Publications

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Refereed Conference Papers	Refereed Journal Papers	Referred Workshop Papers

Refereed Conference Papers

S.D. Stoller, E. Bartocci, J. Seyster, R. Grosu, K. Havelund, S.A. Smolka, and E. Zadok. Runtime Verification with State Estimation. In Proc. of RV'11, the 2nd International Conference on Runtime Verification, San Francisco, September, 2011, Springer LNCS. Best Paper Award

A. Murthy, E. Bartocci, F. Fenton, J. Glimm, R. Gray, S.A. Smolka, and R. Grosu. Curvature Analysis of Cardiac Excitation Wavefronts. In CMSB 2011: Proceedings of the 9th ACM International Conference on Computational Methods in Systems Biology, Paris, France, September 21-23, pages 151-160. ACM, 2011.

E. Bartocci, E. Cherry, J. Glimm, R. Grosu, S.A. Smolka, and F. Fenton. Toward Real-time Simulation of Cardiac Dynamics. In CMSB 2011: Proceedings of the 9th ACM International Conference on Computational Methods in Systems Biology, Paris, France, September 21-23, pages 103-110. ACM, 2011.

R. Grosu, G. Batt, F. Fenton, J. Glimm, C. Le Guernic, S.A. Smolka and E. Bartocci. From Cardiac Cells to Genetic Regulatory Networks. In Proc. of CAV'11, the 23rd International Conference on Computer Aided Verification, Cliff Lodge, Snowbird, Utah, USA, July, 2011, pages 396-411, Springer, LNCS, 6806

E. Bartocci, R. Grosu, P. Katsaros, C.R. Ramakrishnan and S.A. Smolka. Model Repair for Probabilistic Systems. In Proc. of TACAS'11, the 7th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Saarbruecken, Germany, March, 2011, pp. 326-340, Springer, LNCS 6605.

E. Bartocci, D. Cacciagrano, F. Corradini, E. Merelli and L. Vito. A Resourceome for the Automation of In-silico Biological Experiments. In Proc. of the First International Conference on Biosciences, 2010, Cancun, Mexico

E. Bartocci, M. R. Di Berardini, F. Corradini, E. Merelli and L. Tesei. Shape Calculus for Biological Processes. In Proc. of ICTCS'09, the 11th Italian Conference on Theoretical Computer Science, Cremona, Italy, March, 2009

R. Grosu, E. Bartocci, F. Corradini, E. Entcheva, S.A. Smolka and A. Wasilewska. Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes. In Proc. of HSCC'08, the 11th International Conference on Hybrid Systems: Computation and Control, St. Louis, USA, April, 2008, pp. 229-243, Springer, LNCS 4981. To also appear in CACM, the Communications of the ACM, 2009.

E. Bartocci, E. Merelli, L. Mariani. An XML View of the World. In Proc. of ICEIS'03, the 5th International Conference on Enterprise Information Systems, Angers, France, April 22-26, pp. 19-27, 2003.

Refereed Journal Papers

E. Bartocci, R. Singh, F. von Stein, A. Amedome, Alan-Joseph Caceres, J. Castillo, E. Closser, G. Deards, A. Goltsev, R. Sta. Ines, C. Isbilir, J. Marc, D. Moore, D. Pardi, S. Sadhu, S. Sanchez, P. Sharma, A. Singh, J. Rogers, A. Wolinetz, T. Grosso-Applewhite, K. Zhao, A. Filipski, R. Gilmour Jr, R. Grosu, J. Glimm, S. A. Smolka, E. Cherry, E. Clarke, N. Griffeth, and F. Fenton. Teaching cardiac electrophysiology modeling to undergraduate students; using Java Applets and GPU programs to study arrhythmias and spiral wave dynamics. Journal of Advances in Physiology of Education, To appear

E. Bartocci, F. Corradini, M. R. Berardini, E. Merelli, L. Tesei. Shape Calculus. A Spatial Mobile Calculus for 3D Shapes. In Sci. Ann. Comp. Sci., pp. 1-31, vol. 20, 2010.

E. Bartocci, D. R. Cacciagrano, M. R. Di Berardini, E. Merelli, L. Tesei. Timed Operational Semantics and Well-Formedness of Shape Calculus. In Sci. Ann. Comp. Sci., pp. 32-52, vol. 20, 2010.

E. Bartocci, F. Corradini, E. Merelli, L. Tesei. Detecting synchronisation of biological oscillators by model checking. In Theoretical Computer Science, vol. 411(20), pp. 1999-2018, 2010.

E. Bartocci, F. Corradini, M.R. Di Berardini, E. Entcheva, S.A. Smolka and R. Grosu. Modeling and Simulation of Cardiac Tissue using Hybrid I/O Automata. In Theoretical Computer Science (TCS), vol. 410(33-34), pp. 3149-3165, August, 2009.

