Computational Systems Biology Research Group

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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.
2008
Murali T M., Rivera C.G., "Network Legos: Building Blocks of Cellular Wiring Diagrams", Journal of Computational Biology, 2008. Tagged BibTex xml
Dyer M D., Murali T M., Sobral B W., "The landscape of human proteins interacting with viruses and other pathogens.", PLoS Pathog, vol. 4, no. 2, pp. e32, 2008. Abstract Tagged BibTex xml
Jin Y., Murali T M., Ramakrishnan N., "Compositional Mining of Multi-relational Biological Datasets", ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, March, 2008. Tagged BibTex xml
2007
Dyer M.D., Murali T M., Sobral B.W., "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 Tagged BibTex xml
Murali T M., Rivera C.G., "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. Tagged BibTex xml
Shoja V., Murali T M., Zhang L., "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse", Comparative and Functional Genomics, vol. 2007, pp. Article ID 60964, 8 pages, 2007. Tagged BibTex xml
2006
Murali T M., Wu C., Kasif S., "The Art of Gene Function Prediction", Nature Biotechnology, vol. 12, pp. 1474–1475, 2006. Tagged BibTex xml
Grothaus G., Mufti A., Murali T M., "Automatic Layout and Visualisation of Biclusters", Algorithms in Molecular Biology, pp. 15, 2006. Tagged BibTex xml
Li P., Sioson A., Mane S P., Ulanov A., Grothaus G., Heath L S., Murali T M., Bohnert H J., Grene R., "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 Tagged BibTex xml
Massjouni N., Rivera C., Murali T M., "VIRGO: Computational Prediction of Gene Functions", Nucleic Acids Research, vol. 34, pp. W340–W344, 2006. Tagged BibTex xml
Pati A., Vasquez-Robinet C., Heath L S., Grene R., Murali T M., "XcisClique: Analysis of regulatory bicliques.", BMC Bioinformatics, vol. 7, no. 1, pp. 218, 2006. Abstract Tagged BibTex xml
2004
Wu C., Fu Y., Murali T M., Kasif S., "Gene Expression Module Discovery Using Gibbs Sampling", Genome Informatics, vol. 15, no. 1, pp. 239–248, 2004. Tagged BibTex xml
Karaoz U., Murali T M., Letovsky S., Zheng Y., Ding C., Cantor C.R., Kasif S., "Whole genome annotation using evidence integration in functional linkage networks", Proceedings of the National Academy of Sciences, pp. 2888–2893, 2004. Tagged BibTex xml
2003
Murali T M., Kasif S., "Extracting Conserved Gene Expression Motifs from Gene Expression Data", Proceedings of the Pacific Symposium on Biocomputing, pp. 77–88, 2003. Tagged BibTex xml
Su Y., Murali T M., Pavlovic V., Schaffer M., Kasif S., "RankGene: identification of diagnostic genes based on expression data.", Bioinformatics, vol. 19, no. 12, pp. 1578–9, 2003. Tagged BibTex xml
2002
Procopiuc C., Jones M., Agarwal P.K., Murali T M., "A Monte Carlo algorithm for fast projective clustering", Proceedings of the 2002 ACM SIGMOD International Conference on Management of Data, pp. 418-427, 2002. Tagged BibTex xml
Efrat A., Guibas L.J., Har-Peled S., Mitchell J.S B., Murali T M., "New Similarity Measures between Polylines with Applications to Morphing and Polygon Sweeping", Discrete & Computational Geometry, vol. 28, no. 4, pp. 535-569, 2002. Tagged BibTex xml
2001
Efrat A., Har-Peled S., Guibas L.J., Murali T M., "Morphing between polylines", Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 680-689, 2001. Tagged BibTex xml
2000
Efrat A., Guibas L.J., Har-Peled S., Lin D.C., Mitchell J.S B., Murali T M., "Sweeping simple polygons with a chain of guards", Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 927-936, 2000. Tagged BibTex xml
Agarwal P.K., Guibas L.J., Murali T M., Vitter J., "Cylindrical static and kinetic binary space partitions", Computational Geometry: Theory and Applications, vol. 16, no. 2, pp. 103-127, 2000. Tagged BibTex xml
Agarwal P.K., Grove E.F., Murali T M., Vitter J., "Binary Space Partitions for Fat Rectangles", SIAM J. Comput., vol. 29, no. 5, pp. 1422-1448, 2000. Tagged BibTex xml
1999
Gonzalez-Banos H., Mao E., Latombe J C., Murali T M., Efrat A., "Planning robot motion strategies for efficient model construction", Proceedings of the 9th International Symposium on Robotics Research, pp. 345–352, 1999. Tagged BibTex xml
Grove E.F., Murali T M., Vitter J., "The Object Complexity Model for Hidden-Surface Removal", Int. J. Comput. Geometry Appl., vol. 9, no. 2, pp. 207-217, 1999. Tagged BibTex xml
1998
Murali T M., Agarwal P.K., Vitter J., "Constructing Binary Space Partitions for Orthogonal Rectabgles in Practice", Lecture Notes in Computer Science, vol. 1461: Springer-Verlag, pp. 211-222, 1998. Tagged BibTex xml
Murali T M., Efficient Hidden-Surface Removal in Theory and in Practice, : Department of Computer Science, Brown University, June, 1998. Tagged BibTex xml
Agarwal P.K., Arge L., Murali T M., Varadarajan K.R., Vitter J., "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. Tagged BibTex xml
1997
Agarwal P.K., Guibas L.J., Murali T M., Vitter J., "Cylindrical Static and Kinetic Binary Space Partitions", Proceedings of the 13th Annual ACM Symposium on Computational Geometry, pp. 39-48, 1997. Tagged BibTex xml
Agarwal P.K., Murali T M., Vitter J., "Practical Techniques for Constructing Binary Space Partitions for Orthogonal Rectangles", Proceedings of the 13th Annual ACM Symposium on Computational Geometry, pp. 382-384, 1997. Tagged BibTex xml
Murali T M., Funkhouser T.A., "Consistent Solid and Boundary Representations from Arbitrary Polygonal Data", Proceedings of the 1997 Symposium on Interactive 3D Graphics, pp. 155-162, 196, 1997. Tagged BibTex xml
1996
Agarwal P.K., Grove E.F., Murali T M., Vitter J., "Binary Search Partitions for Fat Rectangles", Proceedings of the 37th IEEE Annual Symposium on Foundations of Computer Science, pp. 482-491, 1996. Tagged BibTex xml
1995
Grove E.F., Murali T M., Vitter J., "The Object Complexity Model for Hidden-Surface Elimination", Proc. 7th Canad. Conf. Comput. Geom., pp. 273–278, 1995. Tagged BibTex xml