{"id":83,"date":"2024-03-24T22:07:57","date_gmt":"2024-03-24T22:07:57","guid":{"rendered":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/?page_id=83"},"modified":"2024-03-24T22:08:41","modified_gmt":"2024-03-24T22:08:41","slug":"publications","status":"publish","type":"page","link":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

In my research<\/a>, I focus on problems in bioinformatics and computational biology. In the past, I have done research in the area of computational geometry<\/a>, especially on problems motivated by applications in computer graphics<\/a>, robotics<\/a>, and geographic information systems<\/a>. In my Ph.D. thesis<\/a>, I studied the problem of hidden-surface removal<\/a>. Here is a list of my publications.<\/em><\/p>\n\n\n\n

    \n
  1. ICoN: Integration using Co-attention across Biological Networks<\/a>
    Nure Tasnina and T. M. Murali
    bioRxiv, in review, 2024.<\/li>\n\n\n\n
  2. Current and future directions in network biology<\/a>
    Marinka Zitnik, Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T. M. Murali, Predrag Radivojac, Sushmita Roy, Ana\u00efs Baudot, Serdar Bozdag, Danny Z. Chen, Lenore Cowen, Kapil Devkota, Anthony Gitter, Sara Gosline, Pengfei Gu, Pietro H. Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R. Pico, Nata\u0161a Pr\u017eulj, Teresa M. Przytycka, Benjamin J. Raphael, Anna Ritz, Roded Sharan, Yang Shen, Mona Singh, Donna K. Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenkovi\u0107
    arXiv, in review, 2023.<\/li>\n\n\n\n
  3. Comparative Transcriptomic and Phenotypic Analysis of Induced Pluripotent Stem Cell Hepatocyte-Like Cells and Primary Human Hepatocytes
    Neeti N Gandhi, Lauren Wills, Kyle Akers, Yiqi Su, Parker Niccum, T. M. Murali, Padmavathy Rajagopalan
    Cell and Tissue Research<\/em>, in press, 2024<\/li>\n\n\n\n
  4. Predictive Models of Long COVID<\/a>
    Blessy Antony, Hannah Blau, Elena Casiraghi, Johanna J Loomba, Tiffany J Callahan, Bryan J Laraway, Kenneth J Wilkins, Corneliu C Antonescu, Giorgio Valentini, Andrew E Williams, Peter N Robinson, Justin T Reese, and T. M. Murali
    EBioMedicine<\/em>, 96, 104777, 2023.<\/li>\n\n\n\n
  5. Computational Construction of Toxicant Signaling Networks<\/a>
    Jeffrey Law, Sophia Orbach, Bronson Weston, Peter Steele, Padmavathy Rajagopalan, and T. M. Murali
    Chemical Research in Toxicology<\/em>, 36, 1267-1277, 2023.<\/li>\n\n\n\n
  6. Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes<\/a>
    <\/a>Justin T. Reese, Hannah Blau, Elena Casiraghi, Timothy Bergquist, Johanna J. Loomba, Tiffany J. Callahan, Bryan Laraway, Corneliu Antonescu, Ben Coleman, Michael Gargano, Kenneth J. Wilkins, Luca Cappelletti, Tommaso Fontana, Nariman Ammar, Blessy Antony, T. M. Murali, J. Harry Caufield, Guy Karlebach, Julie A. McMurry, Andrew Williams, Richard Moffitt, Jineta Banerjee, Anthony E. Solomonides, Hannah Davis, Kristin Kostka, Giorgio Valentini, David Sahner, Christopher G. Chute, Charisse Madlock-Brown, Melissa A. Haendel, and Peter N. Robinson
    eBioMedicine<\/em>, 87, 104413, 2023<\/li>\n\n\n\n
  7. Integrating Multimodal Data through Interpretable Heterogeneous Ensembles<\/a>
