Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks. - Heike Siebert; Alexander Bockmayr (CMSB, 2006)

Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks. - Heike Siebert; Alexander Bockmayr (AB, 2007)

Context Sensitivity in Logical Modeling with Time Delays. - Heike Siebert; Alexander Bockmayr (CMSB, 2007)

Local Structure and Behavior of Boolean Bioregulatory Networks. - Heike Siebert (AB, 2008)

Temporal constraints in the logical analysis of regulatory networks. - Heike Siebert; Alexander Bockmayr (Theor. Comput. Sci., 2008)

Analyzing various models of Circadian Clock and Cell Cycle coupling. - Attila Csikász-Nagy; Adrien Fauré; Roberto Larcher; Paola Lecca; Ivan Mura; Ferenc Jordán; Alida Palmisano; Alessandro Romanel; Sean Sedwards; Heike Siebert; Sylvain Soliman; Denis Thieffry; et al. (Formal Methods in Molecular Biology, 2009)

Symbolic Steady States and Dynamically Essential Subnetworks of Discrete Regulatory Networks. - Heike Siebert (Formal Methods in Molecular Biology, 2009)

Dynamical and Structural Modularity of Discrete Regulatory Networks - Heike Siebert (COMPMOD, 2009)

Deriving Behavior of Boolean Bioregulatory Networks from Subnetwork Dynamics. - Heike Siebert (Math. Comput. Sci., 2009)

Stochasticity in reactions: a probabilistic Boolean modeling approach. - Sven Twardziok; Heike Siebert; Alexander Heyl (CMSB, 2010)

Parameter inference for asynchronous logical networks using discrete time series. - Hannes Klarner; Heike Siebert; Alexander Bockmayr (CMSB, 2011)

Parameter Identification and Model Ranking of Thomas Networks. - Hannes Klarner; Adam Streck; David Safránek; Juraj Kolcák; Heike Siebert (CMSB, 2012)

Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks. - Shahrad Jamshidi; Heike Siebert; Alexander Bockmayr (IPCAT, 2012)

Time Series Dependent Analysis of Unparametrized Thomas Networks. - Hannes Klarner; Heike Siebert; Alexander Bockmayr (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Bio-Logics: Logical Analysis of Bioregulatory Networks. - Alexander Bockmayr; Heike Siebert (Programming Logics, 2013)

Preservation of dynamic properties in qualitative modeling frameworks for gene regulatory networks. - Shahrad Jamshidi; Heike Siebert; Alexander Bockmayr (Biosyst., 2013)

Computing Symbolic Steady States of Boolean Networks. - Hannes Klarner; Alexander Bockmayr; Heike Siebert (ACRI, 2014)

Equivalences in Multi-valued Asynchronous Models of Regulatory Networks. - Adam Streck; Heike Siebert (ACRI, 2014)

Model Integration and Crosstalk Analysis of Logical Regulatory Networks. - Kirsten Thobe; Adam Streck; Hannes Klarner; Heike Siebert (CMSB, 2014)

Analysing Cell Line Specific EGFR Signalling via Optimized Automata Based Model Checking. - Adam Streck; Kirsten Thobe; Heike Siebert (CMSB, 2015)

Comparative Statistical Analysis of Qualitative Parametrization Sets. - Adam Streck; Kirsten Thobe; Heike Siebert (HSB, 2015)

Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. - Kaveh Yousef; Adam Streck; Christof Schütte; Heike Siebert; Regine Hengge; Max von Kleist (BMC Syst. Biol., 2015)

Computing maximal and minimal trap spaces of Boolean networks. - Hannes Klarner; Alexander Bockmayr; Heike Siebert (Nat. Comput., 2015)

Minimization and equivalence in multi-valued logical models of regulatory networks. - Adam Streck; Therese Lorenz; Heike Siebert (Nat. Comput., 2015)

Data-driven optimizations for model checking of multi-valued regulatory networks. - Adam Streck; Kirsten Thobe; Heike Siebert (Biosyst., 2016)

Graph Representations of Monotonic Boolean Model Pools. - Robert Schwieger; Heike Siebert (CMSB, 2017)

PyBoolNet: a python package for the generation, analysis and visualization of boolean networks. - Hannes Klarner; Adam Streck; Heike Siebert (Bioinform., 2017)

Erratum to: Computing maximal and minimal trap spaces of Boolean networks. - Hannes Klarner; Alexander Bockmayr; Heike Siebert (Nat. Comput., 2018)

Correspondence of Trap Spaces in Different Models of Bioregulatory Networks. - Robert Schwieger; Heike Siebert; Susanna Röblitz (SIAM J. Appl. Dyn. Syst., 2018)

Designing Distributed Cell Classifier Circuits Using a Genetic Algorithm. - Melania Nowicka; Heike Siebert (CMSB, 2019)

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis. - Denise Thiel; Natasa Djurdjevac Conrad; Evgenia Ntini; Ria X. Peschutter; Heike Siebert; Annalisa Marsico (BMC Bioinform., 2019)

Boolean analysis of lateral inhibition. - Elisa Tonello; Heike Siebert (CoRR, 2019)

Control Strategy Identification via Trap Spaces in Boolean Networks. - Laura Cifuentes Fontanals; Elisa Tonello; Heike Siebert (CMSB, 2020)

Classifier Construction in Boolean Networks Using Algebraic Methods. - Robert Schwieger; Matías R. Bender; Heike Siebert; Christian Haase 001 (CMSB, 2020)

Basins of Attraction, Commitment Sets, and Phenotypes of Boolean Networks. - Hannes Klarner; Frederike Heinitz; Sarah Nee; Heike Siebert (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Structure and behavior in Boolean monotonic model pools. - Robert Schwieger; Heike Siebert (Biosyst., 2022)

Control in Boolean Networks With Model Checking. - Laura Cifuentes Fontanals; Elisa Tonello; Heike Siebert (Frontiers Appl. Math. Stat., 2022)

Uncovering Dynamic Structures Within Cyclic Attractors of Asynchronous Boolean Networks with Spectral Clustering. - