 | T. M. MuraliProfessor
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Research Interests
T. M. Murali is a professor in the Department of Computer Science at Virginia Tech. He co-directs the ICTAS Center for Systems Biology of Engineered Tissues and is the associate director of the Computational Tissue Engineering interdiscplinary graduate education programme. He is also affiliated with the Genetics, Bioinformatics and Computational Biology graduate programme. Murali's research group develops phenomenological and predictive models dealing with the function, behaviour, and properties of large-scale molecular interaction networks in the cell. He received his undergraduate degree in computer science from the Indian Institute of Technology, Madras and his Sc. M. and Ph. D. degrees from Brown University.
Computational Systems Biology Research GroupURL: http://bioinformatics.cs.vt.edu/~murali/research.html 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.
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
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.
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.
2010
Lasher, C. D., C. L. Poirel, and T. M. Murali,
"Networks in Computational Systems Biology",
Problem Solving Handbook in Computational Biology and Bioinformatics, second edition: Springer-Verlag, 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
Murali, T. M., and S. Aluru,
"Computational Systems Biology",
Algorithms and Theory of Computation Handbook, second edition: Chapman & Hall/CRC Press, 2009.
Kim, Y., C. D. Lasher, L. Milford, T. M. Murali, and P. Rajagopalan,
"A Comparative Study of Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures",
American Institute of Chemical Engineers (AIChE) Annual Meeting, 11/2009.
Kidane, Y., T. M. Murali, and O. Crasta,
"Cross-conditional Analysis of Host Response to Pathogen Infection",
17th Annual International Conference on Intelligent Systems for Molecular Biology, 06/2009.
2008
Murali, T. M., and C. G. Rivera,
"Network Legos: Building Blocks of Cellular Wiring Diagrams",
Journal of Computational Biology, 2008.
Z. Ruscio, J., D. Kumar, M. Shukla, M. G. Prisant, T. M. Murali, and A. Onufriev,
"Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin",
Proceedings of the National Academy of Sciences, vol. 105, no. 27, pp. 9204-9209, 2008.
Abstract
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.
Jin, Y., T. M. Murali, and N. Ramakrishnan,
"Compositional Mining of Multirelational Biological Datasets",
ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, 03/2008.
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.
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.",
Comp Funct Genomics, pp. 60964, 2007.
Abstract
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
Li, P. H., 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 [Co2] in the Field",
Plant Molecular Biology, vol. 62, pp. pp. 593-609, 2006.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali,
"XcisClique: Analysis of Regulatory Bicliques",
BMC Bioinformatics, vol. 7, pp. 14 pages in main article; plus 16 pages in 7 additional files, 2006.
2005
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali,
"XcisClique: Analyzing Regulatory Bicliques in Arabidopsis thaliana (Poster)",
8th Annual Conference on Computational Genomics , Cambridge, MA,, 11/2005.
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
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.
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.
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.
Please see projects at: https://bioinformatics.cs.vt.edu/~murali/
ABI Innovation: Bridging the Gap Between the Transcriptome and the Protemome to Study Inter-Cellular Signaling
Granting Institution: National Science Foundation
Amount: $1,102,996
AF: Small: Collaborative Research: Cell Signaling Hypergraphs: Alogrithms and Applications
Granting Institution: NSF
Amount: $287,993.00
Gene Ontology terms and Automated Annotaion for Energy-related Microbial Genomies
Granting Institution: Dept. of Energy
Amount: $1,142,453
GraphCrowd:Using Crowdsourced Design to Visualize Effects of Environmental Chemicals on Signaling Networks
Granting Institution: National Cancer Institute
Amount: $626,159
Integrating Top-Down and Bottom-Up Models in Systems Biology with Applications to Cell Cycle Conrol in Budding Yeast
Granting Institution: National Institutes of Health
Amount: $2,792,278
Microbial ENergy processes Gene Ontology Project
Granting Institution: Department of Energy
Amount: $1,150,000
Multi Scale Modeling of Toxicant Responses in Engineered Liver Mimics
Granting Institution: US EPA
Amount: $750,000
Transcriptional Signatures of 3D Liver Mimetic Architectures
Granting Institution: National Science Foundation
Amount: $304,681