    Yan Chak Li, Linhua Wang, Jeffrey N. Law, T. M. Murali, and Gaurav Pandey
    Bioinformatics Advances<\/em>, 2, vbac065, 2022<\/li>\n\n\n\n
  8. Flud: a hybrid crowd-algorithm approach for visualizing biological networks<\/a>  Presentation at ISMB 2019<\/a>
    Aditya Bharadwaj, David Gwizdala, Yoonjin Kim, Kurt Luther, and T. M. Murali
    ACM Transactions of Computer-Human Interactions<\/em>, 29, 1-53, 2022<\/li>\n\n\n\n
  9. Interpretable Network Propagation with Application to Expanding the Repertoire of Human Proteins that Interact with SARS-CoV-2<\/a>
    Jeffrey N. Law, Kyle Akers, Nure Tasnina, Catherine M. Della Santina, Shay Deutsch, Meghana Kshirsagar, Judith Klein-Seetharaman, Mark Crovella, Padmavathy Rajagopalan, Simon Kasif, and T. M. Murali
    GigaScience<\/em>, 10, giab082, 2021<\/li>\n\n\n\n
  10. Modeling and Analysis of the Macronutrient Signaling Network in Budding Yeast<\/a>
    Amogh P. Jalihal, Pavel Kraikivski, T. M. Murali, John Tyson
    Molecular Biology of the Cell<\/em>, 32, 2021<\/li>\n\n\n\n
  11. Gene Regulatory Network Inference in Single-Cell Biology<\/a>
    Kyle Akers and T. M. Murali
    Current Opinion in Systems Biology<\/em>, 26, 87-97, 2021<\/li>\n\n\n\n
  12. Protein sequence models for prediction and comparative analysis of the SARS-CoV-2\u2212human interactome<\/a>
    Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman, Judith Klein-Seetharaman
    Pacific Symposium on Biocomputing<\/em>, 154-165`, 2021.<\/li>\n\n\n\n
  13. Accurate and Efficient Gene Function Prediction using a Multi-Bacterial Network<\/a>
    Jeffrey N. Law, Shiv D. Kale, and T. M. Murali
    Bioinformatics<\/em>, 37, 800-806, 2021<\/li>\n\n\n\n
  14. Genetic interactions derived from high-throughput phenotyping of 7,350 yeast cell cycle mutants<\/a>
    Jenna E. Gallegos, Neil R. Adames, Mark F. Rogers, Pavel Kraikivski, Aubrey Ibele, Kevin Nurzynski-Loth, Eric Kudlow, T. M. Murali, John Tyson, and Jean Peccoud
    Systems Biology and Applications<\/em>, a Nature Partner journal, 6, Article number 11, 2020<\/li>\n\n\n\n
  15. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data<\/a>  Talk at ISMB 2020<\/a>
    Aditya Pratapa, Amogh P. Jalihal, Jeffrey N. Law, Aditya Bharadwaj, and T. M. Murali
    Nature Methods<\/em>, 17, 147-154, 2020<\/li>\n\n\n\n
  16. Hypergraph-based connectivity measures for signaling pathway topologies<\/a>
    Nicholas Franzese, Adam R. Groce, T. M. Murali, and Anna Ritz
    PLoS Computational Biology<\/em>, 15(10), e1007384, 2019<\/li>\n\n\n\n
  17. Reconstructing Signaling Pathways Using Regular-Language Constrained Paths<\/a>
    Mitchell J. Wagner, Aditya Pratapa, and T. M. Murali
    Bioinformatics<\/em> 35(14), i624\u2013i633, 2019. Special issue on 2019 International Conference on Intelligent Systems for Molecular Biology<\/em>.<\/li>\n\n\n\n
  18. Connectivity Measures for Signaling Pathway Topologies<\/a>
    Nicholas Franzese, Adam Groce, T. M. Murali, and Anna Ritz, Great Lakes Bioinformatics Conference<\/em>, 2019.<\/li>\n\n\n\n
  19. Flud: a hybrid crowd-algorithm approach for visualizing biological networks
