T. M. Murali's Publications

In my research, I focus on problems in bioinformatics and computational biology. In the past, I have done research in the area of computational geometry, especially on problems motivated by applications in computer graphics, robotics, and geographic information systems. In my Ph.D. thesis, I studied the problem of hidden-surface removal. Here is a list of my publications.
  1. Guest Editorial for the special section of papers presented at the 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
    T. M. Murali
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4), 1036, 2018

  2. Efficient Synthesis of Mutants Using Genetic Crosses    bioRxiv version with proofs
    Aditya Pratapa, Amogh Jalihal, S. S. Ravi, and T. M. Murali
    Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, to appear, 2018.

  3. Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models
    Allison N. Tegge, Richard R. Rodrigues, Adam L. Larkin, Lucas Vu, T. M. Murali, and Padmavathy Rajagopalan
    Scientific Reports, 8, 11306, 2018.

  4. Automating the PathLinker app for Cytoscape
    Li Jun Huang, Jeffrey N. Law, and T. M. Murali
    F1000 Research, 7, 727, 2018

  5. CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
    Aditya Pratapa, Neil Adames, Pavel Kraikivski, John J. Tyson, Jean Peccoud, and T. M. Murali
    Bioinformatics, 34 (13), 2237-2244, 2018

  6. CrowdLayout: Crowdsourced Design and Evaluation of Biological Network Visualizations
    Divit P. Singh, Lee Lisle, T. M. Murali, and Kurt Luther
    2018 ACM Conference on Human Factors in Computing Systems (CHI'18), paper 232, 2018

  7. GraphSpace: Stimulating Interdisciplinary Collaborations in Network Biology
    Aditya Bharadwaj, Divit P. Singh, Anna Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel Kraikivski, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson, and T. M. Murali
    Bioinformatics, 13 (19), 3134-3136, 2017

  8. Pathway Analysis with Signaling Hypergraphs
    Anna Ritz, Brendan N. Avent, and T. M. Murali
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(5), 1042-1055, 2017.

  9. The PathLinker app: Connect the dots in protein interaction networks   Cytoscape app  Code
    Daniel P. Gil, Jeffrey N. Law, and T. M. Murali
    F1000 Research, 6, 58, 2017.

  10. XTalkDB: A Database of Signaling Pathway Crosstalk  XTalkDB
    Sarah Sam, Joelle Teel, Allison N. Tegge, Aditya Bharadwaj, and T. M. Murali
    Nucleic Acids Research, 45 (D1), D432-D439, 2016.

  11. Unstable Communities in Network Ensembles
    Ahsanur Rahman, Steve Jan, Hyunju Kim, B. Aditya Prakash, and T. M. Murali
    Proceedings of the 2016 SIAM International Conference on Data Mining, 504-512, 2016.

  12. Pathways on Demand: Automatic Reconstruction of Human Signaling Networks  Supplement  Software  Graphs on GraphSpace
    Anna Ritz, Christopher L. Poirel, Allison N. Tegge, Nicholas Sharp, Allison Powell, Kelsey Simmons, Shiv D. Kale, and T. M. Murali
    npj:Systems Biology and Applications, a Nature Partner Journal, 2, Article number 16002, 2016.

  13. From START to FINISH: Computational Analysis of Cell Cycle Control in Budding Yeast
    Pavel Kraikivski, Katherine C. Chen, Teeraphan Laomettachit, T. M. Murali, and John J. Tyson
    npj Systems Biology and Applications, a Nature Partner Journal, 1, Article number 15016, 2015.

  14. Mining Unstable Communities from Network Ensembles
    Ahsanur Rahman, Steve Jan, Hyunju Kim, B. Aditya Prakash, and T. M. Murali
    2015 IEEE International Conference on Data Mining Workshop (ICDMW), appeared in the 5th IEEE Workshop on Data Mining in Networks, 508-515, 2015.

  15. XTalk: a Path-Based Approach to Identifying Crosstalk between Signaling Pathways  Software  Graphs on GraphSpace
    Allison N. Tegge, Nicholas Sharp, and T. M. Murali
    Bioinformatics, 32(2), 242-251, 2015.

  16. Experimental validation of an integrated model of the budding yeast START transition  Summary on Atlas of Science
    Neil R. Adames, P. Logan Schuck, Katherine C. Chen, T. M. Murali, John J. Tyson, and Jean Peccoud
    In press, Molecular Biology of the Cell, special issue on Quantitative Biology, 26(22), 3966-3984, 2015.

  17. Pathway Analysis with Signaling Hypergraphs  Poster
    Anna Ritz and T. M. Murali
    Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 249-258, 2014.

