Papers
Preprints
- Quantum Computer Benchmarking via Quantum Algorithms [arXiv]
K. Georgopoulos, C. Emary, P. Zuliani. 2021.
- Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network [bioRxiv]
J. Sakkos, J. Weaver, C. Robertson, B. Li, D. Taniguchi, K. Maheshwari, D. Ducat, P. Zuliani, A. S. McGough, T. P Curtis, M. Fuentes-Cabrera. 2021
- Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis [bioRxiv]
F. Shmarov, G.R. Smith, S.C. Weatherhead, N.J. Reynolds, P. Zuliani. 2021
- Formal Verification of Quantum Programs: Theory, Tools and Challenges [arXiv]
M. Lewis, S. Soudjani, P. Zuliani. 2021
Edited Volumes
- Automated Reasoning for Systems Biology and Medicine [doi]
P. Liò and P. Zuliani (Editors). Springer, 2019.
Journals
- Modelling and Simulating the Noisy Behaviour of Near-term Quantum Computers [arXiv]
K. Georgopoulos, C. Emary, P. Zuliani
Physical Review A 104, 062432, 2021.
- The use of psoriasis biomarkers, including trajectory of clinical response, to predict clearance and remission duration to UVB phototherapy
[doi]
N. Watson, N. Wilson, F. Shmarov, P. Zuliani, N. J. Reynolds, S. C. Weatherhead
Journal of the European Academy of Dermatology & Venereology 35: 2250-2258, 2021
- A Comparison of Quantum Walk Implementations on Noisy Intermediate-Scale Quantum Computers [arXiv]
K. Georgopoulos, C. Emary, P. Zuliani
Physical Review A 103, 022408, 2021.
- CFD-DEM modelling of biofilm streamer oscillations and their cohesive failure in fluid flow [doi]
Y. Xia, P. G. Jayathilake, B. Li, P. Zuliani, J. Chen
Biotechnology and Bioengineering 118: 918–929, 2021.
- Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems [doi]
F. Shmarov, S. Soudjani, N. Paoletti, E. Bartocci, S. Lin, S. A. Smolka, P. Zuliani
IEEE Access 8:180825-180843, 2020.
- Pathways to cellular supremacy in biocomputing [doi]
L. Grozinger, M. Amos, T. Gorochowski, P. Carbonell, D. Oyarzún, R. Stoof, H. Fellermann, P. Zuliani, H. Tas, A. Goni-Moreno
Nature Communications 10, 5250 (2019).
- NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities [doi]
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
PLOS Computational Biology, 15(12): e1007125, 2019.
- Modelling bacterial twitching in fluid flows: a CFD-DEM approach [doi]
P. G. Jayathilake, B. Li, P. Zuliani, T. P. Curtis, J. Chen
Scientific Reports 9, 14540 (2019).
- 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 10:1871, 2019.
- 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
- Spatio-temporal model checking for 3D individual-based biofilm simulations [pdf]
B. Li, J. P. Gedara, Y. Xia, T. P. Curtis, P. Zuliani.
In DataMod 2021: 10th Symposium on From Data to Models and Back. To appear.
- Approximate Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes [pdf]
M. Vasileva, F. Shmarov, P. Zuliani
In MEMOCODE 2020: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, pp. 1-11, 2020.
- An Evaluation of Estimation Techniques for Probabilistic Verification [pdf]
M. Vasileva, P. Zuliani
In VECoS 2020: 14th International Conference on Verification and Evaluation of Computer and Communication Systems. LNCS volume 12519, pp. 165-179, 2020.
- ARCH-COMP20 Category Report: Stochastic Models [doi]
A. Abate, H. Blom, N. Cauchi, J. Delicaris, A. Hartmanns, M. Khaled, A. Lavaei, C. Pilch, A. Remke,
S. Schupp, F. Shmarov, S. Soudjani, A. P. Vinod, B. Wooding, M. Zamani, and P. Zuliani
In ARCH20: 7th International Workshop on Applied Verification of Continuous and Hybrid Systems. EPiC volume 74, pp. 76-106, 2020.
- 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.
- 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.
Home