2018 (8)
Lumping of degree-based mean-field and pair-approximation equations for multistate contact processes. Kyriakopoulos, C.; Grossmann, G.; Wolf, V.; and Bortolussi, L. Physical Review E, 97(1). 2018.
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Student performance prediction and optimal course selection: An MDP approach. Backenköhler, M.; and Wolf, V. Volume 10729 LNCS 2018.
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Approximate Adaptive Uniformization of Continuous-Time Markov Chains. Andreychesnko, A.; Sandmann, W.; and Wolf, V. Applied Mathematical Modelling. 5 2018.
Approximate Adaptive Uniformization of Continuous-Time Markov Chains [pdf]Paper   Approximate Adaptive Uniformization of Continuous-Time Markov Chains [link]Website   bibtex   abstract
Simulating the Large-Scale Erosion of Genomic Privacy Over Time. Backes, M.; Berrang, P.; Humbert, M.; Shen, X.; and Wolf, V. IEEE/ACM Transactions on Computational Biology and Bioinformatics,1. 2018.
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Stochastic hybrid models of gene regulatory networks – A PDE approach. Kurasov, P.; Lück, A.; Mugnolo, D.; and Wolf, V. Mathematical Biosciences, 305: 170-177. 2018.
Stochastic hybrid models of gene regulatory networks – A PDE approach [link]Website   bibtex
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing. Giehr, P.; Kyriakopoulos, C.; Lepikhov, K.; Wallner, S.; Wolf, V.; and Walter, J. Nucleic Acids Research, 46(15): e88-e88. 9 2018.
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing [link]Website   bibtex   abstract
Lumping the Approximate Master Equation for Multistate Processes on Complex Networks. Großmann, G.; Kyriakopoulos, C.; Luca Bortolussi, V.; and Wolf, E. In Proceedings of the 15th International Conference on Quantitative Evaluation of SysTems (QEST 2018), 2018.
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Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium. Backenkohler, M.; Bortolussi, L.; and Wolf, V. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 15(4): 1180-1192. 7 2018.
Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium [link]Website   bibtex
  2017 (3)
A stochastic model for the formation of spatial methylation patterns. Lück, A.; Giehr, P.; Walter, J.; and Wolf, V. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 10545 LNBI. 2017.
A stochastic model for the formation of spatial methylation patterns [link]Website   bibtex   abstract
Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium. Backenkohler, M.; Bortolussi, L.; and Wolf, V. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017.
Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium [link]Website   bibtex
Lumping of Degree-Based Mean Field and Pair Approximation Equations for Multi-State Contact Processes. Kyriakopoulos, C.; Grossmann, G.; Wolf, V.; and Bortolussi, L. Physical Review E, 97. 2017.
Lumping of Degree-Based Mean Field and Pair Approximation Equations for Multi-State Contact Processes [pdf]Website   bibtex
  2016 (4)
H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data. Giehr, P.; Kyriakopoulos, C.; and Wolf, V. ,Submitted. 2016.
H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data [link]Website   bibtex
Generalized method of moments for estimating parameters of stochastic reaction networks. Lueck, A.; and Wolf, V. BMC Systems Biology, 10(1). 2016.
Generalized method of moments for estimating parameters of stochastic reaction networks [link]Website   bibtex   abstract
Hybrid stochastic simulation of rule-based polymerization models. Krüger, T.; and Wolf, V. Volume 9957 LNBI 2016.
Hybrid stochastic simulation of rule-based polymerization models [link]Website   bibtex   abstract   buy
The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach. Giehr, P.; Kyriakopoulos, C.; Ficz, G.; Wolf, V.; and Walter, J. PLoS Computational Biology, 12(5). 2016.
The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach [link]Website   bibtex   abstract
  2015 (7)
Model Reconstruction for Moment-Based Stochastic Chemical Kinetics. Andreychenko, A.; Mikeev, L.; and Wolf, V. ACM Transactions on Modeling and Computer Simulation, 25(2): 1-19. 2015.
