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Nagiza Samatova PhD: Mathematics, Computing Center of Russian Academy of Sciences (CCAS), Russia Oak Ridge National Laboratory |
Keywords:
Bioinformatics, functional genomics and proteomics, protein-protein interactions, protein docking, mass spec data analysis, data mining, data integration, algorithms, graph theory, parallel and distributed computing
Research Area:
Description of Research:
(a) Characterization of protein machines. This effort focuses the development and application of bioinformatics tools for discovery and characterization of molecular machines in microbial genomes. The work has two primary objectives: 1) to develop high-performance computational tools for high-throughput discovery and characterization of protein-protein complexes through utilizing knowledge discovery from diverse biological data sets, and 2) to apply these tools, in conjunction with experimental data, to the Synechococcus proteome to aid discovery and functional annotation of its protein complexes. Our approach involves: 1) developing “knowledge fusion” algorithms that combine many sources of experimental, genomic and structural information in a systematic way, 2) coupling these algorithms with modeling and simulation methods, 3) implementing high performance, optimized versions of our algorithms. Specifically algorithms for three interrelated problems are investigated: 1) identification of pair-wise protein interactions, 2) construction of protein-protein interaction maps, and 3) functional characterization of the identified complexes.
(b) Systematic studies of functional mechanisms of molecular machines through utilization of high-throughput biological data. Towards this vision, we are developing data analysis and modeling tools for comprehensive characterization of functional sites in biomolecular machines, especially proteins and protein complexes. We design novel algorithms for recognition of functional sites in biomolecular machines that incorporate diverse high-throughput biological data. This computational capability will permit to answer the question of “where” the interaction between biomolecules occurs in order to carry out a given function. The next more important questions are “how to understand the functional mechanisms governing these interactions” and “how to reduce the search space for possible site-specific mutations.” To address them we develop a computational mutagenesis methodology.
(c) National Bioforensics Encyclopedia: We develop a securely accessible, well-integrated, curated information repository of all data pertinent to a forensic investigation of a chemical or biological terrorist attack. The availability of such a resource will provide analysts and scientists with efficient, timely access to the information needed to accomplish such tasks as locating relevant experts, determining an optimal order of appropriate forensic tests, and comparing the “signature” of the current attack to previous ones. Much of the information required for this repository is scattered across multiple institutions and in multiple formats, is currently being generated, or is proposed as part of new research efforts. Without effective integration and curation, the data is of limited availability and use in a crisis. Despite this type of repository being of great interest to several agencies, including the FBI, there is no existing system that focuses appropriately on the unique aspects of chem/bio forensics.
Selected Publications (of 21):
- B.-H. Park, R. Munavalli, A. Geist, and N. Samatova (2004). Protein Interface Site Prediction from Separated Data Spaces. SIAM International Conference on Data Mining.
- G.-X. Yu, A. Geist, G. Ostrouchov, and N. F. Samatova (2003). An SVM-based Algorithm for Identification of Photosynthesis-Specific Genomes Features. Proceedings of the IEEE Bioinformatics Conference. 235-243.
- B.-H. Park, G. Ostrouchov, G.-X. Yu, A. Geist, A. Gorin, and N. Samatova (2003). Inference of Protein-Protein Interactions by Unlikely Profile Pair. Proceedings of the Third IEEE International Conference on Data Mining,.
- G.-X. Yu, A. Geist, G. Ostrouchov, and N. F. Samatova (2003). KeyGeneMiner for Identification of Biochemical Process-specific Genes. Bioinformatics.
- Heffelfinger, G., Martino, A., Gorin, A., Xu, Y., Rintoul, M. D., Geist, A., Al-Hashimi, M. A., Davidson, G. S., Loup Faulon, J., Frink, L. J., Haaland, D. M., Hart, W. E., Jakobsson, E., Lane, T., Li, M., Locascio, P., Olken, F., Olman, V., Palenik, B., Plimpton, S. J., Roe, D. C., Samatova, N. F., Shah, M., Shoshoni, A., Strauss, C. E. M., Thomas, E. V., Timlin, J. A., and D. Xu (2002). Carbon Sequestration in Synechococcus Sp.: From molecular machines to hierarchical modeling.. OMICS A Journal of Integrative Biology. (6): 305-329.