Associate Professor, Botany and Plant Pathology
KEYWORDS: Bioinformatics, Functional Genomics, Promoter Architecture, Gene Expression, RNA processing, Alternative Splicing, RNA Binding Proteins, Arabidopsis thaliana, Brachypodium distachyon, Flowering Time, Circadian Clock
Promoter Architecture and Genomic Control of Gene Expression. The genome interacts with the environment in the regulation of transcription, and changes in promoter architecture play a role in phenotypic variation observed between and within species. Computational methods will be employed to identify DNA motifs (ie. transcription-factor binding sites) in the regulatory sequences upstream of co-expressed/co-regulated genes in Arabidopsis and other plant species with completed genome sequences, including rice and poplar. Molecular, genetic and biochemical approaches will be used to validate the computational predictions, identify interacting transcription factors, and further dissect the transcriptional networks.
Brachypodium distachyon, an experimental model for cereal genomics. Brachypodium distachyon (Brachypodium.org) is a grass species related to the major cereal grain species wheat, barley, oats, maize, rice, rye, sorghum, and millet. It has many qualities that make it an excellent model organism for functional genomics research in temperate grasses and cereals, and dedicated biofuel crops such as Switchgrass. These attributes include small genome (~300-320Mbp) diploid accessions, a series of polyploid accessions, a small physical stature, self-fertility, a short lifecycle, simple growth requirements, and an efficient transformation system. We will work towards developing genomic, genetic, and bioinformatics resources for Brachypodium and use these tools to facilitate study of flowering time control in grasses.