Model Reconstruction for Moment-Based Stochastic Chemical Kinetics [link]Website   bibtex   abstract
Reconstruction of multimodal distributions for hybrid moment-based chemical kinetics. Andreychenko, A.; Mikeev, L.; and Wolf, V. Journal of Coupled Systems and Multiscale Dynamics, 3(2): 156-163. 2015.
Reconstruction of multimodal distributions for hybrid moment-based chemical kinetics [link]Website   bibtex   abstract
Model reconstruction for moment-based stochastic chemical kinetics. Andreychenko, A.; Mikeev, L.; and Wolf, V. ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2): 12. 2015.
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Model-based whole-genome analysis of dna methylation fidelity. Bock, C.; Bortolussi, L.; Krüger, T.; Mikeev, L.; and Wolf, V. Volume 9271 . pages 141-155. Springer, 2015.
Model-based whole-genome analysis of dna methylation fidelity [link]Website   bibtex   abstract
Modeling of Resilience Properties in Oscillatory Biological Systems Using Parametric Time Petri Nets. Andreychenko, A.; Magnin, M.; and Inoue, K. In Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings, pages 239-250, 2015. Springer International Publishing
Modeling of Resilience Properties in Oscillatory Biological Systems Using Parametric Time Petri Nets [link]Website   bibtex
Rule-based modelling and simulation of drug-administration policies. Bortolussi, L.; Krüger, T.; Lehr, T.; and Wolf, V. In Proceedings of the Symposium on Modeling and Simulation in Medicine, pages 53-60, 2015.
Rule-based modelling and simulation of drug-administration policies [link]Website   bibtex   abstract
Optimal observation time points in stochastic chemical kinetics. Kyriakopoulos, C.; and Wolf, V. Volume 7699 2015.
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  2014 (3)
Optimal Observation Time Points in Stochastic Chemical Kinetics. Kyriakopoulos, C.; and Wolf, V. In Hybrid Systems Biology, pages 83-96, 2014. Springer
Optimal Observation Time Points in Stochastic Chemical Kinetics [link]Website   bibtex   abstract
Analyzing Oscillatory Behavior with Formal Methods. Andreychenko, A.; Krüger, T.; and Spieler, D. pages 1-25. Springer, 2014.
Analyzing Oscillatory Behavior with Formal Methods [link]Website   bibtex   abstract
Model checking CSL for markov population models. Spieler, D.; Hahn, E., M.; and Zhang, L. In QAPL'14, 2014. EPTCS
Model checking CSL for markov population models [pdf]Website   bibtex   abstract
  2013 (8)
Numerical Approximation of Rare Event Probabilities in Biochemically Reacting Systems. Mikeev, L.; Sandmann, W.; and Wolf, V. In Computational Methods in Systems Biology, pages 5-18, 2013.
Numerical Approximation of Rare Event Probabilities in Biochemically Reacting Systems [link]Website   bibtex   abstract
Approximate transient analysis of queueing networks by quasi product forms. Angius, A.; Horvath, A.; and Wolf, V. In Proceedings of the 20th International Conference on Analytic and Stochastic Modelling Techniques and Applications (ASMTA'13), of Lecture Notes of Computer Science, 2013. Springer
Approximate transient analysis of queueing networks by quasi product forms [link]Website   bibtex   abstract
Efficient Steady State Analysis of Multimodal Markov Chains. Spieler, D.; and Wolf, V. In Proceedings of the 20th International Conference on Analytic and Stochastic Modelling Techniques and Applications (ASMTA'13), of Lecture Notes of Computer Science, 2013. Springer
Efficient Steady State Analysis of Multimodal Markov Chains [link]Website   bibtex   abstract
Method of conditional moments (MCM) for the Chemical Master Equation. Hasenauer, J.; Wolf, V.; Kazeroonian, A.; and Theis, F., J. Journal of Mathematical Biology, 69(3): 687-735. 2013.
