Shankar Subramaniam, Ph.D.
Distinguished Professor of Bioengineering, Computer Science and Engineering, Cellular and Molecular Medicine, Computer Science and Engineering, Data Science, and Chemical and Nano Engineering
University of California, San Diego
Seminar Information
In this talk, I plan to provide multi-scale clues on multiple – what appear to be distinct – human pathologies and explore the concepts of “whodunit?”. Let us think about a Rube-Goldberg machine (a machine engineered to perform a task through a chain reaction of complex steps), except with multiple inputs and multiple outputs. The analogy of human physiology to such a device is compelling. Akin to the Rube-Goldberg machine, depending on malfunctioning in distinct parts of the machine in response to distinct inputs, human pathology as we define it arises from dysfunction of parts of our “normal” physiology, albeit affects other parts at the systems level.
We have some notions of the “etiology” of these diseases. We observe the “morphological changes” associated with the disease through imaging or other clinical measurements. Sometimes, we investigate associated “mechanisms” and almost always, we examine the “pathological consequences” which may include malady and sometimes death. But in a complex RG machine-like human physiology, are there fundamental design principles that dictate the dysfunctions associated with pathology?
Towards answering this, I plan to provide clues from measurements and analyses in my laboratory, revealing each principle that is common to pathologies. Furthermore, I will provide nuanced insights into mechanistic causality associated with these pathologies, culminating in posing the biggest mystery of all. I hope to provide clues from human development into the final mystery, albeit leaving the ultimate question for all of us to explore further. Our laboratory has worked over the past two decades or more on liver, muscle, brain, and vascular disorders and cancer and immune pathologies and our investigations form the basis of this talk.
Our work over the past decades has been supported by grants from National Institutes of Health (NHLBI, NIDDK, NIA, NCI, NIGMS, NICHD, NIAID, and OD) and from Wellcome-Leap, Wellcome-Trust, and Chan-Zuckerberg Foundations.
Shankar Subramaniam is a Distinguished Professor of Bioengineering, Computer Science and Engineering, Cellular and Molecular Medicine, Computer Science and Engineering, Data Science, and Chemical and Nano Engineering. He holds the inaugural Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology. He was the Chair of the Bioengineering Department at the University of California at San Diego (2008-13). He was the Founding Director of the Bioinformatics Graduate Program at the University of California at San Diego. 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 chaired the Taskforce which led to the creation of a new School of Computing, Information and Data Sciences at UC San Diego.
He is a Fellow of AAAS, IEEE, AIMBE, and IAMBE. In 2002 he received the Genome Technology All Star Award. He is a recipient of Smithsonian Foundation and Association of Laboratory Automation Awards and his research work is described below. In 2019 he was elected as the diamond jubilee distinguished alumni by the Indian Institute of Technology Kanpur. 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. He has served on the External Advisory Boards for several Bio/ Biomedical Engineering Departments including Johns Hopkins U., Case Western Reserve U., U. Penn, Rice U., and UT Austin. He is currently an overseas advisor for the Department of Biotechnology of the Government of India. In 2012, he was elected as the Chair of the College of Fellows of AIMBE. He also serves on the Scientific Advisory Board of Janssen Pharmaceuticals (the research arm of Johnson and Johnson). He has served on the Scientific Councils of NIGMS and NHGRI (NIH Institutes) and as a Chair of three distinct study sections at the National Institutes of Health. Subramaniam has graduated over 80 Ph.D. students who occupy leading academic and industrial positions. He has trained over 100 postdoctoral researchers. His research is funded by the National Institutes of Health, National Science Foundation, the Wellcome Trust, the Wellcome Leap Foundation, the Chan-Zuckerberg Foundation, and the Chen Foundation.
Subramaniam's innovative work has major impact on research and development in academia and industry by allowing the synthesis of complex biological and medical information from genes and molecules into integrated knowledge at cellular and system levels, thus providing important basis for drug discovery and innovation. He was a pioneer in bioinformatics with his development of the Biology Workbench, the first of its kind in web based infrastructures. He has fostered training and research in systems biology and bioinformatics at the national level, serving on the NIH Director’s Advisory Committee on Bioinformatics and played a key role in the formulation of the NIH Director’s Roadmap which places a major emphasis on the use of quantitative approaches of engineering to biomedical research in health and disease. He has been instrumental in raising national awareness of the roles of these engineering approaches to biomedical research. He founded the UCSD Bioinformatics program and was Chair of the nationally top-ranked bioengineering program from 2008-2013. Subramaniam has collaborated with colleagues in clinical medicine to elucidate the molecular and genomic basis of the pathogenesis of diabetes, inflammation, atherosclerosis, cancer, and myopathies by using modern approaches of systems biology and bioinformatics to analyze physiological and pathophysiological data, leading to the development of novel therapeutic measures and drug discovery. His major research efforts focus on cancer and neurodegenerative disorders.
Subramaniam has made innovative contributions at the interface of engineering and medicine. In addition to inventing new methods for analysis of complex systems, he pioneered a novel technology for RNA sequencing with the smallest quantities of RNA leading to our ability to analyze human tissues at the microscale. His work on brain organoids is revolutionizing our understanding of the mechanisms of neurodegenerative diseases. His most recent innovation in triple-negative breast cancer has now led to a Phase II clinical trial.