Systems Biology, Bioengineering and Medicine – Perspectives and Challenges

Biomedical Engineering Distinguished Lecturer Series sponsored by Stradling Yocca Carlson & Rauth

Speaker:  Chair and Professor Shankar Subramaniam, Ph.D.

UC San Diego

Host: William J. Link Professor and Chair Abe P. Lee, Ph.D.



A survey of all papers that refer to systems biology research over the past decade shows three striking trends. The first is one where “gene expression” studies form the core of the Systems Biology claims, the second is one where Systems Biology is treated synonymously with computational analysis of microbial or yeast systems and the third is characterized as “interactome” research where either through methods such as yeast two-hybrid or through computational “guilt-by-homology” analysis, large protein-protein interaction maps are drawn. The computational systems biologists who are data driven are reluctant to venture into mammalian systems biology since it is neither apparently elegant nor is the biology simple to master. The absence of data also makes entering into this area a more risky proposition. Experimental biologists working on complex eukaryotes, especially mammalian systems, on the other hand, would like to embrace the systems biology paradigm, but find it difficult to attract “card-carrying” systems biologists because of the significant challenges in eukaryotic systems biology.  

In this talk, I will pose the challenges systems biology and medicine research faces with examples and highlight the progress through examples from my laboratory. One example deals with characterizing the parts list of the germ layers during embryonic development using a novel RNA seq methodology. Another example deals with a systems approach to insulin resistance.  Cellular and tissue defects associated with insulin resistance are coincident with transcriptional abnormalities and are improved after insulin sensitization with thiazolidinedione (TZD) PPAR_ ligands. Based on study of human subjects we have identified molecular and functional characteristics of insulin resistant subjects and distinctions between TZD treatment responder and non-responder subjects. Our study towards deciphering responder-non-responder effects in Insulin Resistance at the systemic level serves as a paradigm for pharmacological studies in human subjects. A third example will address a systems approach to muscle pathophysiology.

*Supported by funding from the National Institutes of Health and the National Science Foundation


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.