Method of conditional moments (MCM) for the Chemical Master Equation [link]Website   bibtex   abstract
Characterizing oscillatory and noisy periodic behavior in markov population models. Spieler, D. pages 106-122. Springer, 2013.
Characterizing oscillatory and noisy periodic behavior in markov population models [link]Website   bibtex   abstract
Efficient steady state analysis of multimodal Markov chains. Spieler, D.; and Wolf, V. Volume 7984 LNCS 2013.
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On-the-fly verification and optimization of DTA-properties for large Markov chains. Mikeev, L.; Neuhäußer, M.; Spieler, D.; and Wolf, V. Formal Methods in System Design, 43(2). 2013.
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Numerical approximation of rare event probabilities in biochemically reacting systems. Mikeev, L.; Sandmann, W.; and Wolf, V. Volume 8130 LNBI 2013.
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  2012 (8)
In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. Arand, J.; Spieler, D.; Karius, T.; Branco, M., R.; Meilinger, D.; Meissner, A.; Jenuwein, T.; Xu, G.; Leonhardt, H.; Wolf, V.; and Walter, J. PLoS Genetics, 8(6). 2012.
In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases [link]Website   bibtex   abstract
Approximate maximum likelihood estimation for stochastic chemical kinetics. Andreychenko, A.; Mikeev, L.; Spieler, D.; and Wolf, V. EURASIP Journal on Bioinformatics and Systems Biology, 9. 2012.
Approximate maximum likelihood estimation for stochastic chemical kinetics [link]Website   bibtex   abstract
On-the-fly Verification and Optimization of DTA-properties for Large Markov Chains. Mikeev, L.; Neuhäußer, M.; Spieler, D.; and Wolf, V. Formal Methods in System Design,1-25. 2012.
On-the-fly Verification and Optimization of DTA-properties for Large Markov Chains. [link]Website   bibtex   abstract
Parameter Estimation for Stochastic Hybrid Models of Biochemical Reaction Networks. Mikeev, L.; and Wolf, V. In Proceedings of the 15th International Conference on Hybrid Systems: Computation and Control (HSCC'12), of ACM International Conference Proceeding Series, 2012.
Parameter Estimation for Stochastic Hybrid Models of Biochemical Reaction Networks [link]Website   bibtex   abstract
Parameter estimation for stochastic hybrid models of biochemical reaction networks. Mikeev, L.; and Wolf, V. In HSCC'12 - Proceedings of the 15th ACM International Conference on Hybrid Systems: Computation and Control, 2012.
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Quasi product form approximation for markov models of reaction networks. Angius, A.; Horváth, A.; and Wolf, V. Volume 7625 LNBI 2012.
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  2011 (14)
Infinite Level-Dependent QBDs and Matrix Analytic Solutions for Stochastic Chemical Kinetics. Dayar, T.; Sandmann, W.; Spieler, D.; and Wolf, V. Advances in Applied Probability, 43(4). 2011.
Infinite Level-Dependent QBDs and Matrix Analytic Solutions for Stochastic Chemical Kinetics [link]Website   bibtex   abstract
Approximation of Event Probabilities in Noisy Cellular Processes. Didier, F.; Henzinger, T., A.; Mateescu, M.; and Wolf, V. Journal of Theoretical Computer Science, 412(21): 2128-2141. 2011.
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On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models. Andreychenko, A.; Crouzen, P.; and Wolf, V. In Proceedings of the 9th International Workshop on Quantitative Aspects of Programming Languages (QAPL'11), of Electronic Proceedings in Theoretical Computer Science, 2011.
On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models [pdf]Website   bibtex   abstract
Formalisms for Specifying Markovian Population Models. Henzinger, T., A.; Jobstmann, B.; and Wolf, V. Journal of Foundations of Computer Science, 22(4). 2011.
Formalisms for Specifying Markovian Population Models [link]Website   bibtex   abstract
Efficient Calculation of Rare Event Probabilities in Markovian Queueing Networks. Mikeev, L.; Sandmann, W.; and Wolf, V. In Proceedings of the 5th International ICST Conference on Performance Evaluation Methodologies and Tools (VALUETOOLS'11), of ACM International Conference Proceeding Series, 2011.
