**Papers**

**Preprints**

**NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities**[bioRxiv]

B. Li, D. Taniguchi, J. P. Gedara, V. Gogulancea, R. Gonzalez-Cabaleiro, J. Chen, A. S. McGough, I. D. Ofiteru, T. P. Curtis, P. Zuliani

**Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems**[arXiv]

F. Shmarov, S. Soudjani, N. Paoletti, E. Bartocci, S. Lin, S. A. Smolka, P. Zuliani

**Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth**[doi]

V. Gogulancea, R. Gonzalez-Cabaleiro, B. Li, D. Taniguchi, P. G. Jayathilake, J. Chen, D. Wilkinson, D. Swailes, A. S. McGough, P. Zuliani, I. D. Ofiteru, T. P. Curtis

*Frontiers Microbiology*, 2019, to appear.**Bayesian emulation and calibration of an individual-based model of microbial communities**[doi]

O. Oyebamiji, D. Wilkinson, B. Li, P. G. Jayathilake, P. Zuliani, T. P. Curtis

*Journal of Computational Science*30:194-208, 2019.**A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation**[doi]

O. Oyebamiji, D. Wilkinson, P. G. Jayathilake, S. Rushton, B. Bridgens, B. Li, P. Zuliani

*PLoS ONE*13(4): e0195484, 2018.**A Mechanistic Individual-based Model of Microbial Communities**[doi]

P. G. Jayathilake, P. Gupta, B. Li, C. Madsen, O. Oyebamiji, R. González-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, S. McGough, P. Zuliani, I. D. Ofiteru, D. Wilkinson, J. Chen, T. Curtis

*PLoS ONE*12(8): e0181965, 2017.**Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation**[doi]

G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, A. Wipat

*Bioinformatics*, 32(6):908-917, 2016.**Statistical Model Checking for Biological Applications**[pdf]

P. Zuliani

*Software Tools for Technology Transfer*, 17(4):527-536, 2015.**Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features**[pdf]

J. Rusakovica, J. Hallinan, A. Wipat, P. Zuliani

*Journal of Integrative Bioinformatics*, 11(2):243, 2014.**Bayesian Statistical Model Checking with Application to Stateflow/Simulink Verification**[pdf]

P. Zuliani, A. Platzer, E. M. Clarke

*Formal Methods in System Design*, 43(2):338-367, 2013.**Model checking of a synchronous diabetes-cancer logical network**[pdf]

H. Gong, P. Zuliani, E. M. Clarke

*Current Bioinformatics*, 8(1):9-15, 2013.**Analysis and Verification of the HMGB1 Signaling Pathway**[doi]

H. Gong, P. Zuliani, A. Komuravelli, J. R. Faeder, E. M. Clarke

*BMC Bioinformatics*2010, 11(Suppl 7):S10. (Best Paper Award at InCoB 2010.)**Reasoning about faulty quantum programs**[pdf]

P. Zuliani

*Acta Informatica*, 46(6):403-432, 2009.**Compiling quantum programs**[pdf]

P. Zuliani

*Acta Informatica*, 41(7-8):435-474, 2005.**An empirical exploration of the distributions of the Chidamber and Kemerer object-oriented metrics suite**[doi]

G. Succi, W. Pedrycz, S. Djokic, P. Zuliani, B. Russo

*Empirical Software Engineering*, 10(1):81-104, 2005.**Logical reversibility**[pdf]

P. Zuliani

*IBM Journal of Research and Development*, 45(6):807-818, 2001.

**Tutorials**

**Model checking and the state explosion problem**[pdf]

E. M. Clarke, W. Klieber, M. Nováček, P. Zuliani

In*8th LASER Summer School on Software Engineering*, Sept. 4-10, 2011. LNCS volume 7682, pp. 1-30, 2012.

