Shankar Subramaniam, Ph.D.


Shankar Subramaniam is a Distinguished Professor of Bioengineering, Computer Science and Engineering, Cellular and Molecular Medicine and Nano Engineering. He was recently the Chair of the Bioengineering Department at the University of California at San Diego (2008-13). He holds the inaugural Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology. He was the Founding Director of the Bioinformatics Graduate Program at the University of California at San Diego. He also has adjunct Professorships at the Salk Institute for Biological Studies and the San Diego Supercomputer Center. He is also a Professor at the Center for Cardiovascular Bioinformatics and Modeling at Johns Hopkins University and was a Guest Professor at the Center for Molecular Biology and Neuroscience at the University of Oslo in Norway. Prior to moving to UC San Diego, Dr. Subramaniam was a Professor of Biophysics, Biochemistry, Molecular and Integrative Physiology, Chemical Engineering and Electrical and Computer Engineering at the University of Illinois at Urbana-Champaign (UIUC). He was the Director of the Bioinformatics and Computational Biology Program at the National Center for Supercomputing Applications and the Co-Director of the W.M. Keck Center for Comparative and Functional Genomics at UIUC. He is a fellow of the American Institute for Medical and Biological Engineering (AIMBE) and is a recipient of Smithsonian Foundation and Association of Laboratory Automation Awards and his research work is described below. In 2013 he was elected as a Fellow of AAAS. In 2002 he received the Genome Technology All Star Award. In 2008 he was awarded the Faculty Excellence in Research Award at the University of California at San Diego. In 2011 he was appointed as a Distinguished Scientist at the San Diego Supercomputer Center. In 2014 he was appointed as a Distinguished Professor. His research spans several areas of bioinformatics and systems biology.

Subramaniam has played a key role in raising national awareness for training and research in bioinformatics. He served as a member of the National Institute for Health (NIH) Director’s Advisory Committee on Bioinformatics, which resulted in the BIOMEDICAL INFORMATION SCIENCE AND TECHNOLOGY INITIATIVE (BISTI) report. The report recognized the dire need for trained professionals in Bioinformatics and recommended the launching of a strong NIH funding initiative. Dr. Subramaniam served as the Chair of a NIH BISTI Study Section. Dr. Subramaniam has also served on Bioinformatics and Biotechnology Advisory Councils for Virginia Tech, the University of Illinois at Chicago, and on the Scientific Advisory Board of several Biotech and Bioinformatics Companies. Dr. Subramaniam has served as a member of the State of Illinois Governor’s initiative in Biotechnology and an advisor and reviewer of the State of North Carolina initiative in Biotechnology. He is currently an overseas advisor for the Department of Biotechnology of the Government of India, and a member of a European Science Foundation Panel. In 2012, he was elected as the Chair of the College of Fellows of AIMBE. He serves on the External Advisory Boards for several Bio/Biomedical Engineering Departments including Johns Hopkins U., Case Western Reserve U., U. Penn, Georgia Tech, Rice U. and UT Austin.


Research in 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 recent work on systems medicine involves diseases of the skeletal muscle, liver and the immune system. 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.

He 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 cu ration has led to the Molecule Pages Database that provides comprehensive information on all known functional states of signaling molecules. The LIPID MAPS 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. He was recently awarded the NIH Data Coordination Center for Metabolomics of the Common Funds Initiative. For a list of resources, see,

Subramaniam laboratory is funded by grants from NIGMS, NHLBI, NIAID and NIDDK in the National Institutes of Health and the National Science Foundation.