Efficient Calculation of Rare Event Probabilities in Markovian Queueing Networks [link]Website   bibtex   abstract
Parameter Identification for Markov Models of Biochemical Reactions. Andreychenko, A.; Mikeev, L.; Spieler, D.; and Wolf, V. In Proceedings of the 23rd International Conference on Computer Aided Verification (CAV'11), volume 6806, of Lecture Notes of Computer Science, pages 83-98, 2011. Springer
Parameter Identification for Markov Models of Biochemical Reactions [link]Website   bibtex   abstract
Bounding the Equilibrium Distribution of Markov Population Models. Dayar, T.; Hermanns, H.; Spieler, D.; and Wolf, V. Numerical Linear Algebra with Applications, 18(6): 931-946. 2011.
Bounding the Equilibrium Distribution of Markov Population Models. [link]Website   bibtex   abstract
SHAVE -- Stochastic Hybrid Analysis of Markov Population Models. Lapin, M.; Mikeev, L.; and Wolf, V. In Proceedings of the 14th International Conference on Hybrid Systems: Computation and Control (HSCC'11), of ACM International Conference Proceeding Series, 2011.
SHAVE -- Stochastic Hybrid Analysis of Markov Population Models [link]Website   bibtex   abstract
Infinite level-dependent QBD processes and matrix-analytic solutions for stochastic chemical kinetics. Dayar, T.; Sandmann, W.; Spieler, D.; and Wolf, V. Advances in Applied Probability, 43(4). 2011.
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SHAVE - Stochastic hybrid analysis of Markov population models. Lapin, M.; Mikeev, L.; and Wolf, V. In HSCC'11 - Proceedings of the 2011 ACM/SIGBED Hybrid Systems: Computation and Control, 2011.
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Efficient calculation of rare event probabilities in Markovian queueing networks. Mikeev, L.; Sandmann, W.; and Wolf, V. In VALUETOOLS 2011 - 5th International ICST Conference on Performance Evaluation Methodologies and Tools, 2011.
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Approximation of event probabilities in noisy cellular processes. Didier, F.; Henzinger, T.; Mateescu, M.; and Wolf, V. Theoretical Computer Science, 412(21). 2011.
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Parameter identification for Markov models of biochemical reactions. Andreychenko, A.; Mikeev, L.; Spieler, D.; and Wolf, V. Volume 6806 LNCS 2011.
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Formalisms for specifying Markovian population models. Henzinger, T.; Jobstmann, B.; and Wolf, V. International Journal of Foundations of Computer Science, 22(4). 2011.
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  2010 (8)
On the Numerical Analysis of Stochastic Lotka-Volterra Models. Dayar, T.; Mikeev, L.; and Wolf, V. In Proceedings of the Workshop on Computer Aspects of Numerical Algorithms (CANA'10), 2010. IMCSIT
On the Numerical Analysis of Stochastic Lotka-Volterra Models [link]Website   bibtex   abstract
Solving the Chemical Master Equation Using Sliding Windows. Wolf, V.; Goel, R.; Mateescu, M.; and Henzinger, T., A. BMC Systems Biology Journal, 4(42). 2010.
Solving the Chemical Master Equation Using Sliding Windows [link]Website   bibtex   abstract
SABRE: A Tool for Stochastic Analysis of Biochemical Reaction Networks. Didier, F.; Henzinger, T., A.; Mateescu, M.; and Wolf, V. In Proceedings of the 7th International Conference on Quantitative Evaluation of Systems (QEST'10), pages 193-194, 2010. IEEE Computer Society
SABRE: A Tool for Stochastic Analysis of Biochemical Reaction Networks [pdf]Website   bibtex   abstract
Hybrid Numerical Solution of the Chemical Master Equation. Henzinger, T., A.; Mateescu, M.; Mikeev, L.; and Wolf, V. In Proceedings of the 8th International Conference on Computational Methods in Systems Biology (CMSB '10), of ACM International Conference Proceeding Series, pages 55-65, 2010.