    Aditya Bharadwaj, David Gwizdala, Yoonjin Kim, Kurt Luther, and T. M. Murali
    Where is the Human? Bridging the Gap Between AI and HCI<\/a>, CHI 2019 Workshop, 2019.<\/li>\n\n\n\n
  20. Large-scale protein function prediction using heterogeneous ensembles<\/a>
    Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, and Gaurav Pandey, F1000 Research<\/em>, 7 (ISCB Comm J), 1577, 2018.<\/li>\n\n\n\n
  21. Guest Editorial<\/a> 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.<\/li>\n\n\n\n
  22. Efficient Synthesis of Mutants Using Genetic Crosses<\/a>    bioRxiv version with proofs<\/a>
    Aditya Pratapa, Amogh Jalihal, S. S. Ravi, and T. M. Murali
    Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 53-62, 2018.<\/li>\n\n\n\n
  23. Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models<\/a>
    Allison N. Tegge, Richard R. Rodrigues, Adam L. Larkin, Lucas Vu, T. M. Murali, and Padmavathy Rajagopalan
    Scientific Reports<\/em>, 8, 11306, 2018.<\/li>\n\n\n\n
  24. Automating the PathLinker app for Cytoscape<\/a>
    Li Jun Huang, Jeffrey N. Law, and T. M. Murali
    F1000 Research<\/em>, 7, 727, 2018<\/li>\n\n\n\n
  25. CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models<\/a>
    Aditya Pratapa, Neil Adames, Pavel Kraikivski, John J. Tyson, Jean Peccoud, and T. M. Murali
    Bioinformatics<\/em>, 34 (13), 2237-2244, 2018<\/li>\n\n\n\n
  26. CrowdLayout: Crowdsourced Design and Evaluation of Biological Network Visualizations<\/a>
    Divit P. Singh, Lee Lisle, T. M. Murali, and Kurt Luther
    2018 ACM Conference on Human Factors in Computing Systems (CHI’18)<\/em>, paper 232, 2018<\/li>\n\n\n\n
  27. GraphSpace: Stimulating Interdisciplinary Collaborations in Network Biology<\/a>
    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<\/em>, 13 (19), 3134-3136, 2017<\/li>\n\n\n\n
  28. Pathway Analysis with Signaling Hypergraphs<\/a>
    Anna Ritz, Brendan N. Avent, and T. M. Murali
    IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>, 14(5), 1042-1055, 2017.<\/li>\n\n\n\n
  29. The PathLinker app: Connect the dots in protein interaction networks<\/a>   Cytoscape app<\/a>  Code<\/a>
    Daniel P. Gil, Jeffrey N. Law, and T. M. Murali
    F1000 Research<\/em>, 6, 58, 2017.<\/li>\n\n\n\n
  30. XTalkDB: A Database of Signaling Pathway Crosstalk<\/a>  XTalkDB<\/a>
    Sarah Sam, Joelle Teel, Allison N. Tegge, Aditya Bharadwaj, and T. M. Murali
    Nucleic Acids Research<\/em>, 45 (D1), D432-D439, 2016.<\/li>\n\n\n\n
  31. 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<\/em><\/a>, 504-512, 2016.<\/li>\n\n\n\n
  32. Pathways on Demand: Automatic Reconstruction of Human Signaling Networks<\/a>  Supplement<\/a>  Software<\/a>  Graphs on GraphSpace<\/a>
    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<\/em><\/a>, a Nature Partner Journal, 2, Article number 16002, 2016.<\/li>\n\n\n\n
  33. From START to FINISH: Computational Analysis of Cell Cycle Control in Budding Yeast<\/a>
    Pavel Kraikivski, Katherine C. Chen, Teeraphan Laomettachit, T. M. Murali, and John J. Tyson
    npj Systems Biology and Applications<\/em><\/a>, a Nature Partner Journal, 1, Article number 15016, 2015.<\/li>\n\n\n\n
