T. M. Murali

Publication Activity (10 Years)

Years Active: 1996-2022
Publications (10 Years): 21

Top Topics

Signaling Pathways

Reverse Engineer

Mathematical Models

Regulatory Networks

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

J. Comput. Biol.

Publications

Aditya Bharadwaj, David Gwizdala, Yoonjin Kim, Kurt Luther, T. M. Murali
Flud: A Hybrid Crowd-Algorithm Approach for Visualizing Biological Networks. ACM Trans. Comput. Hum. Interact. 29 (1) (2022)
Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019). J. Comput. Biol. 28 (2) (2021)
Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman, Judith Klein-Seetharaman
Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 - human interactome. PSB (2021)
Jeffrey N. Law, Shiv D. Kale, T. M. Murali
Accurate and efficient gene function prediction using a multi-bacterial network. Bioinform. 37 (6) (2021)
Aditya Pratapa, Amogh P. Jalihal, Jeffrey N. Law, Aditya Bharadwaj, T. M. Murali
How to build regulatory networks from single-cell gene expression data. BCB (2020)
Mitchell J. Wagner, Aditya Pratapa, T. M. Murali
Reconstructing signaling pathways using regular language constrained paths. Bioinform. 35 (14) (2019)
Nicholas Franzese, Adam Groce, T. M. Murali, Anna M. Ritz
Hypergraph-based connectivity measures for signaling pathway topologies. PLoS Comput. Biol. 15 (10) (2019)
Aditya Bharadwaj, David Gwizdala, Yoonjin Kim, Kurt Luther, T. M. Murali
Flud: a hybrid crowd-algorithm approach for visualizing biological networks. CoRR (2019)
Li Jun Huang, Jeffrey N. Law, T. M. Murali
Automating the PathLinker app for Cytoscape. F1000Research 7 (2018)
Divit P. Singh, Lee Lisle, T. M. Murali, Kurt Luther
CrowdLayout: Crowdsourced Design and Evaluation of Biological Network Visualizations. CHI (2018)
T. M. Murali
Guest Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Aditya Pratapa, Neil Adames, Pavel K. Brazhnik, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
CrossPlan: systematic planning of genetic crosses to validate mathematical models. Bioinform. 34 (13) (2018)
Linhua Wang, Jeffrey N. Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Large-scale protein function prediction using heterogeneous ensembles. F1000Research 7 (2018)
Aditya Pratapa, Amogh P. Jalihal, S. S. Ravi, T. M. Murali
Efficient Synthesis of Mutants Using Genetic Crosses. BCB (2018)
Aditya Pratapa, Neil Adames, Pavel K. Kraikivski, Nicholas Franzese, John J. Tyson, Jean Peccoud, T. M. Murali
CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. BCB (2018)
Aditya Bharadwaj, Divit P. Singh, Anna M. Ritz, Allison N. Tegge, Christopher L. Poirel, Pavel K. Brazhnik, Neil Adames, Kurt Luther, Shiv D. Kale, Jean Peccoud, John J. Tyson, T. M. Murali
GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinform. 33 (19) (2017)
Sarah A. Sam, Joelle Teel, Allison N. Tegge, Aditya Bharadwaj, T. M. Murali
XTalkDB: a database of signaling pathway crosstalk. Nucleic Acids Res. 45 (Database-Issue) (2017)
Anna M. Ritz, Brendan Avent, T. M. Murali
Pathway Analysis with Signaling Hypergraphs. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (5) (2017)
Ahsanur Rahman, Steve T. K. Jan, Hyunju Kim, B. Aditya Prakash, T. M. Murali
Unstable Communities in Network Ensembles. SDM (2016)
Allison N. Tegge, Nicholas Sharp, T. M. Murali
Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinform. 32 (2) (2016)
Ahsanur Rahman, Steve T. K. Jan, Hyunju Kim, B. Aditya Prakash, T. M. Murali
Mining Unstable Communities from Network Ensembles. ICDM Workshops (2015)
Anna M. Ritz, T. M. Murali
Pathway analysis with signaling hypergraphs. BCB (2014)
Craig Estep, Jaeil Yi, Anna M. Ritz, T. M. Murali
GraphSpace: sharing and collaborating through networks on the web. BCB (2014)
Ahsanur Rahman, Christopher L. Poirel, David Badger, Craig Estep, T. M. Murali
Reverse Engineering Molecular Hypergraphs. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (5) (2013)
Christopher D. Lasher, Padmavathy Rajagopalan, T. M. Murali
Summarizing cellular responses as biological process networks. BMC Syst. Biol. 7 (2013)
Christopher L. Poirel, Ahsanur Rahman, Richard R. Rodrigues, Arjun Krishnan, Jacqueline R. Addesa, T. M. Murali
Reconciling differential gene expression data with molecular interaction networks. Bioinform. 29 (5) (2013)
Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, T. M. Murali
Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. J. Comput. Biol. 20 (5) (2013)
