Computational Systems Biology Research Group

URL: http://bioinformatics.cs.vt.edu/~murali/research.html

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.
2013
Poirel, C. L., A. Rahman, R. R. Rodrigues, A. Krishnan, J. R. Addesa, and T. M. Murali, "Reconciling differential gene expression data with molecular interaction networks", Bioinformatics, vol. 29, issue 5, pp. 622 - 629, 03/2013.
Kidane, Y. H., C. Lawrence, and T. M. Murali, "The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Bacterial Pathogens: Towards Host-Oriented Broad-Spectrum Drug Targets", PLoS ONE, vol. 8, issue 3, pp. e58553, 3/2013.
2012
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
Rivera, C., B. M. Tyler, and T. M. Murali, "Sensitive detection of pathway perturbations in cancers", BMC Bioinformatics, vol. 13, no. Suppl 3, pp. S9+, 2012.
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.
2011
Lasher, C. D., P. Rajagopalan, and T. M. Murali, "Discovering networks of perturbed biological processes in hepatocyte cultures.", PLoS one, vol. 6, no. 1, 2011.
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.
2010
Zhang, J., L. T. Watson, C. A. Beattie, and Y. Cao, "Radial basis function collocation for the chemical master equation", Internat. J. Comput. Methods, vol. 7, pp. 477-498, 2010.
2009
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
2008
Panning, T. D., L. T. Watson, N. A. Allen, K. C. Chen, C. A. Shaffer, and J. J. Tyson, "Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle", Journal of Global Optimization, vol. 40, no. 4, Hingham, MA, USA, Kluwer Academic Publishers, pp. 719–738, 2008.
Murali, T. M., and C. G. Rivera, "Network Legos: Building Blocks of Cellular Wiring Diagrams", Journal of Computational Biology, 2008.
Dyer, M. D., T. M. Murali, and B. W. Sobral, "The landscape of human proteins interacting with viruses and other pathogens.", PLoS Pathog, vol. 4, no. 2, pp. e32, 2008. Abstract
Jin, Y., T. M. Murali, and N. Ramakrishnan, "Compositional Mining of Multi-relational Biological Datasets", ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, March, 2008.
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. dyermd@vbi.vt.edu, 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.
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.
2006
Murali, T. M., C. - J. Wu, and S. Kasif, "The Art of Gene Function Prediction", Nature Biotechnology, vol. 12, pp. 1474–1475, 2006.
Grothaus, G., A. Mufti, and T. M. Murali, "Automatic Layout and Visualisation of Biclusters", Algorithms in Molecular Biology, pp. 15, 2006.
Li, P., A. Sioson, S. P. Mane, A. Ulanov, G. Grothaus, L. S. Heath, T. M. Murali, H. J. Bohnert, and R. Grene, "Response diversity of Arabidopsis thaliana ecotypes in elevated CO/2 in the field.", Plant Mol Biol, vol. 62, no. 4-5, pp. 593-609, 2006. Abstract
Massjouni, N., C. Rivera, and T. M. Murali, "VIRGO: Computational Prediction of Gene Functions", Nucleic Acids Research, vol. 34, pp. W340–W344, 2006.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali, "XcisClique: Analysis of regulatory bicliques.", BMC Bioinformatics, vol. 7, no. 1, pp. 218, 2006. Abstract
2004
Wu, C. - J., Y. Fu, T. M. Murali, and S. Kasif, "Gene Expression Module Discovery Using Gibbs Sampling", Genome Informatics, vol. 15, no. 1, pp. 239–248, 2004.
Karaoz, U., T. M. Murali, S. Letovsky, Y. Zheng, C. Ding, C. R. Cantor, and S. Kasif, "Whole genome annotation using evidence integration in functional linkage networks", Proceedings of the National Academy of Sciences, pp. 2888–2893, 2004.
2003
Murali, T. M., and S. Kasif, "Extracting Conserved Gene Expression Motifs from Gene Expression Data", Proceedings of the Pacific Symposium on Biocomputing, pp. 77–88, 2003.
Su, Y., T. M. Murali, V. Pavlovic, M. Schaffer, and S. Kasif, "RankGene: identification of diagnostic genes based on expression data.", Bioinformatics, vol. 19, no. 12, pp. 1578–9, 2003.
2002
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., L. J. Guibas, S. Har-Peled, J. S. B. Mitchell, and T. M. Murali, "New Similarity Measures between Polylines with Applications to Morphing and Polygon Sweeping", Discrete & Computational Geometry, vol. 28, no. 4, pp. 535-569, 2002.
2001
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.
2000
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.
Agarwal, P. K., E. F. Grove, T. M. Murali, and J. S. Vitter, "Binary Space Partitions for Fat Rectangles", SIAM J. Comput., vol. 29, no. 5, pp. 1422-1448, 2000.
1999
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.
1998
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. Arge, T. M. Murali, K. R. Varadarajan, and J. S. Vitter, "I/O-Efficient Algorithms for Contour-line Extraction and Planar Graph Blocking (Extended Abstract)", Proceedings of the 9th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 117-126, 1998.
1997
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.
1996
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.
1995
Grove, E. F., T. M. Murali, and J. S. Vitter, "The Object Complexity Model for Hidden-Surface Elimination", Proc. 7th Canad. Conf. Comput. Geom., pp. 273–278, 1995.