Subramaniam’s research is focused on systems biology (i.e. computational and mathematical modeling of biological systems) and systems medicine (an interdisciplinary approach at looking systems of the body as part of an integrated whole). His laboratory focuses on understanding mechanisms, reconstructing networks, building quantitative models and predicting phenotypes in mammalian systems. Areas of recent focus include quantitative transcriptomics (the sum of an organism’s RNA transcripts), neuropathology (i.e. Duchenne Muscular Dystrophy and Alzheimer’s disease), skeletal muscle myopathies, liver regeneration and pathologies, stress and endothelial physiology, and systems vaccinology. His laboratory is interested in mapping the circuitry of cells to mechanisms and phenotypes in physiology and pathology and in developing quantitative models of cellular pathways.
Subramaniam is the principal investigator on a $12 million, four-year grant from the National Institutes of Health to expand the Metabolomics Workbench, a searchable, interactive repository of data for all research in the field of metabolomics—the study of the small molecules called metabolites that are found within cells and biological systems. “Blood is our first window into human physiology,” said Subramaniam, who is the Joan and Irwin Jacobs Professor of Bioengineering and Systems Biology at UC San Diego. “The next generation of the Workbench will allow us to get a clearer and more complete view of biological systems, rooted in clinical data.”
Subramaniam is supported by 10 federally funded grants and has a large research portfolio. He is also engaged in developing state-of-the-art infrastructure for bioinformatics and systems biology. The Molecule Pages Database developed by him 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 Metabolomics Workbench is the internationally recognized resource which is a one-stop infrastructure for all researchers in metabolism and systems biology.
Areas of Expertise (7)
Gene Expression and Regulation
Genetics and Genomics
Appointed as a Distinguished Professor
Appointed as a Distinguished Scientist
2011 - San Diego Supercomputer Center
Faculty Excellence in Research Award
2008 - UC San Diego
Genome Technology All Star Award
Indian Institute of Technology: Ph.D., Chemistry 1992
- Fellow - American Institute for Medical and Biological Engineering (AIMBE)
- External Advisory Board - Johns Hopkins U.
- External Advisory Board - Case Western Reserve U.
- External Advisory Board - U. Penn
- External Advisory Board - Georgia Tech
- External Advisory Board - Rice U.
- External Advisory Board - UT Austin
Media Appearances (4)
UCSD Researchers Led by Shankar Subramaniam Receive $12M Grant to Study Human Metabolism
India West online
Researchers at U.C. San Diego, led by the university’s Jacobs School of Engineering bioengineering professor Shankar Subramaniam, have been provided a sizeable grant from the National Institutes of Health to further research on human metabolism.
Nonalcoholic liver diseases focus of new UCSD center
The San Diego Union-Tribune online
Other UCSD members include Dr. David Brenner, MD, dean of the School of Medicine; Larry Smarr, founding director of California Institute for Telecommunications and Information Technology; and Shankar Subramaniam, a bioengineering professor at the Jacobs School of Engineering.
UC San Diego Launches New Nonalcoholic Fatty Liver Disease Research Center
UC San Diego Health Newsroom online
UC San Diego researchers and colleagues elsewhere are also investigating the use of low-cost ultrasound diagnostics and biomarkers based upon metabolomics – the chemical fingerprints left by specific cellular processes – and microbiomics, specifically analyses of stool samples to predict NASH and hepatic fibrosis, the accumulation of scar tissue resulting from chronic liver disease.
Why flu shot is less effective for elderly
The San Diego Union-Tribune online
These differences could be used to determine in advance how effective the vaccine is likely to be, said UCSD's Shankar Subramaniam, a co-senior author of the paper with Emory's Bali Pulendran. The first author was Helder I. Nakaya, also of Emory. Moreover, it may be possible to reverse-engineer the immune differences to develop varieties of flu vaccine better attuned to provoking the immune system of older people into making more powerful antibodies to flu viruses, Subramaniam said.
A direct comparison of particle-resolved and point-particle methods in decaying turbulenceJournal of Fluid Mechanics
M Mehrabadi, JAK Horwitz, S Subramaniam, A Mani
2018 We use particle-resolved direct numerical simulation (PR-DNS) as a model-free physics-based numerical approach to validate particle acceleration modelling in gas-solid suspensions.
Rheological transition in simple shear of moderately dense assemblies of dry cohesive granulesPhysical Review E
Eric Murphy, Sriram Sundararajan, Shankar Subramaniam
2018 The rheology of homogeneous cohesive granular assemblies under shear at moderate volume fractions is investigated using the discrete element method for both frictionless and frictional granules. A transition in rheology from inertial to quasistatic scaling is observed at volume fractions below the jamming point of noncohesive systems, which is a function of the granular temperature, energy dissipation, and cohesive potential. The transition is found to be the result of growing clusters, which eventually percolate the domain, and change the mode of momentum transport in the system.
Investigation and quantification of flow unsteadiness in shock-particle cloud interactionInternational Journal of Multiphase Flow
Zahra Hosseinzadeh-Nik, Shankar Subramaniam, Jonathan D Regele
2018 This work aims to study the interaction of a shock wave with a cloud of particles to quantify flow unsteadiness and velocity fluctuations using particle-resolved direct numerical simulation (PR-DNS). Three cases are studied, with each case revealing one aspect of the intricate flow phenomena involved in this interaction. The unsteady interaction of a shock wave with a transverse array of particles reveals the origin of unsteadiness under the effect of mutual wave-wave and wave-wake interactions between the particles.
Mechanism of kinetic energy transfer in homogeneous bidisperse gas-solid flow and its implications for segregationPhysics of Fluids
Mohammad Mehrabadi, Shankar Subramaniam
2017 Most gas–solid flows encountered in nature and industrial applications are polydisperse, and the segregation or mixing of particle classes in polydisperse gas–solid flows is a phenomenon of great practical importance. A statistically homogeneous gas–solid flow with a bidisperse distribution (in size or density) of particles is a canonical representation of polydisperse flows.
Binary collision outcomes for inelastic soft-sphere models with cohesionPowder Technology
Eric Murphy, Shankar Subramaniam
2017 We present an in-depth study on the restitution coefficient and sticking behavior of two models commonly used in the Discrete Element Method (DEM) community for simulating fine cohesive powders. The cohesion in this study is the result of the van der Waals force which is added to commonly used contact force models. We obtain a collapse of the restitution behavior depending on four independent non-dimensional variables governing the dynamics of the system, and a quantitative model for the restitution behavior is presented.