Shankar Subramaniam: Research Interests, Bioinformatics
Bioinformatics: An area of growing interest in modern biology deals with processing of the
myriad information associated with genomics and sequencing. The large volume of data
necessitates involvement of high performance computing as well as data manipulation and
analysis. The Biology Workbench, a seamless biology analysis environment on the world
wide web, (http://biology.ncsa.uiuc.edu), was designed by Subramaniam and developed in
his laboratory. This web-based problem-solving environment for the biologist involves
innovative design of both database federation and wrapping of a large number of sequence
and structure tools into a web-environment. The biology workbench has been released to
the national biology research community, in 1996 and is used by thousands of users each
day. NCSA and SDSC provide the compute server and storage facilities for the community
to use. The biology workbench is also now being mirrored in numerous national
laboratories, international centers and major pharmaceutical companies. Further extensions
of this problem-solving environment include extensions to genomics and automated
macromolecular structure refinement and modeling. A scientific grand challenge which has
emerged from the potential of the biology workbench is the new science called
phylogenomics - the study of comparative genetic organization, function and evolution of
genomes for extant life forms. In collaboration with leading genome scientists,
Subramaniam is working on a) developing and implementing the necessary bioinformatics
tools to perform large-scale phylogenomic analysis, and b) annotating genomes and
delineating gene participation in biochemical pathways.