**Conferences**

**Stochastic Rate Parameter Inference using the Cross-Entropy Method**[doi] [tool page]

J. Revell, P. Zuliani

In*CMSB 2018: 16th International Conference on Computational Methods in Systems Biology.*LNCS volume 11095, pp. 146-164, 2018.**An Evaluation of Estimation Techniques for Probabilistic Reachability**[pdf]

M. Vasileva, P. Zuliani

In*SNR 2018, to appear***Entangλe: A Translation Framework from Quipper Programs to Quantum Markov Chains**[pdf]

L. Anticoli, C. Piazza, L. Taglialegne, P. Zuliani

In*InfQ 2017: 7th Workshop on Quantitative Methods in Informatics*. Springer CCIS, volume 825, pp. 113-126, 2017.**SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems**[pdf]

F. Shmarov, N. Paoletti, E. Bartocci, S. Lin, S. A. Smolka, P. Zuliani

In*HVC 2017: 13th Haifa Verification Conference*. LNCS volume 10629, pp. 131-146, 2017.**Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques**[pdf]

F. Shmarov, P. Zuliani

In*HVC 2016: 12th Haifa Verification Conference*. LNCS volume 10028, pp. 152-168, 2016.**High-level modeling and verification of cellular signaling**[doi]

N. Miskov-Zivanov, P. Zuliani, Q. Wang, E. M. Clarke, J. R. Faeder

In*HLDVT 2016: 18th IEEE International High Level Design Validation and Test Workshop*. IEEE, pp. 162-169, 2016.**Verifying Quantum Programs: From Quipper Circuits to QPMC**[pdf]

L. Anticoli, C. Piazza, L. Taglialegne, P. Zuliani

In*RC 2016: 8th Conference on Reversible Computation*. LNCS volume 9720, pp. 213-219, 2016.**SMT-Based Reasoning for Uncertain Hybrid Domains**[pdf]

F. Shmarov, P. Zuliani

In*AAAI-16 Workshop on Planning for Hybrid Systems, 30th AAAI Conference on Artificial Intelligence*, 2016.**BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models**[pdf] [tool page]

C. Madsen, F. Shmarov, P. Zuliani

In*CMSB 2015: 13th Conference on Computational Methods in Systems Biology*. LNCS volume 9308, pp. 182-194, 2015.**SReach: A Bounded Model Checker for Stochastic Hybrid Systems**[pdf] [tool page]

Q. Wang, P. Zuliani, S. Kong, S. Gao, E. M. Clarke

In*CMSB 2015: 13th Conference on Computational Methods in Systems Biology*. LNCS volume 9308, pp. 15-27, 2015.**ProbReach: Verified Probabilistic Delta-Reachability for Stochastic Hybrid Systems**[pdf] [tool page]

F. Shmarov, P. Zuliani

In*HSCC 2015: 18th International Conference on Hybrid Systems: Computation and Control*. ACM, pp. 134-139, 2015.**Towards Personalized Prostate Cancer Therapy Using Delta-Reachability Analysis**[pdf]

B. Liu, S. Kong, S. Gao, P. Zuliani, E. M. Clarke

In*HSCC 2015: 18th International Conference on Hybrid Systems: Computation and Control*. ACM, pp. 227-232, 2015.**Parameter Synthesis for Cardiac Cell Hybrid Models Using Delta-Decisions**[pdf]

B. Liu, S. Kong, S. Gao, P. Zuliani, E. M. Clarke

In*CMSB 2014: 12th Conference on Computational Methods in Systems Biology*. LNCS volume 8859, pp. 99-113, 2014.**Studies of biological networks with statistical model checking: application to immune system cells**[doi]

N. Miskov-Zivanov, P. Zuliani, E. M. Clarke, J. R. Faeder

In*ACM-BCB 2013: ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics*. (Poster)**Statistical model checking for Markov decision processes**[pdf] [tool page]

D. Henriques, J. Martins, P. Zuliani, A. Platzer, E. M. Clarke

In*QEST 2012: 9th International Conference on Quantitative Evaluation of SysTems*. IEEE, pp. 84-93.**Model checking for studying timing of events in T cell differentiation**[pdf]

P. Zuliani, N. Miskov-Zivanov, J. R. Faeder, E. M. Clarke

In*IWBDA 2012: 4th International Workshop on Bio-Design Automation, with 49th ACM/EDAC/IEEE Design Automation Conference*(Abstract).**Rare-Event Verification for Stochastic Hybrid Systems**[pdf]

P. Zuliani, C. Baier, E.M. Clarke

In*HSCC 2012: 15th ACM International Conference on Hybrid Systems: Computation and Control*, pp. 217-226, 2012.**Formal Analysis for Logical Models of Pancreatic Cancer**[pdf]

