Computational Systems Biology Research Group


Contact: T. M. Murali

The functioning of a living cell is governed by intricate networks of physical, functional, and regulatory interactions among different types of molecules. The goal of our research is to build phenomenological and predictive models of these networks by developing approaches based on graph theory, data mining, and machine learning. We drive this work through collaborations with computer scientists and with life science researchers spanning diverse fields including biochemistry, infectious diseases, plant pathology, and tissue engineering.

Murali, T. M., "Guest Editor's Introduction: Computationally Driven Experimental Biology", Computer, vol. 45, Los Alamitos, CA, USA, IEEE Computer Society, pp. 22-23, 2012. Abstract
Pu, Y., S. Lee, L. T. Watson, and Y. Cao, "The effect of unhealthy-cells in synchronized insulin secretion", 2012 IEEE Internat. Conf. on Bioinformatics and Biomedicine, Philadelphia, PA, pp. 416--419, 2012.
Rahman, A., C. L. Poirel, D. J. Badger, and T. M. Murali, "Reverse Engineering Molecular Hypergraphs", Proceedings of the ACM Conference on Bioinformatics, Computational Biology, and Biomedicine, Chicago IL, Association for Computing Machinery, 10/2012.
Murali, T. M., M. D. Dyer, D. Badger, B. M. Tyler, and M. G. Katze, "Network-Based Prediction and Analysis of HIV Dependency Factors", PLoS Comput Biol, vol. 7, no. 9: Public Library of Science, pp. e1002164+, 2011.
Dyer, M. D., T. M. Murali, and B. W. Sobral, "Supervised learning and prediction of physical interactions between human and {HIV} proteins.", Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol. 11, no. 5, pp. 917–923, 2011.
Poirel, C. L., C. C. Owens, and T. M. Murali, "Network-based functional enrichment", BMC Bioinformatics, vol. 12, no. Suppl 13, pp. S9+, 2011.
III, C. C. O., T. M. Murali, and N. Ramakrishnan, "Capturing Truthiness: Mining Truth Tables in Binary Datasets", Proceedings of the 24th Annual ACM Symposium on Applied Computing (SAC'09; Data Mining Track): ACM, pp. 1467–1474, March, 2009.
Driscoll, T., M. D. Dyer, T. M. Murali, and B. W. Sobral, "PIG–the pathogen interaction gateway.", Nucleic Acids Res, vol. 37, no. Database issue, pp. D647-50, 2009. Abstract
Shoja, V., T. M. Murali, and L. Zhang, "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse", Comparative and Functional Genomics, vol. 2007, pp. Article ID 60964, 8 pages, 2007.
Dyer, M. D., T. M. Murali, and B. W. Sobral, "Computational prediction of host-pathogen protein-protein interactions.", Bioinformatics, vol. 23, no. 13, Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA., pp. i159-66, 2007. Abstract
Murali, T. M., and C. G. Rivera, "Network Legos: Building Blocks of Cellular Wiring Diagrams", Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 47–61, 2007.
Procopiuc, C. M., M. Jones, P. K. Agarwal, and T. M. Murali, "A Monte Carlo algorithm for fast projective clustering", Proceedings of the 2002 ACM SIGMOD International Conference on Management of Data, pp. 418-427, 2002.
Efrat, A., S. Har-Peled, L. J. Guibas, and T. M. Murali, "Morphing between polylines", Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 680-689, 2001.
Efrat, A., L. J. Guibas, S. Har-Peled, D. C. Lin, J. S. B. Mitchell, and T. M. Murali, "Sweeping simple polygons with a chain of guards", Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 927-936, 2000.
Agarwal, P. K., L. J. Guibas, T. M. Murali, and J. S. Vitter, "Cylindrical static and kinetic binary space partitions", Computational Geometry: Theory and Applications, vol. 16, no. 2, pp. 103-127, 2000.
Gonzalez-Banos, H., E. Mao, J. C. Latombe, T. M. Murali, and A. Efrat, "Planning robot motion strategies for efficient model construction", Proceedings of the 9th International Symposium on Robotics Research, pp. 345–352, 1999.
Grove, E. F., T. M. Murali, and J. S. Vitter, "The Object Complexity Model for Hidden-Surface Removal", Int. J. Comput. Geometry Appl., vol. 9, no. 2, pp. 207-217, 1999.
Murali, T. M., P. K. Agarwal, and J. S. Vitter, "Constructing Binary Space Partitions for Orthogonal Rectabgles in Practice", Lecture Notes in Computer Science, vol. 1461: Springer-Verlag, pp. 211-222, 1998.
Murali, T. M., Efficient Hidden-Surface Removal in Theory and in Practice, : Department of Computer Science, Brown University, June, 1998.
Agarwal, P. K., L. J. Guibas, T. M. Murali, and J. S. Vitter, "Cylindrical Static and Kinetic Binary Space Partitions", Proceedings of the 13th Annual ACM Symposium on Computational Geometry, pp. 39-48, 1997.
Agarwal, P. K., T. M. Murali, and J. S. Vitter, "Practical Techniques for Constructing Binary Space Partitions for Orthogonal Rectangles", Proceedings of the 13th Annual ACM Symposium on Computational Geometry, pp. 382-384, 1997.
Murali, T. M., and T. A. Funkhouser, "Consistent Solid and Boundary Representations from Arbitrary Polygonal Data", Proceedings of the 1997 Symposium on Interactive 3D Graphics, pp. 155-162, 196, 1997.
Agarwal, P. K., E. F. Grove, T. M. Murali, and J. S. Vitter, "Binary Search Partitions for Fat Rectangles", Proceedings of the 37th IEEE Annual Symposium on Foundations of Computer Science, pp. 482-491, 1996.