  18. Signaling Hypergraphs
    Anna Ritz, Allison Tegge, Hyunju Kim, Christopher L. Poirel, and T. M. Murali
    Trends in Biotechnology, 32(7), 356-362, 2014.

  19. Reverse Engineering Molecular Hypergraphs
    Ahsanur Rahman, Christopher L. Poirel, David J. Badger, Craig Estep, and T. M. Murali
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(5), 1113-1124, 2013. (Full version of the conference publication.)

  20. Designing a Multi-cellular Organotypic 3D Liver Model with a Detachable, Nanoscale Polymeric Space of Disse
    Adam L. Larkin, Richard R. Rodrigues, T. M. Murali, and Padmavathy Rajagopalan
    Tissue Engineering Part C: Methods, 19(11), 875-884, 2013.

  21. Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions
    Yared H Kidane, Christopher Lawrence, and T. M. Murali
    BMC Microbiology, 13, 224, 2013.

  22. Summarizing cellular responses as biological process networks
    Christopher D. Lasher, Padma Rajagopalan, and T. M. Murali
    BMC Systems Biology, 7, 68, 2013.

  23. Systems Biology Characterization of Engineered Tissues
    Padmavathy Rajagopalan, Simon Kasif, and T. M. Murali
    Annual Reviews of Biomedical Engineering, 15, 55-70, 2013.

  24. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes  Supplementary website  Graphs on GraphSpace
    Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, and T. M. Murali
    Journal of Computational Biology, 20(5), 409-418, 2013, special issue on the 5th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges.

  25. The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Bacterial Pathogens:Towards Host-Oriented Broad-Spectrum Drug Targets  Supplementary website
    Yared H. Kidane, Christopher Lawrence, and T. M. Murali
    PLoS One, 8(3), e58553, 2013

  26. Reconciling Differential Gene Expression Data with Molecular Interaction Networks
    Christopher L. Poirel, Ahsanur Rahman, Richard R. Rodrigues, Arjun Krishnan, Jacqueline R. Addesa, and T. M. Murali.
    Bioinformatics, 29(5), 622-629, 2013.

  27. Reverse Engineering Molecular Hypergraphs  Supplementary website
    Ahsanur Rahman, Christopher L. Poirel, David J. Badger, and T. M. Murali
    Proceedings of ACM Conference on Bioinformatics, Computational Biology, and Biomedicine 2012, 68-75, October 7-10, 2012, Orlando FL
    Winner of the best paper award

  28. Guest Editor's Introduction: Computationally Driven Experimental Biology
    T. M. Murali
    Computer, 45(3), 22-23, 2012

  29. Network-Based Functional Enrichment  Supplementary website
    Christopher L. Poirel, Clifford Conley Owens III, and T. M. Murali
    BMC Bioinformatics, 12(Suppl 13), S14, 2011, part of the supplement on the 10th International Conference on Bioinformatics

  30. Network-Based Prediction and Analysis of HIV Dependency Factors
    T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, and Michael G. Katze
    PLoS Computational Biology, 7(9), e1002164, 2011
    Please also see the coverage at ProteoMonitor

  31. Sensitive Detection of Pathway Perturbations in Cancers
    Corban G. Rivera, Brett M. Tyler, and T. M. Murali
    BMC Bioinformatics, 13(Suppl 3), S9, 2012, part of the supplement on the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011

  32. Supervised Prediction and Learning of Physical Interactions between Human and HIV Proteins
    Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    Infection, Genetics, and Evolution, 11, 917-923, 2011

  33. Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures
    Christopher D. Lasher, Padma Rajagopalan, and T. M. Murali
    PLoS One, 6(1), e15247, 2011

  34. A Comparative Study of Genome Wide Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures  Supplementary website
    Yeonhee Kim, Christopher D. Lasher, Logan M. Milford, T. M. Murali, and Padmavathy Rajagopalan
    Tissue Engineering Part C Methods, 16(6), 1449-1460, 2010

  35. Cellular Response Networks
    Christopher D. Lasher, Christopher L. Poirel, and T. M. Murali
    Invited chapter in The Problem Solving Handbook for Computational Biology and Bioinformatics, edited by Lenwood S. Heath and Naren Ramakrishnan, 233-250, Springer-Verlag, 2010

  36. The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
    Matthew D. Dyer, Chris Neff, Max Dufford, Corban G. Rivera, Donna Shattuck, Josep Bassaganya-Riera, T. M. Murali, and Bruno W. Sobral
    PLoS One, 5(8), e12089, 2010

  37. Computational Systems Biology
    T. M. Murali and Srinivas Aluru
    Invited chapter in Algorithms and Theory of Computation Handbook, second edition, edited by Mikhail J. Atallah and Marina Blanton, Chapter 32, CRC Press, 2009.