  34. Mining Unstable Communities from Network Ensembles<\/a>
    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<\/em><\/a>, 508-515, 2015.<\/li>\n\n\n\n
  35. XTalk: a Path-Based Approach to Identifying Crosstalk between Signaling Pathways<\/a>  Software<\/a>  Graphs on GraphSpace<\/a>
    Allison N. Tegge, Nicholas Sharp, and T. M. Murali
    Bioinformatics<\/em><\/a>, 32(2), 242-251, 2015.<\/li>\n\n\n\n
  36. Experimental validation of an integrated model of the budding yeast START transition<\/a>  Summary on Atlas of Science<\/a>
    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<\/em>, special issue on Quantitative Biology, 26(22), 3966-3984, 2015.<\/li>\n\n\n\n
  37. Pathway Analysis with Signaling Hypergraphs<\/a>  Poster<\/a>
    Anna Ritz and T. M. Murali
    Proceedings of the     5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics<\/a><\/em>, 249-258, 2014.<\/a><\/li>\n\n\n\n
  38. Signaling Hypergraphs<\/a>
    Anna Ritz, Allison Tegge, Hyunju Kim, Christopher L. Poirel, and T. M. Murali
    Trends in Biotechnology<\/em>, 32(7), 356-362, 2014.<\/li>\n\n\n\n
  39. Reverse Engineering Molecular Hypergraphs<\/a>
    Ahsanur Rahman, Christopher L. Poirel, David J. Badger, Craig Estep, and T. M. Murali
    IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>, 10(5), 1113-1124, 2013. (Full version of the     conference publication<\/a>.)<\/li>\n\n\n\n
  40. Designing a Multi-cellular Organotypic 3D Liver Model with a Detachable, Nanoscale Polymeric Space of Disse<\/a>
    Adam L. Larkin, Richard R. Rodrigues, T. M. Murali, and Padmavathy Rajagopalan
    Tissue Engineering Part C: Methods<\/em>, 19(11), 875-884, 2013.<\/li>\n\n\n\n
  41. Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions<\/a>
    Yared H Kidane, Christopher Lawrence, and T. M. Murali
    BMC Microbiology<\/em>, 13, 224, 2013.<\/li>\n\n\n\n
  42. Summarizing cellular responses as biological process networks<\/a>
    Christopher D. Lasher, Padma Rajagopalan, and T. M. Murali
    BMC Systems Biology<\/em>, 7, 68, 2013.<\/li>\n\n\n\n
  43. Systems Biology Characterization of Engineered Tissues<\/a>
    Padmavathy Rajagopalan, Simon Kasif, and T. M. Murali
    Annual Reviews of Biomedical Engineering<\/a><\/em>, 15, 55-70, 2013.<\/li>\n\n\n\n
  44. Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes<\/a>  Supplementary website<\/a>  Graphs on GraphSpace<\/a>
    Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, and T. M. Murali
    Journal of Computational Biology<\/a><\/em>, 20(5), 409-418, 2013, special issue on the 5th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges<\/a><\/em>.<\/li>\n\n\n\n
  45. The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Bacterial Pathogens:Towards Host-Oriented Broad-Spectrum Drug Targets<\/a>  Supplementary website<\/a>
    Yared H. Kidane, Christopher Lawrence, and T. M. Murali
    PLoS One<\/a><\/em>, 8(3), e58553, 2013<\/li>\n\n\n\n
  46. Reconciling Differential Gene Expression Data with Molecular Interaction Networks<\/a>
    Christopher L. Poirel, Ahsanur Rahman, Richard R. Rodrigues, Arjun Krishnan, Jacqueline R. Addesa, and T. M. Murali.
