Professor, Departments of Medicine and BioEngineering, UCSD
Towards an artificially intelligent model of the cell for patient data translation
The overall objective of our laboratory is to develop an artificially intelligent model of the cell able to translate a patient’s data into precision diagnosis and treatment. Towards this goal, we are developing methods that learn how to structure cell models directly from genomics data sets (Dutkowski et al. Nature Biotechnology 31.1 pp. 38-45, 2013; Carvunis and Ideker, Cell 157.3 pp. 534-538 2014). For this purpose, we run an experimental facility for systematic measurement of gene and protein interaction networks (Bandyopadhyay et al. Science 330.6009 pp, 1385-1389 2010; Srivas, Shen et al. Molecular Cell 2016). A second big challenge is to work out the functional logic by which these models process information, e.g. from genotype to phenotype. Here too, we have made recent progress (Yu et al. Cell Systems 2.2 pp. 77-88 2016) but much remains to be done before we have a cell model capable of making robust predictions about patients. As supporting software, we are developers of Cytoscape, a popular platform for visualization and modeling of biological networks (http://www.cytoscape.org/) as well as NDEx, a database of network models (http://ndexbio.org/).
Trey Ideker, Ph. D. is Professor of Genetics in the Department of Medicine at the University of California at San Diego. He serves as Director of the National Resource for Network Biology and Director of the San Diego Center for Systems Biology, as well as being Adjunct Professor of Computer Science and Bioengineering and Member of the Moores UCSD Cancer Center. Ideker received Bachelor’s and Master’s degrees from MIT in Electrical Engineering and Computer Science and his Ph.D. from the University of Washington in Molecular Biology under the supervision of Dr. Leroy Hood.
Dr. Ideker’s research is led by the vision that given the right experimentation and analysis, it will be possible to automatically assemble maps of pathways just as we now assemble maps of genomes. During graduate work, he developed a general iterative framework for how biological systems can be systematically perturbed, interrogated and modeled. This framework laid the foundation for many studies in the discipline of Systems Biology. He demonstrated that biological networks could be integrated with gene expression to systematically map pathways and aligned, like sequences, to reveal conserved and divergent functions. He showed that the best biomarkers of disease are typically not single proteins but aggregates of proteins in networks.
Dr. Ideker has founded influential bioinformatic tools including Cytoscape, a popular network analysis platform which has been cited >12,000 times. Ideker serves on the Editorial Boards for Cell, Cell Reports, Nature Scientific Data, EMBO Molecular Systems Biology, and PLoS Computational Biology and is a Fellow of AAAS and AIMBE.
He was named one of the Top 10 Innovators of 2006 by Technology Review magazine and was the recipient of the 2009 Overton Prize from the International Society for Computational Biology. His work has been featured in news outlets such as The Scientist, the San Diego Union Tribune, Forbes magazine, and the New York Times.