Hybrid Numerical Solution of the Chemical Master Equation [link]Website   bibtex   abstract
Fast adaptive uniformisation of the chemical master equation. Mateescu, M.; Wolf, V.; Didier, F.; and Henzinger, T. IET Systems Biology, 4(6). 2010.
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SABRE: A tool for stochastic analysis of biochemical reaction networks. Didier, F.; Henzinger, T.; Mateescu, M.; and Wolf, V. In Proceedings - 7th International Conference on the Quantitative Evaluation of Systems, QEST 2010, 2010.
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Hybrid numerical solution of the chemical master equation. Henzinger, T.; Mateescu, M.; Mikeev, L.; and Wolf, V. In CMSB 2010 - Proceedings of the 8th International Conference on Computational Methods in Systems Biology, 2010.
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Solving the chemical master equation using sliding windows. Wolf, V.; Goel, R.; Mateescu, M.; and Henzinger, T. BMC Systems Biology, 4. 2010.
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  2009 (8)
Formalisms for Specifying Markovian Population Models. Henzinger, T., A.; Jobstmann, B.; and Wolf, V. In Proceedings of the 3rd International Workshop on Reachability Problems (RP'09), volume 5797, of Lecture Notes in Computer Science, 2009. Springer
Formalisms for Specifying Markovian Population Models [link]Website   bibtex   abstract
Fast Adaptive Uniformization of the Chemical Master Equation. Didier, F.; Henzinger, T., A.; Mateescu, M.; and Wolf, V. In Proceedings of the High Performance Computational Systems Biology Workshop (HIBI'09), pages 118-127, 2009. IEEE Computer Society
Fast Adaptive Uniformization of the Chemical Master Equation [link]Website   bibtex   abstract
Approximation of Event Probabilities in Noisy Cellular Processes. Didier, F.; Henzinger, T., A.; Mateescu, M.; and Wolf, V. In Proceedings of the 7th International Conference on Computational Methods in Systems Biology (CMSB'09), volume 5688, of Lecture Notes in Bioinformatics, pages 173-183, 2009. Springer
Approximation of Event Probabilities in Noisy Cellular Processes [link]Website   bibtex   abstract
Sliding Window Abstraction for Infinite Markov Chains. Henzinger, T.; Mateescu, M.; and Wolf, V. In Proceedings of the 21st International Conference on Computer Aided Verification (CAV'09), volume 5643, of Lecture Notes in Computer Science, pages 337-352, 2009. Springer
Sliding Window Abstraction for Infinite Markov Chains [link]Website   bibtex   abstract
Approximation of event probabilities in noisy cellular processes. Didier, F.; Henzinger, T.; Mateescu, M.; and Wolf, V. Volume 5688 LNBI 2009.
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Fast adaptive uniformization of the chemical master equation. Didier, F.; Henzinger, T.; Mateescu, M.; and Wolf, V. In HiBi09 - 2009 International Workshop on High Performance Computational Systems Biology, 2009.
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Sliding window abstraction for infinite markov chains. Henzinger, T.; Mateescu, M.; and Wolf, V. Volume 5643 LNCS 2009.
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Formalisms for specifying Markovian population models. Henzinger, T.; Jobstmann, B.; and Wolf, V. Volume 5797 LNCS 2009.
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  2008 (3)
Equivalences on Phase Type Processes. Wolf, V. 2008.
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Computational Probability for Systems Biology. Sandmann, W.; and Wolf, V. In Proceedings of the International Workshop on Formal Methods in Systems Biology (FMSB'08), volume 5054, of Lecture Notes in Bioinformatics, pages 33-47, 2008. Springer
Computational Probability for Systems Biology [link]Website   bibtex   abstract
  2007 (4)
Modelling of Biochemical Reactions by Stochastic Automata Networks. Wolf, V. Electronic Notes in Theoretical Computer Science, 171(2 SPEC. ISS.): 197-208. 2007.