T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze
Network-Based Prediction and Analysis of HIV Dependency Factors. RECOMB (2012)
Corban G. Rivera, Brett M. Tyler, T. M. Murali
Sensitive detection of pathway perturbations in cancers. BMC Bioinform. 13 (S-3) (2012)
Ahsanur Rahman, Christopher L. Poirel, David Badger, T. M. Murali
Reverse engineering molecular hypergraphs. BCB (2012)
T. M. Murali
Guest Editor's Introduction: Computationally Driven Experimental Biology. Computer 45 (3) (2012)
Christopher L. Poirel, Clifford Conley Owens III, T. M. Murali
Network-based functional enrichment. BMC Bioinform. 12 (S-13) (2011)
Corban G. Rivera, Brett M. Tyler, T. M. Murali
Sensitive detection of pathway perturbations in cancers: extended abstract. BCB (2011)
T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze
Network-Based Prediction and Analysis of HIV Dependency Factors. PLoS Comput. Biol. 7 (9) (2011)
Tim Driscoll, Matthew D. Dyer, T. M. Murali, Bruno W. S. Sobral
PIG - the pathogen interaction gateway. Nucleic Acids Res. 37 (Database-Issue) (2009)
Corban G. Rivera, T. M. Murali
Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper. BICoB (2009)
Clifford Conley Owens III, T. M. Murali, Naren Ramakrishnan
Capturing truthiness: mining truth tables in binary datasets. SAC (2009)
T. M. Murali, Corban G. Rivera
Network Legos: Building Blocks of Cellular Wiring Diagrams. J. Comput. Biol. 15 (7) (2008)
Ying Jin, T. M. Murali, Naren Ramakrishnan
Compositional mining of multirelational biological datasets. ACM Trans. Knowl. Discov. Data 2 (1) (2008)
T. M. Murali, Corban G. Rivera
Network Legos: Building Blocks of Cellular Wiring Diagrams. RECOMB (2007)
Matthew D. Dyer, T. M. Murali, Bruno W. S. Sobral
Computational prediction of host-pathogen protein-protein interactions. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Gregory A. Grothaus, Adeel Mufti, T. M. Murali
Automatic layout and visualization of biclusters. Algorithms Mol. Biol. 1 (2006)
Naveed Massjouni, Corban G. Rivera, T. M. Murali
VIRGO: computational prediction of gene functions. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, T. M. Murali
XcisClique: analysis of regulatory bicliques. BMC Bioinform. 7 (2006)
Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, Simon Kasif
RankGene: identification of diagnostic genes based on expression data. Bioinform. 19 (12) (2003)
T. M. Murali, Simon Kasif
Extracting Conserved Gene Expression Motifs from Gene Expression Data. Pacific Symposium on Biocomputing (2003)
Cecilia Magdalena Procopiuc, Michael Jones, Pankaj K. Agarwal, T. M. Murali
A Monte Carlo algorithm for fast projective clustering. SIGMOD Conference (2002)
Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, Joseph S. B. Mitchell, T. M. Murali
New Similarity Measures between Polylines with Applications to Morphing and Polygon Sweeping. Discret. Comput. Geom. 28 (4) (2002)
Alon Efrat, Sariel Har-Peled, Leonidas J. Guibas, T. M. Murali
Morphing between polylines. SODA (2001)
Pankaj K. Agarwal, Edward F. Grove, T. M. Murali, Jeffrey Scott Vitter
Binary Space Partitions for Fat Rectangles. SIAM J. Comput. 29 (5) (2000)
Alon Efrat, Leonidas J. Guibas, Sariel Har-Peled, David C. Lin, Joseph S. B. Mitchell, T. M. Murali
Sweeping simple polygons with a chain of guards. SODA (2000)
Pankaj K. Agarwal, Leonidas J. Guibas, T. M. Murali, Jeffrey Scott Vitter
Cylindrical static and kinetic binary space partitions. Comput. Geom. 16 (2) (2000)
Edward F. Grove, T. M. Murali, Jeffrey Scott Vitter
The Object Complexity Model for Hidden-Surface Removal. Int. J. Comput. Geom. Appl. 9 (2) (1999)
Pankaj K. Agarwal, Lars Arge, T. M. Murali, Kasturi R. Varadarajan, Jeffrey Scott Vitter
I/O-Efficient Algorithms for Contour-line Extraction and Planar Graph Blocking (Extended Abstract). SODA (1998)
T. M. Murali, Pankaj K. Agarwal, Jeffrey Scott Vitter
Constructing Binary Space Partitions for Orthogonal Rectabgles in Practice. ESA (1998)
Pankaj K. Agarwal, T. M. Murali, Jeffrey Scott Vitter
Practical Techniques for Constructing Binary Space Partitions for Orthogonal Rectangles. SCG (1997)
T. M. Murali, Thomas A. Funkhouser
Consistent Solid and Boundary Representations from Arbitrary Polygonal Data. SI3D (1997)
Pankaj K. Agarwal, Leonidas J. Guibas, T. M. Murali, Jeffrey Scott Vitter
Cylindrical Static and Kinetic Binary Space Partitions. SCG (1997)
Pankaj K. Agarwal, Edward F. Grove, T. M. Murali, Jeffrey Scott Vitter
Binary Search Partitions for Fat Rectangles. FOCS (1996)