    Bioinformatics<\/a><\/em>, 29(5), 622-629, 2013.<\/li>\n\n\n\n
  47. Reverse Engineering Molecular Hypergraphs<\/a>  Supplementary website<\/a>
    Ahsanur Rahman, Christopher L. Poirel, David J. Badger, and T. M. Murali
    Proceedings of ACM Conference on Bioinformatics, Computational Biology, and Biomedicine 2012<\/em><\/a>, 68-75, October 7-10, 2012, Orlando FL
    Winner of the     best paper award<\/a><\/strong><\/li>\n\n\n\n
  48. Guest Editor’s Introduction: Computationally Driven Experimental Biology<\/a>
    T. M. Murali
    Computer<\/a><\/em>, 45(3), 22-23, 2012<\/li>\n\n\n\n
  49. Network-Based Functional Enrichment<\/a>  Supplementary website<\/a>
    Christopher L. Poirel, Clifford Conley Owens III, and T. M. Murali
    BMC Bioinformatics<\/a><\/em>, 12(Suppl 13), S14, 2011, part of the supplement on the 10th International Conference on Bioinformatics<\/em><\/li>\n\n\n\n
  50. Network-Based Prediction and Analysis of HIV Dependency Factors<\/a>
    T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, and Michael G. Katze
    PLoS Computational Biology<\/a><\/em>, 7(9), e1002164, 2011
    Please also see the coverage at     ProteoMonitor<\/a><\/li>\n\n\n\n
  51. Sensitive Detection of Pathway Perturbations in Cancers<\/a>
    Corban G. Rivera, Brett M. Tyler, and T. M. Murali
    BMC Bioinformatics<\/a><\/em>, 13(Suppl 3), S9, 2012, part of the supplement on the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011<\/em><\/a><\/li>\n\n\n\n
  52. Supervised Prediction and Learning of Physical Interactions between Human and HIV Proteins<\/a>
    Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    Infection, Genetics, and Evolution<\/a><\/em>, 11, 917-923, 2011<\/li>\n\n\n\n
  53. Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures<\/a>
    Christopher D. Lasher, Padma Rajagopalan, and T. M. Murali
    PLoS One<\/a><\/em>, 6(1), e15247, 2011<\/li>\n\n\n\n
  54. A Comparative Study of Genome Wide Transcriptional Profiles of Primary Hepatocytes in Collagen Sandwich and Monolayer Cultures<\/a>  Supplementary website<\/a>
    Yeonhee Kim, Christopher D. Lasher, Logan M. Milford, T. M. Murali, and Padmavathy Rajagopalan
    Tissue Engineering Part C Methods<\/em><\/a>, 16(6), 1449-1460, 2010<\/li>\n\n\n\n
  55. 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<\/a><\/em>, edited by Lenwood S. Heath and Naren Ramakrishnan, 233-250, Springer-Verlag, 2010<\/li>\n\n\n\n
  56. The human-bacterial pathogen protein interaction networks of Bacillus anthracis<\/em>, Francisella tularensis<\/em>, and Yersinia pestis<\/em><\/a>
    Matthew D. Dyer, Chris Neff, Max Dufford, Corban G. Rivera, Donna Shattuck, Josep Bassaganya-Riera, T. M. Murali, and Bruno W. Sobral
    PLoS One<\/a><\/em>, 5(8), e12089, 2010<\/li>\n\n\n\n
  57. Computational Systems Biology<\/a>
    T. M. Murali and     Srinivas Aluru<\/a>
    Invited chapter in     Algorithms and Theory of Computation Handbook<\/a><\/em>, second edition, edited by Mikhail J. Atallah and Marina Blanton, Chapter 32, CRC Press, 2009.<\/li>\n\n\n\n
  58. Finding Conserved Protein Interaction Modules using GraphHopper<\/a>     Slides<\/a>
    Corban G. Rivera and T. M. Murali
    Proceedings of the 1st International Conference on Bioinformatics and Computational Biology<\/em><\/a> (BICoB), volume 5462 of Lecture Notes in Computer Science<\/em>, 67-78, 2009<\/li>\n\n\n\n