R. Grosu, S.A. Smolka, F. Corradini, A. Wasilewska, E. Entcheva and E. Bartocci. Learning and Detecting Emergent Behavior in Networks of Cardiac Myocytes. In CACM, the Communications of the ACM, vol. 52(3), pp. 1-10, March, 2009. Shorter version also in Proc. of HSCC'08, the 11th International Conference on Hybrid Systems: Computation and Control, St. Louis, USA, April, 2008, pp. 229-243, Springer, LNCS 4981.

E. Bartocci, F. Corradini, E. Entcheva, R. Grosu, S. A. Smolka. CellExcite: An Efficient Simulation Environment for Excitable Cells. In BMC Bioinformatics, vol. 9(Suppl 2), 2008.

E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, E. Merelli, L. Milanesi, P. Romano. An Agent-based Multilayer Architecture for Bioinformatics Grids. IEEE transactions on Nanobioscience, vol. 6(2), 2007.

E. Bartocci, F. Corradini, E. Merelli, Lorenzo Scortichini . BioWMS: a web-based Workflow Management System for bioinformatics. In BMC Bioinformatics, vol. 8(Suppl 1), 2007.

P. Romano, E. Bartocci, G. Bertolini, F. De Paoli, D. Marra, G. Mauri, E. Merelli, L. Milanesi. BioWep: a Workflow Management portal for bionformatics applications. In BMC Bioinformatics, vol. 8(Suppl 1), 2007.

G. Fischer, S. Ibrahim, G. Brockmann, J. Pahnke, E. Bartocci, Hans-Jurgen Thiesen, S. Moller, P. Serrano-Fernandez. Expressionview: visualization of quantitative trait loci and gene-expression data in Ensembl. In Genome Biology, vol. 4(11), pp. R77, 2003.

Refereed Workshop

E. Bartocci, F. Corradini, E. Merelli, L. Tesei. Model Checking Biological Oscillators. In Proc. of FBTC'08, the 2th International Workshop From Biology to Concurrency and Back, Lisbon, July, 2008. ENTCS vol. 229(1), pp. 41-58, 2009.

E. Bartocci, F. Corradini, M.R. Di Berardini, E. Entcheva, R. Grosu and S.A. Smolka. Spatial Networks of Hybrid I/O Automata for Modeling Excitable Tissue. In Proc. of FBTC'07, the International Workshop From Biology to Concurrency and Back, Lisbon, September, 2007. ENTCS vol. 194(3), pp. 51-67, 2007.

E. Bartocci, F. Corradini, E, Merelli, L. Vito. Model driven design and implementation of activity-based applications in Hermes. In Proc. of Workshop From Object to Agents - WOA 2006 - Demo Session, September 26-27, 2006, Catania, Italy.

E. Bartocci, F. Corradini, E, Merelli. Building a Multiagent System from User Workflow Specification. In Proc. of Workshop From Object to Agents - WOA 2006, September 26-27, 2006, Catania, Italy.

E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, E. Merelli, L. Milanesi, P. Romano, A GRID-based multilayer architecture for bioinfomratics. In Proc. of the NETTAB'06 Network Tools and Application in Biology, Santa Margheita di Pula, Cagliari, Italy

E. Bartocci, F. Corradini, E, Merelli. Enacting proactive workflows engine in e-Science. In Proc. of the 1st International Workshop on Workflow Systems in e-Science (WSES 06) ICCS 2006, Part III, LNCS 3993-1012, Springer-Verlag

Invited Papers

E. Bartocci, F. Corradini, E. Merelli, R. Grosu, O. Riganelli, S. A. Smolka. StonyCam: a Formal Framework for Modeling, Analyzing and Regulating Cardiac Myocytes. Concurrency, Graphs and Models 2008, Lecture Notes in Computer Science vol. 5065, pp. 493-502, Springer-Verlag

Submitted Papers

E. Bartocci, D. Cacciagrano, M. R. Di Berardini, E. Merelli, L. Vito UBILab: a web-based tool for ubiquitous in-silico experiments Journal of Integrative Bioinformatics

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Runtime Verification with State Estimation

Toward Realtime Simulation of Cardiac Dynamics

From Cardiac Cells to Genetic Regulatory Networks

Modeling the cell cycle: From deterministic models to hybrid systems

Model Repair for Probabilistic Systems

Curvature Analysis of Cardiac Excitation Wavefronts

Shape Calculus. A Spatial Mobile Calculus for 3D Shapes

Timed Operational Semantics and Well-Formedness of Shape Calculus

Shape Calculus: Timed Operational Semantics and Well-formedness

Detecting synchronisation of biological oscillators by model checking

A Resourceome for the Automation of In-silico Biological Experiments

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