  38. Finding Conserved Protein Interaction Modules using GraphHopper     Slides
    Corban G. Rivera and T. M. Murali
    Proceedings of the 1st International Conference on Bioinformatics and Computational Biology (BICoB), volume 5462 of Lecture Notes in Computer Science, 67-78, 2009

  39. Capturing Truthiness: Mining Truth Tables in Binary Datasets
    Clifford Conley Owens III, T. M. Murali, and Naren Ramakrishnan
    24th Annual ACM Symposium on Applied Computing, 1467-1474, 2009

  40. PIG: The Pathogen Interaction Gateway  The PIG website
    Tim Driscoll, Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    Nucleic Acids Research, 37(Database issue), D647-D650, 2009.

  41. Network Legos: Building Blocks of Cellular Wiring Diagrams
    T. M. Murali and Corban G. Rivera
    Journal of Computational Biology, 15(7), 829-844, 2008.

  42. Atomic level computational identification of ligand migration pathways between solvent and heme iron in myoglobin
    Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. Murali and Alexey Onufriev
    Proceedings of the National Academy of Sciences, 105(27) 27, 9204-9209, 2008.   

  43. Compositional Mining of Multi-relational Biological Datasets
    Ying Jin, T. M. Murali, and Naren Ramakrishnan
    ACM Transactions on Knowledge Discovery from Data, 2(1), 1-35, 2008

  44. The Landscape of Human Proteins Interacting with Viruses and Other PathogensWebsite
    Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    PLoS Pathogens, 4(2), e32, 2008

  45. Expression Divergence of Tandemly Arrayed Genes in Human and Mouse
    Valia Shoja, T. M. Murali, and Liqing Zhang
    Comparative and Functional Genomics, 2007, article ID 60964, 2007.

  46. Computational Prediction of Host-Pathogen Protein-Protein Interactions     Website     Slides (17 MB)
    Matthew D. Dyer, T. M. Murali and Bruno W. Sobral
    Bioinformatics, 23(13), i159-i166, issue on Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2007

  47. Network Legos: Building Blocks of Cellular Wiring Diagrams      Slides of RECOMB talk, Slides of longer (1 hour) talk
    T. M. Murali and Corban G. Rivera
    Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), volume 4453 of Lecture Notes in Computer Science, 47-61, 2007

  48. The Art of Gene Function Prediction     Website
    T. M. Murali, Chang-Jiun Wu, and Simon Kasif
    Nature Biotechnology, 24, 1474--1475, 2006

  49. Automatic Layout and Visualisation of Biclusters     Website
    Gregory A. Grothaus, Adeel Mufti, and T. M. Murali
    Algorithms for Molecular Biology, 1, 15, 2006

  50. Response Diversity of Arabidopsis thaliana Ecotypes in Elevated [CO2] in the Field
    Pinghua Li, Allan Sioson, Shrinivasrao Mane, Alexander Ulanov, Gregory Grothaus, Lenwood Heath, T. M. Murali, Hans Bohnert, and Ruth Grene
    Plant Molecular Biology, 62, 593--609, 2006

  51. Automatic Layout and Visualisation of Biclusters     Website
    Gregory A. Grothaus, Adeel Mufti, and T. M. Murali
    In Proceedings of the 6th SIGKDD Workshop on Data Mining in Biology, 23--30, 2006

  52. VIRGO: Computational Prediction of Gene Functions     The VIRGO web server
    Naveed Massjouni, Corban Rivera, and T. M. Murali
    Nucleic Acids Research, Web server issue, 4, W340-W344, 2006

  53. XcisClique: Analysis of Regulatory Bicliques     Website
    Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, and T. M. Murali
    BMC Bioinformatics, 7, 218, 2006

  54. Gene Expression Module Discovery Using Gibbs Sampling
    Chang-Jiun Wu, Yutao Fu, T. M. Murali, and Simon Kasif
    Genome Informatics, 15, 239--248, 2004

  55. Whole Genome Annotation using Evidence Integration in Functional Linkage NetworksWebsite
    Ulas Karaoz, T. M. Murali, Stan Letovsky, Yu Zheng, Chunming Ding, Charles R. Cantor, and Simon Kasif
    Proceedings of the National Academy of Sciences, 101, 2888--2893, 2004.

  56. RankGene: Identification of Diagnostic Genes Based on Expression Data
    Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, and Simon Kasif,
    Bioinformatics, 19, 2003, 1578-1579.