  59. Capturing Truthiness: Mining Truth Tables in Binary Datasets<\/a>
    Clifford Conley Owens III, T. M. Murali, and Naren Ramakrishnan
    24th Annual ACM Symposium on Applied Computing<\/a><\/em>, 1467-1474, 2009<\/li>\n\n\n\n
  60. PIG: The Pathogen Interaction Gateway<\/a>  The PIG website<\/a>
    Tim Driscoll, Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    Nucleic Acids Research<\/a><\/em>, 37(Database issue), D647-D650, 2009.<\/li>\n\n\n\n
  61. Network Legos: Building Blocks of Cellular Wiring Diagrams<\/a>
    T. M. Murali and Corban G. Rivera
    Journal of Computational Biology<\/a><\/em>, 15(7), 829-844, 2008.<\/li>\n\n\n\n
  62. Atomic level computational identification of ligand migration pathways between solvent and heme iron in myoglobin<\/a>
    Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. Murali and Alexey Onufriev
    Proceedings of the National Academy of Sciences<\/a><\/em>, 105(27) 27, 9204-9209, 2008.   <\/li>\n\n\n\n
  63. Compositional Mining of Multi-relational Biological Datasets<\/a>
    Ying Jin, T. M. Murali, and Naren Ramakrishnan
    ACM Transactions on Knowledge Discovery from Data<\/a><\/em>, 2(1), 1-35, 2008<\/li>\n\n\n\n
  64. The Landscape of Human Proteins Interacting with Viruses and Other Pathogens<\/a>
    Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral
    PLoS Pathogens<\/a><\/em>, 4(2), e32, 2008<\/li>\n\n\n\n
  65. Expression Divergence of Tandemly Arrayed Genes in Human and Mouse<\/a>
    Valia Shoja, T. M. Murali, and Liqing Zhang
    Comparative and Functional Genomics<\/a><\/em>, 2007, article ID 60964, 2007.
    <\/li>\n\n\n\n
  66. Computational Prediction of Host-Pathogen Protein-Protein Interactions<\/a>     Website<\/a>     Slides<\/a> (17 MB)
    Matthew D. Dyer, T. M. Murali and Bruno W. Sobral
    Bioinformatics<\/em><\/a>, 23(13), i159-i166, issue on Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology<\/em><\/a> (ISMB), 2007<\/li>\n\n\n\n
  67. Network Legos: Building Blocks of Cellular Wiring Diagrams<\/a>      Slides of RECOMB talk<\/a>, Slides of longer (1 hour) talk<\/a>
    T. M. Murali and Corban G. Rivera
    Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology<\/em><\/a> (RECOMB), volume 4453 of Lecture Notes in Computer Science<\/em>, 47-61, 2007<\/li>\n\n\n\n
  68. The Art of Gene Function Prediction<\/a>     Website<\/a>
    T. M. Murali, Chang-Jiun Wu, and Simon Kasif
    Nature Biotechnology<\/a><\/em>, 24, 1474–1475, 2006<\/li>\n\n\n\n
  69. Automatic Layout and Visualisation of Biclusters<\/a>     Website<\/a>
    Gregory A. Grothaus, Adeel Mufti, and T. M. Murali
    Algorithms for Molecular Biology<\/em><\/a>, 1, 15, 2006<\/li>\n\n\n\n
  70. Response Diversity of Arabidopsis thaliana<\/em> Ecotypes in Elevated [CO2] in the Field<\/a>
    Pinghua Li, Allan Sioson, Shrinivasrao Mane, Alexander Ulanov, Gregory Grothaus, Lenwood Heath, T. M. Murali, Hans Bohnert, and Ruth Grene
    Plant Molecular Biology<\/a><\/em>, 62, 593–609, 2006<\/li>\n\n\n\n
  71. Automatic Layout and Visualisation of Biclusters<\/a>     Website<\/a>
    Gregory A. Grothaus, Adeel Mufti, and T. M. Murali
    In Proceedings of the     6th SIGKDD Workshop on Data Mining in Biology<\/em><\/a>, 23–30, 2006<\/li>\n\n\n\n
  72. VIRGO: Computational Prediction of Gene Functions<\/a>     The VIRGO web server<\/a>
    Naveed Massjouni, Corban Rivera, and T. M. Murali
