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Publications

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Articles, Book Chapters

2016

Streck A, Thobe K, Siebert H: Data-driven optimizations for model checking of multi-valued regulatory networks. Biosystems, Jun 2016.

2015

Streck A, Thobe K, Siebert H: Comparative Statistical Analysis of Qualitative Parametrization Set. Hybrid Systems Biology, 4th International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. Lecture Notes in Bioinformatics, 9271, 20-34, 2015.

Klarner H, Bockmayr A, Siebert H: Computing maximal and minimal trap spaces of Boolean networks. Natural Computing, 14(4): 535-544, Dec 2015.

Streck A, Lorenz T, Siebert H: Minimization and equivalence in multi-valued logical models of regulatory networks. Natural Computing, 14(4): 555-566, Dec 2015.

Stötzel C, Röblitz S, Siebert H: Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation, PLoS ONE 10(10):e0140954, Oct 2015.

Streck A, Thobe K, Siebert H: Analysing Cell Line Specific EGFR Signalling via Optimized Automata Based Model Checking. Computational Methods in Systems Biology, 13th International Conference, CMSB 2015, Nantes, France. Springer International, LNCS 9308, 264-276, Sept 2015.

Klarner H, Siebert H: Approximating attractors of Boolean networks by iterative CTL model checking. Frontiers in Bioengineering and Biotechnology, 3:130, Aug 2015.

Yousef KP, Streck A, Schütte Ch, Siebert H, Hengge R, von Kleist M: Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9:39, Jul 2015.

Streck A, Siebert H: Extensions for LTL model checking of Thomas networks. Strasbourg Spring School on Advances in Systems and Synthetic Biology, Strasbourg, 101-114, Mar 2015.

2014

Thobe K, Streck A, Klarner H, Siebert H: Model Integration and Crosstalk Analysis of Logical Regulatory Networks. Computational Methods in Systems Biology, 12th International Conference, CMSB 2014, Manchester, UK. Springer, LNCS 8859, 32-44, Nov 2014.

Streck A, Siebert H: Equivalences in Multi-valued Asynchronous Models of Regulatory Networks. Cellular Automata, ACRI 2014, Krakow, Poland, Springer, LNCS 8751, 571-575, Sep 2014.

Klarner H, Bockmayr A, Siebert H: Computing Symbolic Steady States of Boolean Networks. Cellular Automata, ACRI 2014, Krakow, Poland, Springer, LNCS 8751, 561-570, Sep 2014.

Bockmayr A, Siebert H., Röblitz S, Schütte Ch, Deuflhard P: Advanced mathematical modeling in systems biology. MATHEON-Mathematics for Key Technologies, volume 1, pages 29-44, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Christof Schütte, Martin Skutela, Jürgen Sprekels (Editors), European Mathematical Society, 2014.

2013

Jamshidi S, Siebert H, Bockmayr A: Preservation of Dynamic Properties in Qualitative Modeling Frameworks for Gene Regulatory Networks. Biosystems, 112/2, 171-179, 2013.

Lorenz, Therese and Siebert, Heike and Bockmayr, Alexander: Analysis and characterization of asynchronous state transition graphs using extremal states. Bulletin of Mathematical Biology, 75/6, 920-938, 2013.

Bockmayr A, Siebert H: Bio-Logics: Logical Analysis of Bioregulatory Networks. Programming Logics. Essays in Memory of Harald Ganzinger. Springer, LNCS 7797, 19-34, 2013.

2012

Klarner H, Siebert H, Bockmayr A: Time Series Dependent Analysis of Unparametrized Thomas Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012.

Klarner H, Streck A, Safránek D, Kolcák J, Siebert H: Parameter Identification and Model Ranking of Thomas Networks. CMSB 2012: 207-226.

S. Jamshidi, Siebert H, Bockmayr A: Comparing discrete and piecewise affine differential equation models of gene regulatory networks. In Proc. 9th Int. Conf. Information Processing in Cells and Tissues, IPCAT 2012, Cambridge, UK, Springer, LNCS 7223, 17-24, 2012.

2006 - 2011

Klarner H, Siebert H, Bockmayr A: Parameter inference for asynchronous logical networks using discrete time series, in Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'11, Paris, France, ACM, NY, USA, pages 121-130, 2011.

Siebert H:  Analysis of discrete bioregulatory networks using symbolic steady states, Bull. Math. Biol., 73 (4): 873-898, 2011. (Preprint)

Twardziok S, Siebert S, Heyl Alexander: Stochasticity in reactions: a probabilistic Boolean modeling approach, in Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB'10, Trento, Italy, ACM, NY, USA, pages 76-85, 2010. (Preprint)

Siebert H: Dynamical and structural modularity of discrete regulatory networks, in Computational Models for Cell Processes, CompMod 2009, Eindhoven, Netherlands, volume 6 of EPTCS, pages 109-124, 2009.

Siebert H: Deriving behavior of Boolean bioregulatory networks from subnetwork dynamics, Math. Comput. Sci., 2(3): 421-442, 2009.

Siebert H: Local Structure and Behavior of Boolean Bioregulatory Networks, in Algebraic Biology, AB 2008, Castle of Hagenberg, Austria, volume 5147 of LNCS, pages 185-199, Springer, 2008.

Siebert H, Bockmayr A: Temporal constraints in the logical analysis of regulatory networks, Theoret. Comput. Sci., 391(3): 258-275, 2008.

Siebert H, Bockmayr A: Context sensitivity in logical modelling with time delays, in Computational Methods in Systems Biology, CMSB 2007, Edinburgh, Scotland, volume 4695 of LNCS, Springer, 2007.

Siebert H, Bockmayr A: Relating attractors and singular steady states in the logical analysis of bioregulatory networks, in Algebraic Biology, AB 2007, Castle of Hagenberg, Austria, volume 4545 of LNCS, pages 36-50, Springer, 2007.

Siebert H, Bockmayr A: Incorporating time delays into the logical analysis of gene regulatory networks, in Computational Methods in Systems Biology, CMSB 2006, Trento, Italy, volume 4210 of LNBI, pages 169-183. Springer, 2006.

Siebert H: Fixed points and normal families of quasiregular mappings, J. Analyse Math. 98 (2006), 145-168.

Miscellaneous

Thobe K, Siebert H: Discrete modeling of the MAPK-mTor pathway connection in cancer, 11th Bioinformatics Research and Education Workshop, 2013.

Csikasz-Nagy A et al. Analyzing various models of circadian clock and cell cycle coupling, in Formal Methods in Molecular Biology, number 09091 of Dagstuhl Seminar Proceedings, 2009.

Siebert H: Symbolic steady states and dynamically essential subnetworks of discrete regulatory networks, in Formal Methods in Molecular Biology, number 09091 of Dagstuhl Seminar Proceedings, 2009.

Popular

Mit Mathe durch das Netz der Algen und Bakterien Interview mit Alexander Bockmayr und Heike Siebert im Wissenschaftsmagazin fundiert, 2012.

Heike Siebert. Roboter und Zuckerstangen, in Besser als Mathe, Eds. M. Grötschel, B. Lutz-Westphal, K. Biermann, Vieweg 2009.

Theses

Heike Siebert, Logic-based modeling in systems biology, Habilitationsschrift, FU Berlin, 2011.

Heike Siebert, Fixpunkte und normale Familien quasiregulärer Abbildungen, Dissertation, CAU Kiel, 2004.

Heike Siebert, Vergrabene Komponenten der Juliamenge ganzer transzendenter Funktionen, Diplomarbeit, CAU Kiel, 2002.