Publications

• Benjamin M. Gyori, Gireedhar Venkatachalam, P.S. Thiagarajan, David Hsu, Marie-Veronique Clement. OpenComet: An automated tool for comet image analysis in Redox Biology, (Accepted) (2014).
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• Andrei Hagiescu, Bing Liu, R. Ramanathan, Sucheendra K. Palaniappan, Zheng Cui, Bipasa Chatopadhyay, P.S. Thiagarajan, Weng-Fai Wong. GPU code generation for ODEs based applications with phased shared-data access patterns in ACM Transactions on Architecture and code optimization (ACM TACO), 10(4) (2013).
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• Sucheendra K Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu and P. S. Thiagarajan. Statistical model checking based calibration and analysis of bio-pathway models in Proceedings of the 11th international conference on computational methods in systems biology (CMSB'2013).
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• Sucheendra K. Palaniappan and P. S. Thiagarajan, “Dynamic Bayesian Networks: A Factored Model of Probabilistic Dynamics” in Automated Technology for Verification and Analysis, S. Chakraborty and M. Mukund, Eds. Springer Berlin Heidelberg, 2012, pp. 17–25.
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• Chuan Hock Koh, Sucheendra K. Palaniappan, P. S. Thiagarajan, and Limsoon Wong. Improved statistical model checking methods for pathways analysis. BMC Bioinformatics 13(Suppl 17) (Dec 2012) S15
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• Benjamin Gyori, David Hsu. Bayesian Estimation and Analysis of Pathway Models using Kernel-enhanced Particle Filters. In the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012), Poster, 2012.
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• Sucheendra K. Palaniappan, S. Akshay, Bing Liu, Blaise Genest, P.S.Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathway Application. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Special Section on the Ninth International Conference on Computational Methods in Systems Biology),1352–1365, September 2012.
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• Bing Liu, P.S. Thiagarajan. Modeling and Analysis of Biopathways Dynamics. Journal of Bioinformatics and Computational Biology, 10(4):1231001, August 2012.
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• Bing Liu, Andrei Hagiescu, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng Fai Wong, P.S. Thiagarajan. Approximate Probabilistic Analysis of Biopathway Dynamics. Bioinformatics, 28(11):1508–1516, June 2012.
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• Sucheendra K. Palaniappan, S. Akshay, Blaise Genest, P.S. Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Network Models of Biopathways. In Proc. of the 9th Computational Methods in Systems Biology (CMSB 2011), 2011.
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• Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding, P. S. Thiagarajan. A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System. PLoS Computational Biology, 7(1):e1001059, 2011.
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• Geoffrey Koh, David Hsu, P.S. Thiagarajan. Component-based Construction of Bio-pathway Models: The Parameter Estimation Problem. Theoretical Computer Science (Special Issue on Foundations of Formal Reconstruction of Biochemical Networks), 2011.
  PDF   Supplementary Website.
• Bing Liu, David Hsu, P. S. Thiagarajan. Probabilistic Approximations of ODEs based Bio-Pathway Dynamics. Theoretical Computer Science, 412(21):2188-2206, 2011.
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• Geoffrey Koh, David Hsu, P.S. Thiagarajan. Incremental Signaling Pathway Modeling by Data Integration. In Proc. of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010) , 2010.
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• Bing Liu, P.S. Thiagarajan, David Hsu. Probabilistic Approximations of Signaling Pathway Dynamics. In Proc. of the 7th Computational Methods in Systems Biology (CMSB 2009) , 2009.
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• Bing Liu, David Hsu, P.S. Thiagarajan. Probabilistic Approximations of Bio-pathway Dynamics. In the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009) Poster Book, 2009.
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• Geoffrey Koh, David Hsu, P.S. Thiagarajan. Composition of signaling pathway models and its application to parameter estimation. In the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008) Poster Book, 2008.
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• Geoffrey Koh, Lisa Tucker-Kellogg, David Hsu, and P.S. Thiagarajan. Composing globally consistent pathway parameter estimates through belief propagation. In Proc. of the 7th Workshop on Algorithms in Bioinformatics (WABI 2007) , 2007.
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• Geoffrey Koh, Huey Fern Carol Teong, Marie-Veronique Clement, David Hsu, P.S. Thiagarajan. A decompositional approach to parameter estimation in pathway modeling: A case study of the AKT and MAPK pathways and their crosstalk. Bioinformatics, 22:e271--e280, 2006.
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