    Nucleic Acids Research<\/em>, Web server issue, 4, W340-W344, 2006<\/li>\n\n\n\n
  73. XcisClique: Analysis of Regulatory Bicliques<\/a>     Website<\/a>
    Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, and T. M. Murali
    BMC Bioinformatics<\/em>, 7, 218, 2006<\/li>\n\n\n\n
  74. Gene Expression Module Discovery Using Gibbs Sampling<\/a>
    Chang-Jiun Wu, Yutao Fu, T. M. Murali, and Simon Kasif
    Genome Informatics<\/a><\/em>, 15, 239–248, 2004
    <\/li>\n\n\n\n
  75. Whole Genome Annotation using Evidence Integration in Functional Linkage Networks<\/a>\u2003Website<\/a>
    Ulas Karaoz, T. M. Murali, Stan Letovsky, Yu Zheng, Chunming Ding, Charles R. Cantor, and Simon Kasif
    Proceedings of the National Academy of Sciences<\/a><\/em>, 101, 2888–2893, 2004.<\/li>\n\n\n\n
  76. RankGene: Identification of Diagnostic Genes Based on Expression Data<\/a>
    Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, and Simon Kasif,
    Bioinformatics<\/a><\/em>, 19, 2003, 1578-1579.<\/li>\n\n\n\n
  77. Extracting Conserved Gene Expression Motifs from Gene Expression Data<\/a>
    T. M. Murali<\/a> and Simon Kasif<\/a>
    In Proceedings of the     Pacific Symposium on Biocomputing<\/em><\/a>, 77–88, 2003<\/li>\n\n\n\n
  78. A Monte-Carlo Algorithm for Fast Projective Clustering<\/a>
    Magda Procopiuc<\/a>, Michael Jones<\/a>, Pankaj Agarwal<\/a>, and T. M. Murali<\/a>
    In Proceedings of the     2002 International Conference on Management of Data<\/em><\/a>, 418–427, 2002<\/li>\n\n\n\n
  79. New Similarity Measures between Polylines with Applications to Morphing and Polygon Sweeping<\/a>
    Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, Joseph S. B. Mitchell, and T. M. Murali,
    Discrete and Computational Geometry<\/a><\/em>, 28, 2002, 535–569
    This paper combines the results of     Morphing between Polylines<\/a> and Sweeping Simple Polygons with a Chain of Guards<\/a>.<\/li>\n\n\n\n
  80. Morphing between Polylines<\/a>
    Alon Efrat<\/a>, Leonidas J. Guibas<\/a>, Sariel Har-Peled<\/a>, and T. M. Murali<\/a>
    In Proceedings of the     12th Annual ACM-SIAM Symposium on Discrete Algorithms<\/em><\/a>, 680–689, 2001<\/li>\n\n\n\n
  81. Sweeping Simple Polygons with a Chain of Guards<\/a>
    Alon Efrat<\/a>, Leonidas J. Guibas<\/a>, Sariel Har-Peled<\/a>, David C. Lin<\/a>, Joseph S. B. Mitchell<\/a>, and T. M. Murali<\/a>
    In Proceedings of the     11th Annual ACM-SIAM Symposium on Discrete Algorithms<\/em><\/a>, 927–936, 2000<\/li>\n\n\n\n
  82. Cylindrical Static and Kinetic Binary Space Partitions<\/a>
    Pankaj K. Agarwal<\/a>, Leonidas J. Guibas<\/a>, T. M. Murali<\/a>, and Jeffrey Scott Vitter<\/a>
    Computational Geometry: Theory and Applications<\/em><\/a>, 16, 2000, 103–127<\/li>\n\n\n\n
  83. Binary Space Partitions for Fat Rectangles<\/a>
    Pankaj K. Agarwal<\/a>, Edward F. Grove, T. M. Murali<\/a>, and Jeffrey Scott Vitter<\/a>
    SIAM Journal on Computing<\/a><\/em>, 29, 1422–1448, 2000<\/li>\n\n\n\n
  84. Planning Robot Motion Strategies for Efficient Model Construction<\/a>
    Hector Hugo Gonzalez-Banos<\/a>, Alon Efrat<\/a>, Jean-Claude Latombe<\/a>, Eric Mao<\/a>, and T. M. Murali<\/a>
    In Proceedings of the     9th International Symposium of Robotics Research<\/em><\/a>, 1999, 345–352<\/li>\n\n\n\n
  85. The Object Complexity Model for Hidden-Surface Removal<\/a>
    Edward F. Grove,     T. M. Murali<\/a>. and Jeffrey Scott Vitter<\/a>
