A fundamental biological challenge is to understand how the linear information in an organism's genome is processed to produce the resulting behavior or phenotype. Genes are transcribed and translated into proteins that adopt three-dimensional conformations. Evolutionary processes ensure that a folded protein conformation interacts with its environment in a manner that is beneficial to the organism, using the protein to catalyze reactions, recognize cellular signals, build cellular structures, and to perform a host of other diverse biological functions.
Our research aims to understand these processes by using computational techniques to perform sophisticated analyses on genomic sequence data to annotate and understand relationships between the sequence, structure, and function of DNA, RNA, proteins and metabolites, at both the molecular and the genomic/systems levels. The goal is to develop a coherent picture of molecular and organismal structure, function, networks, and evolution within a fundamental scientific framework. We have applied our methods to the genomes/proteomes of more than forty organisms, encapsulated by the object-oriented Bioverse database and webserver (http://bioverse.compbio.washington.edu). The talk will detail our current progress and provide an overview of the methodologies being pursued by our group to achieve the above goals, as well as applications and discoveries made using this framework.