H. Gong, P. Zuliani, Q. Wang, E. M. Clarke

In*CDC-ECC 2011: 50th IEEE Conference on Decision and Control and European Control Conference*. IEEE, pp. 4855-4860, 2011.**Statistical Model Checking for Cyber-Physical Systems**[pdf]

E. M. Clarke, P. Zuliani

In*ATVA 2011: 9th International Symposium on Automated Technology for Verification and Analysis*. LNCS volume 6996, pp. 1-12, 2011. (Invited paper.)**Model Checking of a Diabetes-Cancer Model**[pdf]

H. Gong, P. Zuliani, E. M. Clarke

In*CMLS 2011: 3rd International Symposium on Computational Models for Life Sciences*, AIP Conf. Proc. 1371, pp. 234-243, 2011.**Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer**[pdf]

H. Gong, Q. Wang, P. Zuliani, J. R. Faeder, M. T. Lotze, E. M. Clarke

In*BiCoB 2011: 3rd International Conference on Bioinformatics and Computational Biology*, March 23-25, 2011, New Orleans, LA.**Analog Circuit Verification by Statistical Model Checking**[pdf]

Y.-C. Wang, A. Komuravelli, P. Zuliani, E. M. Clarke

In*ASP-DAC 2011: 16th Asia and South Pacific Design Automation Conference*. IEEE, pp. 1-6, 2011. (Best Paper Award nomination.)**Statistical Verification of Probabilistic Properties with Unbounded Until**[pdf]

H. L. S. Younes, E. M. Clarke, P. Zuliani

In*SBMF 2010: 13th Brazilian Symposium on Formal Methods*. LNCS volume 6527, pp. 144-160, 2011.**Computational Modeling and Verification of Signaling Pathways in Cancer**[pdf]

H. Gong, P. Zuliani, A. Komuravelli, J. R. Faeder, E. M. Clarke

In*ANB 2010: 4th International Conference on Algebraic and Numeric Biology*. LNCS volume 6479, pp. 117-135, 2010.**Bayesian Statistical Model Checking with Application to Stateflow/Simulink Verification**[pdf]

P. Zuliani, A. Platzer, E. M. Clarke

In*HSCC 2010: 13th ACM International Conference on Hybrid Systems: Computation and Control*, pp. 243-252, 2010.**A Bayesian approach to model checking biological systems**[pdf]

S. K. Jha, E. M. Clarke, C. J. Langmead, A. Legay, A. Platzer, P. Zuliani

In*CMSB 2009: 7th Conference on Computational Methods in Systems Biology*. LNCS volume 5688, pp. 218-234, 2009.**A formal derivation of Grover's quantum search algorithm**[pdf]

P. Zuliani

In*TASE 2007: 1st IEEE & IFIP International Symposium on Theoretical Aspects of Software Engineering*, pp. 67-74, 2007.**Quantum programming with mixed states**[pdf]

P. Zuliani

In*QPL 2005: 3rd International Workshop on Quantum Programming Languages*. ENTCS, volume 170, pp. 185-199, 2007.**On counterfactual computation**[pdf]

P. Zuliani

In*UC 2005: 4th International Conference on Unconventional Computation*. LNCS, volume 3699, pp. 251-266, 2005.**On the transition to an open source solution for desktop automation**[doi]

B. Rossi, B. Russo, P. Zuliani, G. Succi

In*TCGOV 2005: ESF-TCD Conference on e-Government*. LNCS, volume 3416, pp. 277-285, 2005.**Non-deterministic quantum programming**[pdf]

P. Zuliani

In*QPL 2004: 2nd International Workshop on Quantum Programming Languages*, pp. 179-195. TUCS Publication 33, Turku, Finland, 2004.-
**An empirical analysis on the discontinuous use of pair programming**[doi]

A. Janes, B. Russo, P. Zuliani, G. Succi

In*XP 2003: 4th International Conference on eXtreme Programming and Agile Processes in Software Engineering*. LNCS, volume 2675, pp. 205-214, 2003. **Quantum programming**[pdf]

J. W. Sanders, P. Zuliani

In*MPC 2000: Mathematics of Program Construction*. LNCS, volume 1837, pp. 80-99, 2000.