis-regulatory modules in terms of the types and arrangements of binding sites within them. The educational component focuses on (1) development of an educational software package for probabilistic analysis of regulatory DNA sequences, to be used to train graduate students, (2) outreach activities that motivate middle school girls to consider future careers in science and engineering, and (3) development of courses on bioinformatics at the undergraduate and graduate levels.