Trey Ideker

Associate Professor, Bioengineering , School of Medicine

Bioinformatics and systems biology; computational modeling of cellular regulatory networks; yeast genetics

Trey Ideker is a pioneer in the nascent field known as systems biology. Through the use of high-throughput experimental technologies, systems biology aims to understand and map all of the molecular components and interactions that control the inner workings of cells. These interactions form a vast signaling and regulatory network that govern every aspect our biological lives, from the function of our immune system to our risk for disease. Ideker's goal is to create computational models that provide researchers with a more global perspective of what goes wrong in disease and in turn, enable them to design better therapies.His work involves the use of high-throughput experimental technologies such as DNA microarrays and mass spectrometry-enabled proteomics, to gather new information about genes, proteins and their direct interactions. Recently, he and his collaborators developed CYTOSCAPE (www.cytoscape.org), a software program being used by several hundred labs to visualize and integrate such data into models of cellular pathways and networks. Ideker and his graduate advisor Leroy Hood published a landmark paper in Science (May 2001) in which they built a computational model of yeast metabolism through systematic perturbations of the cell using DNA microarrays, proteomics, and databases of known physical interactions. The paper was one of the first demonstrations of the process of systems biology and continues to define this emerging field. 

Capsule Bio:
Trey Ideker became an assistant professor of bioengineering at the UCSD Jacobs School of Engineering in 2003. He received his Ph.D. in Molecular Biotechnology in 2001 at the University of Washington. From 2001-2003, he was a Pfizer Fellow of Computational Biology at the Whitehead Institute for Biomedical Research. Ideker is an advisor to the NIH Study Section for the Biomedical Information Science and Technology Initiative and the DOE Genomes to Life project. He serves on the advisory boards of Genstruct and BioCyc, and holds several patents in microarray analysis and systems biology.

Institute Affiliation:
Whitaker Institute of Biomedical Engineering »