Protein Interaction Networks: Integration and Alignment

Stanford University, Stanford CA

Investigators

Abstract

Stanford University is awarded a grant to computationally predict, compare, and analyze functional associations between proteins in sequenced microbes. Protein interaction networks have emerged as a canonical way to represent functional associations between proteins in a cell. In such a network, proteins are nodes and edges connect proteins that physically interact, or more broadly participate in the same biological process. For the molecular biologist, protein interaction networks are an invaluable resource, as they can aid in functionally annotating hypothetical proteins that are connected to proteins of known functions, identifying new multiprotein complexes, and suggesting promising target proteins for experimentation. This project will computationally predict interaction networks that integrate all available functional genomics data sources, compare predicted networks across microbes to extract functional modules, and generate concrete experimental recommendations. It will develop novel methodology for inferring transcriptional cascades on a global level and aligning these cascades to find conserved regulons. In addition it will create tools for computer-guided experimental validation in Caulobacter crescentus, which will guide efforts in two experimental laboratories. The result will be an experimentally tested means of predicting protein interactions ? and hence biology ? directly from genome sequence. The team will develop a powerful and user-friendly web interface where protein interaction networks from all sequenced microbes will be browsed and compared across species. The resulting data will be downloadable in convenient formats, and the software will be available through the General Public Licence (GPL). The team will directly involve several undergraduate students in the research, through the CURIS undergraduate research program at the Computer Science department. Research will be conducted at the Clark Center, a new building that is part of the BioX initiative at Stanford University. The BioX initiative's goal is to foster cooperation across disciplines such as biology and computer science, and to educate a new generation of students that will be bilingual in the languages of both the biological and computational sciences.