    International Journal of Computational Geometry and Applications<\/a><\/em>, 9, 207-217, 1999<\/li>\n\n\n\n
  86. Constructing Binary Space Partitions for Orthogonal Rectangles in Practice<\/a>
    T. M. Murali<\/a>, Pankaj K. Agarwal<\/a>, and Jeffrey Scott Vitter<\/a>
    In Proceedings of the     6th Annual European Symposium on Algorithms<\/a><\/em>, 211–222, 1998<\/li>\n\n\n\n
  87. Efficient Hidden-Surface Removal in Theory and in Practice<\/a>
    Ph. D. Thesis, Department of Computer Science, Brown University, June 1998<\/li>\n\n\n\n
  88. I\/O-Efficient Algorithms for Contour Line Extraction and Planar Graph Blocking<\/a>
    Pankaj K. Agarwal<\/a>, Lars Arge<\/a>, T. M. Murali<\/a>, Kasturi R. Varadarajan<\/a>, and Jeffrey Scott Vitter<\/a>
    In Proceedings of the     9th Annual ACM-SIAM Symposium on Discrete Algorithms<\/a><\/em>, 211–222, 1998<\/li>\n\n\n\n
  89. Cylindrical Static and Kinetic Binary Space Partitions<\/a>
    Pankaj K. Agarwal<\/a>, Leonidas J. Guibas<\/a>, T. M. Murali<\/a>, and Jeffrey Scott Vitter<\/a>
    Proceedings of the     13th Annual ACM Symposium on Computational Geometry<\/a><\/em>, 39-48, 1997<\/li>\n\n\n\n
  90. Practical Techniques for Constructing Binary Space Partitions for Orthogonal Rectangles<\/a>
    Pankaj K. Agarwal<\/a>, T. M. Murali<\/a>, and Jeffrey Scott Vitter<\/a>
    In Proceedings of the     13th Annual ACM Symposium on Computational Geometry<\/a><\/em>, 382–384, 1997<\/li>\n\n\n\n
  91. Consistent Solid and Boundary Representations from Arbitrary Polygonal Data
    T. M. Murali<\/a> and Thomas A. Funkhouser<\/a>
    In Proceedings of the     1997 Symposium on Interactive 3D Graphics<\/a><\/em>, Providence, Rhode Island, April 1997
    Since the size of this paper is more than 21MB when uncompressed, you can download it in three forms:\n
      \n
    1. The full paper<\/a> (a little more than 21Mb when uncompressed),<\/li>\n\n\n\n
    2. The paper without the colour page<\/a> (200 Kb when uncompressed), or<\/li>\n\n\n\n
    3. The colour page<\/a> (nearly 21Mb when uncompressed).<\/li>\n<\/ol>\n<\/li>\n\n\n\n
    4. Binary Space Partitions for Fat Rectangles<\/a>
      Pankaj K. Agarwal<\/a>, Edward F. Grove, T. M. Murali<\/a>, and Jeffrey Scott Vitter<\/a>
      Proceedings of the       37th IEEE Annual Symposium on Foundations of Computer Science<\/a><\/em>, 482-491, 1996<\/li>\n\n\n\n
    5. The Object Complexity Model for Hidden-Surface Removal<\/a>
      Edward F. Grove,       T. M. Murali<\/a>. and Jeffrey Scott Vitter<\/a>
      Proceedings of the       Seventh Canadian Conference on Computational Geometry<\/a><\/em>, 273-278, 1995<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

      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.<\/p>\n","protected":false},"author":447,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-83","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/83","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/users\/447"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/comments?post=83"}],"version-history":[{"count":2,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/83\/revisions"}],"predecessor-version":[{"id":85,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/83\/revisions\/85"}],"wp:attachment":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/media?parent=83"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}