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Faculty Profiles

Shankar Subramaniam

Professor, Bioengineering

Faculty, Computer Science and Engineering




Bioinformatics, Systems Biology and Medicine

Research in the Subramaniam laboratory spans several areas of bioinformatics, systems biology and medicine. In bioinformatics, he is involved in developing novel strategies for identifying protein interaction networks, intracellular localization of proteins and identification of functional networks in cells. In systems biology, he is involved in deciphering mammalian cellular networks from high throughput and phenotypic data and in developing strategies for modeling cellular signaling networks. In systems medicine, he collaborates with biomedical scientists towards understanding diseases associated with insulin resistance and inflammation. His laboratory is interested in mapping the circuitry of cells to mechanisms and phenotypes in physiology and pathology and to develop quantitative models of cellular pathways.

Subramaniam continues to be engaged in developing state-of-the-art infrastructure for bioinformatics. The Molecule Pages Database has been recognized as the most innovative informatics resource for signaling proteins and received the ALSIP award. The integration of highly innovative and complex computer science strategies with expert-driven curation has led to the Molecule Pages Database that provides comprehensive information on all known functional states of signaling molecules. The LipidMaps database serves as the first and only integrated resource for mammalian lipids along with their complementary gene and protein data. The microarray server, widely used by the research community, combines sophisticated statistical analysis methods developed in the Subramaniam laboratory with biochemical annotations and pathways to provide biological insights into consequences of transcriptional changes in mammalian cells.

Capsule Bio:

Subramaniam is the Chair of the Bioengineering Department and the Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology. In addition, he holds joint appointments in Cellular and Molecular Medicine, Chemistry and Biochemistry and Nanoengineering at UCSD and the Salk Institute for Biological Studies. He was the founding Director of the Bioinformatics and Systems Biology Interdisciplinary Program. He was named a distinguished scientist at the San Diego Supercomputer Center in 2010. He is a Fellow of the American Institute for Medical and Biological Engineering and is a recipient of the UCSD Chancellor’s Award for Research Excellence, and Genome All Star, Smithsonian Foundation and Laboratory Automation awards. Subramaniam received a Ph.D. in Chemistry in 1982 from the Indian Institute of Technology.

Selected Publications:

Google Scholar Publications


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