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Shankar Subramaniam
Bioinformatics and computational biology
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| Contact Information |
| Office: EBU1 5406 |
| Phone: (858) 822-0986 |
| Fax: (858) 822-3752 |
| Email: shsubramaniam@ucsd.edu |
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| Education and Appointments |
| 1982 |
Ph.D., Indian Institute of Technology
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| 1972 |
B.Sc., Osmania Univeristy
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| Awards and Academic Honors |
| 1999 |
Elected Fellow, Institute for Biomedical Engineering |
| 1999 |
Appointed to faculty, Bioengineering, and adjunct faculty, Chemistry and Biochemistry |
| 1991-1999 |
Appointed to faculty, University of Illinois at Urbana-Champaign |
| 1990 |
Visiting Scientist, Princeton University and Senior Research Scientists, Squibb Institute for Med. Research |
| 1986-1990 |
Asst. Director Scientific Development and Visiting Assistant Prof. of Chemistry, University of Houston |
| 1974-1976 |
Council of Scientific and Industrial Research Fellowship |
| 1972-1974 |
Indian National Merit Scholarship |
| Research Interests |
The major mandate of genome research is to identify all the coding protein sequences, understand their function and perhaps their association with molecular diseases. Even if the steps towards this task can be outlined, they are not easily accomplished. First, it is necessary to identify all the genes. Then, the structure and function of all the gene products are to be discovered. And finally the role of the gene product in a functional pathway and its role in the functioning of the organism have to be deciphered.
The human genome alone is estimated to contain 3 billion base pairs coding for about 100,000 proteins. Myriad species have comparable genome sizes. Understanding how genomes work requires sophisticated computer-based information handling tools - bioinformatics - and new high throughput technologies for understanding the function of genes on a genome-wide scale (functional genomics). Due to the complexity of this new paradigm in biology, i.e., understanding the organization, evolution and function of whole genomes rather than single genes, entirely new sets of tools and human resources will be necessary. Thus, future developments in genomics, and the applications that derive from genomics, will be dependent upon the scientific progress at the interface of three major disciplines; biology, engineering, and computer science.
My laboratory works in this interdisciplinary area of bioinformatics. Bioinformatics characterizes the flow of information in living systems.
The flow of information in living systems is Genome->Gene Products->Function->Pathways. Our laboratory is associated with specific projects in these areas.
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| Selected Publications |
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Knowledge-based potentials for protein structure. With A. Rojnuckarin. Proteins - Structure, Function and Genetics. 36, 54 (1999).
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A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. With R. Ramarathnam. Microbial and Comparative Genomics. 5, 1 (2000).
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The Molecule Pages database. With J. Li, Y. Ning, W. Hedley, B. Saunders, Y. Chen, N. Tindill, and T. Hannay. Nature 420, 716 (2002).
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Protein Local Structure Prediction from Sequence. With C.G. Hunter. Proteins: Structure, Function and Genetics. 50, 572 (2003).
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Conservation of Electrostatic Properties within Enzyme Families and Superfamilies. With D.R. Livesay, P. Jambeck, and A. Rojnuckarin. Biochemistry. 42, 3464 (2003).
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Sequence-Function Analysis of the K+-Selective Family of Ion Channels Using a Comprehensive Alignment and the KcsA Channel Structure. With R.T. Shealy, A.D. Murphy, R. Ramarathnam, E. Jakobsson. Biophys. J. 84, 1 (2003).
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