Papers

    • Julia Klein, Alberto D’Onofrio, Tatjana Petrov: “Exploring Consensus Robustness in Swarms with Disruptive Individuals”, to appear
    • Luca Bortolussi, Francesca Cairoli, Julia Klein, Tatjana Petrov. “Data-Driven Inference of Chemical Reaction Networks via Graph-Based Variational Autoencoders.” International Conference on Quantitative Evaluation of Systems. Cham: Springer Nature Switzerland, 2023.
    • Julia Klein, Huy-Nhat Phung, Matej Hajnal, David Šafránek, Tatjana Petrov (2023). Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state data. Plos one, 18(11), e0291151.
    • Tatjana Petrov, Matej Hajnal, Julia Klein, Davide Safranek, Morgane Nouvian: Extracting individual characteristics from population data reveals a negative social effect during honeybee defence, PLOS Computational Biology (2022)
    • Matej Hajnal, Tatjana Petrov, David Safranek: DiPS: A Tool for Data-informed Parameter Synthesis for Discrete-Time Stochastic Processes from Multiple-Property Specifications 2021 [doi, pdf]
    • Tatjana Petrov, Stefano Tognazzi: Exact and Approximate Role Assignment for Multi-Layer Networks Journal of Complex Networks 2021 [doi, pdf]
    • Tatjana Petrov, Denis Repin: Automated Deep Abstractions for Stochastic Chemical Reaction Networks
      Information and Computation, 2021 [doi, pdf]

    • Tatjana Petrov, Claudia Igler, Ali Sezgin, Thomas A. Henzinger, Calin C. Guet: Long-lived Transients in Gene Regulatory Networks, Theoretical Computer Science, 2021 [doi, pdf]

    • Tatjana Petrov, Stefano Tognazzi: Centrality-Preserving Exact Reductions of Multi-Layer Networks
      Leveraging Applications of Formal Methods, Verification and Validation: Engineering Principles (ISoLA 2020) [doi, pdf]

    • Pavol Bokes, Julia Klein, Tatjana Petrov: Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression, Computational Methods in Systems Biology (CMSB 2020) [doi, pdf]

    • Repin Denis, Phung N Huy, Petrov Tatjana: StochNetV2: A Tool for Automated Deep Abstractions for Stochastic Reaction Networks, Quantitative Evaluation of Systems (QEST 2020) [doi, pdf]

    • Calin Guet, Thomas A. Henzinger, Claudia Igler, Tatjana Petrov, Ali Sezgin: Transient Memory in Gene Regulatory Networks, Computational Methods in Systems Biology (CMSB 2019) [doi, pdf]

    • Matej Hajnal, Morgane Nouvian, David Šafránek, Tatjana Petrov. Data-informed parameter synthesis for population markov chains. In International Workshop on Hybrid Systems Biology (HSB 2019) [doi pdf poster]

    • Andreea Beica, Jérôme Feret, Tatjana Petrov: Tropical Abstraction of Biochemical Reaction Networks with Guarantees,The Ninth International Workshop on Static Analysis in Systems Biology (SASB 2018) [doi, pdf, poster]