  57. Extracting Conserved Gene Expression Motifs from Gene Expression Data
    T. M. Murali and Simon Kasif
    In Proceedings of the Pacific Symposium on Biocomputing, 77--88, 2003

  58. A Monte-Carlo Algorithm for Fast Projective Clustering
    Magda Procopiuc, Michael Jones, Pankaj Agarwal, and T. M. Murali
    In Proceedings of the 2002 International Conference on Management of Data, 418--427, 2002

  59. New Similarity Measures between Polylines with Applications to Morphing and Polygon Sweeping
    Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, Joseph S. B. Mitchell, and T. M. Murali,
    Discrete and Computational Geometry, 28, 2002, 535--569
    This paper combines the results of Morphing between Polylines and Sweeping Simple Polygons with a Chain of Guards.

  60. Morphing between Polylines
    Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, and T. M. Murali
    In Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms, 680--689, 2001

  61. Sweeping Simple Polygons with a Chain of Guards
    Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, David C. Lin, Joseph S. B. Mitchell, and T. M. Murali
    In Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, 927--936, 2000

  62. Cylindrical Static and Kinetic Binary Space Partitions
    Pankaj K. Agarwal, Leonidas J. Guibas, T. M. Murali, and Jeffrey Scott Vitter
    Computational Geometry: Theory and Applications, 16, 2000, 103--127

  63. Binary Space Partitions for Fat Rectangles
    Pankaj K. Agarwal, Edward F. Grove, T. M. Murali, and Jeffrey Scott Vitter
    SIAM Journal on Computing, 29, 1422--1448, 2000

  64. Planning Robot Motion Strategies for Efficient Model Construction
    Hector Hugo Gonzalez-Banos, Alon Efrat, Jean-Claude Latombe, Eric Mao, and T. M. Murali
    In Proceedings of the 9th International Symposium of Robotics Research, 1999, 345--352

  65. The Object Complexity Model for Hidden-Surface Removal
    Edward F. Grove, T. M. Murali. and Jeffrey Scott Vitter
    International Journal of Computational Geometry and Applications, 9, 207-217, 1999

  66. Constructing Binary Space Partitions for Orthogonal Rectangles in Practice
    T. M. Murali, Pankaj K. Agarwal, and Jeffrey Scott Vitter
    In Proceedings of the 6th Annual European Symposium on Algorithms, 211--222, 1998

  67. Efficient Hidden-Surface Removal in Theory and in Practice
    Ph. D. Thesis, Department of Computer Science, Brown University, June 1998

  68. I/O-Efficient Algorithms for Contour Line Extraction and Planar Graph Blocking
    Pankaj K. Agarwal, Lars Arge, T. M. Murali, Kasturi R. Varadarajan, and Jeffrey Scott Vitter
    In Proceedings of the 9th Annual ACM-SIAM Symposium on Discrete Algorithms, 211--222, 1998

  69. Cylindrical Static and Kinetic Binary Space Partitions
    Pankaj K. Agarwal, Leonidas J. Guibas, T. M. Murali, and Jeffrey Scott Vitter
    Proceedings of the 13th Annual ACM Symposium on Computational Geometry, 39-48, 1997

  70. Practical Techniques for Constructing Binary Space Partitions for Orthogonal Rectangles
    Pankaj K. Agarwal, T. M. Murali, and Jeffrey Scott Vitter
    In Proceedings of the 13th Annual ACM Symposium on Computational Geometry, 382--384, 1997

  71. Consistent Solid and Boundary Representations from Arbitrary Polygonal Data
    T. M. Murali and Thomas A. Funkhouser
    In Proceedings of the 1997 Symposium on Interactive 3D Graphics, Providence, Rhode Island, April 1997
    Since the size of this paper is more than 21MB when uncompressed, you can download it in three forms:
    1. The full paper (a little more than 21Mb when uncompressed),
    2. The paper without the colour page (200 Kb when uncompressed), or
    3. The colour page (nearly 21Mb when uncompressed).

  72. Binary Space Partitions for Fat Rectangles
    Pankaj K. Agarwal, Edward F. Grove, T. M. Murali, and Jeffrey Scott Vitter
    Proceedings of the 37th IEEE Annual Symposium on Foundations of Computer Science, 482-491, 1996

  73. The Object Complexity Model for Hidden-Surface Removal
    Edward F. Grove, T. M. Murali. and Jeffrey Scott Vitter
    Proceedings of the Seventh Canadian Conference on Computational Geometry, 273-278, 1995


T. M. Murali (murali at cs dot vt dot edu) Last modified: Mon Mar 14 11:01:45 EDT 2016