Modelling of Biochemical Reactions by Stochastic Automata Networks [link]Website   bibtex   abstract
Interaction Models for Biochemical Reactions. Majster-Cederbaum, M., E.; Semmelrock, N.; and Wolf, V. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BIOCOMP'07), pages 480-486, 2007. CSREA Press
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  2006 (8)
A Numerical Aggregation Algorithm for the Enzyme-Catalyzed Substrate Conversion. Busch, H.; Sandmann, W.; and Wolf, V. In Computational Methods in Systems Biology, volume 4210, of Lecture Notes in Computer Science, pages 298-311, 2006. Springer
A Numerical Aggregation Algorithm for the Enzyme-Catalyzed Substrate Conversion [pdf]Website   bibtex   abstract
Trace Semantics for Stochastic Systems with Nondeterminism. Wolf, V.; Baier, C.; and Majster-Cederbaum, M. Electronic Notes in Theoretical Computer Science, 164(3 SPEC. ISS.): 187-204. 2006.
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Stochastic Reasoning About Channel-based Component Connectors. Baier, C.; and Wolf, V. In Proceedings of the 8th International Conference on Coordination Models and Languages (COORDINATION'06), volume 4038, of Lecture Notes in Computer Science, pages 1-15, 2006. Springer
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Don't know in probabilistic systems. Fecher, H.; Leucker, M.; and Wolf, V. In Proceedings of 13th International SPIN Workshop on Model Checking of Software (SPIN'06), volume 3925, of Lecture Notes in Computer Science, pages 71-88, 2006. Springer
Don't know in probabilistic systems [link]Website   bibtex   abstract
Bisimulation and Simulation Relations for Markov Chains. Baier, C.; Hermanns, H.; Katoen, J.; and Wolf, V. In Proceedings of the Workshop Essays on Algebraic Process Calculi (ACP'06), volume 162, of Electronic Notes in Theoretical Computer Science, pages 73-78, 2006. Elsevier
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Stochastic reasoning about channel-based component connectors. Baier, C.; and Wolf, V. Volume 4038 LNCS 2006.
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A numerical aggregation algorithm for the enzyme-catalyzed substrate conversion. Busch, H.; Sandmann, W.; and Wolf, V. Volume 4210 LNBI 2006.
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Trace Machines for Observing Continuous-Time Markov Chains. Wolf, V.; Baier, C.; and Majster-Cederbaum, M. Electronic Notes in Theoretical Computer Science, 153(2 SPEC. ISS.). 2006.
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  2005 (2)
Testing theory for probabilistic systems. Wolf, V. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3472 LNCS: 233-275. 2005.
Testing theory for probabilistic systems [link]Website   bibtex   abstract
Comparative branching-time semantics for Markov chains. Baier, C.; Katoen, J.; Hermanns, H.; and Wolf, V. Information and Computation, 200: 149-214. 2005.
Comparative branching-time semantics for Markov chains [link]Website   bibtex   abstract
  2004 (1)
Trace machines for observing continuous-time Markov chains. Wolf, V.; Baier, C.; and Majster-Cederbaum, M. In Proceedings of the International Workshop on Quantitative Aspects of Programming Languages (QAPL'04), volume 153, of Electronic Notes in Theoretical Computer Science, pages 259-277, 2004. Elsevier
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  2003 (3)
Bisimulation und Simulation für Markovmodelle. Wolf, V. 2003.
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Comparative Branching Time Semantics for Markov Chains. Baier, C.; Katoen, J.; Hermanns, H.; and Wolf, V. In Proceedings of the 14th International Conference on Concurrency Theory (CONCUR'03), volume 2761, of Lecture Notes in Computer Science, pages 492-508, 2003. Springer
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Comparative branching-time semantics for Markov chains (extended abstract). Baier, C.; Hermanns, H.; Katoen, J.; and Wolf, V. Volume 2761 2003.
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