    • Przemyslaw Daca, Thomas A. Henzinger, Jan Kretinsky, Tatjana Petrov: Faster Statistical Model Checking for Unbounded Temporal Properties, ACM Transactions on Computational Logic, 2017 [doi, pdf]
    • Przemyslaw Daca, Thomas A. Henzinger, Jan Kretinsky, Tatjana Petrov: Linear Distances between Markov Chains, In 27th International Conference on Concurrency Theory (CONCUR 2016) [doi, pdf, slides]
    • Przemyslaw Daca, Thomas A. Henzinger, Jan Kretinsky, Tatjana Petrov: Faster Statistical Model Checking for Unbounded Temporal Properties, In 22nd International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2016), nomination for best paper award [doi, pdf  slides]
    • Andreea Beica, Calin C. Guet, Tatjana Petrov: Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set, Lecture Notes in Computer Science, Revised Selected Papers from Hybrid Systems Biology (HSB 2015) [doi, pdf]
    • Mirco Giacobbe, Calin C. Guet, Ashutosh Gupta, Thomas A. Henzinger, Tiago Paixao, Tatjana Petrov: Model checking the evolution of gene regulatory networks, In Acta Informatica, 2017 [doi pdf]
    • Mirco Giacobbe, Calin C. Guet, Ashutosh Gupta, Thomas A. Henzinger, Tiago Paixao, Tatjana Petrov: Model Checking Gene Regulatory Networks, 21st International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2015), best paper award [doi pdf slides]
    • Bernhard Geiger, Tatjana Petrov, Heinz Koeppl, and Gernot Kubin: Optimal Kullback-Leibler Aggregation via Information Bottleneck, IEEE Transactions on Automatic Control (TAC), 2014 [doi pdf]
    • Ivan Milenkovic, Tatjana Petrov, Gabor G. Kovacz: Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias, Dementia and Geriatric Cognitive Disorders, 2014 [doi pdf]
    • Arnab Ganguly*, Tatjana Petrov*, Heinz Koeppl: Markov chain aggregation and its applications to combinatorial reaction networks (authors marked * with equal contributions), Journal of Mathematical Biology (JMB), 2014 [doi pdf]
    • Tatjana Petrov: Formal reductions of stochastic rule-based models of biochemical systems (PhD thesis)
      ETH Zurich, 2013 [doi]
    • Tatjana Petrov, Heinz Koeppl: Approximate reductions of rule-based models, In Proceedings of ECC (European Control Conference), 2013 [doi pdf]
    • Tatjana Petrov, Jerome Feret and Heinz Koeppl: Reconstructing species-based dynamics from reduced stochastic rule-based models, In Proceedings of Winter Simulation Conference (WSC), 2012 [doi pdf]
    • Tom Henzinger, Jerome Feret, Heinz Koeppl, Tatjana Petrov: Lumpability abstractions of Rule-based systems, Journal of Theoretical Computer Science, 2011 [doi pdf]
    • Marc Hafner, James Lu, Heinz Koeppl, Tatjana Petrov: Rational design of robust biomolecular circuits: from specification to parameters, in Design and Analysis of Bio-Molecular Circuits, 2011 [doi pdf]
    • Michael Klann, Loic Pauleve, Tatjana Petrov, Heinz Koeppl: Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models
      in Proceedings of the 11th Computational Methods in Systems Biology (CMSB), 2013 [doi pdf slides]
    • Arnab Ganguly, Heinz Koeppl, Tatjana Petrov: Model Decomposition and Stochastic Fragments
      Electronic Notes in Theoretical Computer Science, 2012 [doi pdf]
    • Ferdinanda Camporesi, Jerome Feret, Heinz Koeppl, Tatjana Petrov: Combining model reductions
      26th Conference on the Mathematical Foundations of Programming Semantics – MFPS, 2010 [doi pdf]
    • Heinz Koeppl, Tatjana Petrov: Stochastic Semantics of Signalling as a Composition of Agent-view Automata
      Electronic Notes in Theoretical Computer Science, 2011 [doi pdf]
    • Heinz Koeppl, Tatjana Petrov: Maximal Reduction of ODE Semantics of Rule-based Models: Syntax-Independent Setup
      in Proceedings of the 7th International Workshop on Computational Systems Biology (WCSB), 2010 [pdf]
    • H. Koeppl, G. Setti, S. Pelet, M. Mangia, T. Petrov, M. Peter: Probability Metrics to Calibrate Stochastic Chemical Kinetics
      International Conference of Numerical Analysis and Applied Mathematics (NAAM), 2010 [doi pdf]
    • Ferdinanda Camporesi, Jerome Feret, Heinz Koeppl, Tatjana Petrov: Automatic reduction of stochastic rules-based models in a nutshell
      in Proceedings of the IEEE International Symposium on Circuits and Systems Proceedings (ISCAS), 2010 [doi pdf]
    • Laurent Doyen, Tom Henzinger, Barbara Jobstman, Tatjana Petrov: Interface theories with component reuse,
      in Proceedings of EMSOFT (The International Conference on Embedded Software), 2008 [doi pdf slides]