# Computational Systems Biology

A theorem proving approach for automatically synthesizing visualizations of flow cytometry data
,” BMC Bioinformatics, vol. 18, no. 8, pp. 245, 2017. Publisher's VersionAbstract flowcytometry_bmcbioinformatics2017.pdf

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Stochastic computational model parameter synthesis system
”, US Patent: US9558300 B2, 2017.Abstract

, “US Patent App. 13/673,575

Automated parameter estimation for biological models using Bayesian statistical model checking
,” BMC bioinformatics, vol. 16, no. 17, pp. S8, 2015.Abstract bmcbioinformatics_discovery.pdf

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**BEST PAPER AWARD at IEEE ICCABS 2014**

SANJAY: Automatically synthesizing visualizations of flow cytometry data using decision procedures
,” in Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on, 2015, pp. 1–1.

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EpiSpec: A formal specification language for parameterized agent-based models against epidemiological ground truth
,” in Computational Advances in Bio and Medical Sciences (ICCABS), 2014 IEEE 4th International Conference on, 2014, pp. 1–6.

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Parameter discovery for stochastic computational models in systems biology using Bayesian model checking
,” in Computational Advances in Bio and Medical Sciences (ICCABS), 2014 IEEE 4th International Conference on, 2014, pp. 1–2.

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Parameter discovery in stochastic biological models using simulated annealing and statistical model checking
,” International Journal of Bioinformatics Research and Applications 2, vol. 10, no. 4-5, pp. 519–539, 2014.

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Putting humpty-dumpty together: Mining causal mechanistic biochemical models from big data
,” in Computational Advances in Bio and Medical Sciences (ICCABS), 2014 IEEE 4th International Conference on, 2014, pp. 1–6.

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A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readout
,” in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012, pp. 530–532.

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Exploring behaviors of stochastic differential equation models of biological systems using change of measures
,” BMC bioinformatics, vol. 13, no. 5, pp. S8, 2012.

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**BEST PAPER AWARD**

Quantifying uncertainty in epidemiological models
,” in BioMedical Computing (BioMedCom), 2012 ASE/IEEE International Conference on, 2012, pp. 80–85. quantifyinguncertainty.pdf

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Parameter estimation and synthesis for systems biology: New algorithms for nonlinear and stochastic models
,” Journal of critical care, vol. 26, no. 2, pp. e8, 2011.

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Synthesis and infeasibility analysis for stochastic models of biochemical systems using statistical model checking and abstraction refinement
,” Theoretical Computer Science, vol. 412, no. 21, pp. 2162–2187, 2011.

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A bayesian approach to model checking biological systems
,” in International Conference on Computational Methods in Systems Biology, 2009, pp. 218–234. cmsb09_bayesianstatisticalmodelchecking_jha.pdf

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Symbolic approaches for finding control strategies in Boolean networks
,” Journal of Bioinformatics and Computational Biology, vol. 7, no. 02, pp. 323–338, 2009.Abstract 2009_jbcb_and_apbc_paper_underlined.pdf

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Statistical model checking in biolab: Applications to the automated analysis of t-cell receptor signaling pathway
,” in International Conference on Computational Methods in Systems Biology, 2008, pp. 231–250.Abstract 2008_cmsb_underlined.pdf

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Predicting protein folding kinetics via temporal logic model checking
,” in International Workshop on Algorithms in Bioinformatics, 2007, pp. 252–264.Abstract 2007_wabi_underlined.pdf

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