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Shankar Subramaniam, Ph.D.

AIMBE College of Fellows Class of 2000
For innovative research on modeling protein homology and molecular recognition, and contributions to the definition and advancement of bioinformatics.

Bioinformatics Breakthrough: High Quality Transcriptome from as Few as Fifty Cells

Via UC San Diego | October 24, 2013

Bioengineers from the University of California, San Diego have created a new method for analyzing RNA transcripts from samples of 50 to 100 cells. The approach could be used to develop inexpensive and rapid methods for diagnosing cancers at early stages, as well as better tools for forensics, drug discovery and developmental biology.

The protocols, which were published in April 2013 in the journal Nature Scientific Reports, are now being applied to a wide range of biological and medical research questions from brain cancer, to liver function and stem cell biology.

The approach from the UC San Diego bioengineers is called Designed Primer-based RNA sequencing or “DP-seq.” It’s a new tool for generating comprehensive snapshots of RNA — the “transcriptome” — collected from as little as 50 picograms of RNA. Analysis of the transcriptome provides insights into what biological processes are occurring at a specific moment in time. RNA transcripts serve as a proxy for which genes are being expressed and at what levels.

“In the months since we published the DP-seq protocol, there has been tremendous interest from the scientific community,” said Shankar Subramaniam a bioengineering professor at the UC San Diego Jacobs School of Engineering and the corresponding author on the paper. “When you are not restricted to samples of thousands of cells, there are so many more system-wide gene expression questions you can ask, and answer,” said Subramaniam. Questions like: What transcription factors will determine cell fates, such as cancer versus normal? and what pathways are likely to be activated in a tissue upon treatment with a drug?

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New Way of Fighting High Cholesterol Upends Assumptions

Via UC San Diego | September 27, 2012

Atherosclerosis – the hardening of arteries that is a primary cause of cardiovascular disease and death – has long been presumed to be the fateful consequence of complicated interactions between overabundant cholesterol and resulting inflammation in the heart and blood vessels.

However, researchers at the University of California, San Diego School of Medicine and the Jacobs School of Engineering, with colleagues at institutions across the country, say the relationship is not exactly what it appears, and that a precursor to cholesterol actually suppresses inflammatory response genes. This precursor molecule could provide a new target for drugs designed to treat atherosclerosis, which kills tens of thousands of Americans annually.

The findings are published in the September 28, 2012 issue of Cell…

… The systems biology approach that identified the lipid molecules came from analysis of the vast amounts of data from the transcriptome and metabolome. “The interaction between researchers in medicine and engineering has the potential to lead to such discoveries and is the future,” said Shankar Subramaniam, professor and chair in the Department of Bioengineering, who is also a senior co-author in this paper. Subramanian was recently awarded a $6 million grant by the National Institutes of Health to accelerate the study of “metabolomics,” an emerging field of biomedical research that could transform how doctor’s assess patient health and diagnose disease.

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With $6M Grant, UC San Diego Bioengineers Take On Key Role in New NIH Common Funds Metabolomics Program

Via UC San Diego | September 21, 2012

With a $6 million grant over five years, bioengineers from the University of California, San Diego will play a central role in a new program from theNational Institutes of Health (NIH) to accelerate “metabolomics”, an emerging field of biomedical research that offers a path to a wealth of information about a person’s nutrition, infection, health, disease status and more. In addition to powerful tools for diagnosis and disease follow-up, metabolomics technologies will transform researchers’ ability to define the mechanisms underlying disease, such as diabetes and obesity, and to develop new strategies for treatment.

Metabolomics is the study of small molecules called metabolites, found within cells and biological systems. Metabolites are produced or consumed in the chemical reactions that take place in the body to sustain life. The sum of all metabolites at any given moment — the metabolome — is a form of chemical readout of the state of health of the cell or body. One of the expected outcomes of this project is the ability to “metabo-type” individuals in order to get a detailed picture of their current metabolite profile, and recognize problems such as insulin resistance at an early stage. The effects of interventions such as changes in diet and exercise as well as pharmaceuticals could then be seen in updated metabo-type readings.

Shankar Subramaniam, professor and chair of the Department of Bioengineering at the UC San Diego Jacobs School of Engineering leads the metabolomics effort at UC San Diego, which involves coordinating the research cores and running the metabolome project’s Data Repository and Coordination Center (DRCC).

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Shankar Subramaniam Named Distinguished Scientist at the San Diego Supercomputer Center

Via UC San Diego | June 7, 2010

Shankar Subramaniam has been named a Distinguished Scientist at the San Diego Supercomputer Center (SDSC), to assist the Organized Research Unit of the University of California, San Diego, in identifying new opportunities and solutions in the area of bioinformatics. Subramaniam’s appointment is effective June 1, 2010.

Subramaniam, a professor of bioengineering, chemistry and biochemistry, cellular and molecular medicine and nano engineering, is currently Chair of UC San Diego’s Bioengineering Department. He holds the inaugural Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology, and was the founding director of the Bioinformatics Graduate Program at the university, participating in campus-wide recruitment of leading researchers in systems biology.

“All of us at SDSC look forward to working with Dr. Subramaniam in his new role as a Distinguished Scientist,” said Michael L. Norman, SDSC’s interim director. “As a true pioneer in bioinformatics and systems biology, Dr. Subramaniam is uniquely qualified to identify new opportunities and propose innovative solutions as SDSC broadens its expertise in these exciting areas of scientific research.”

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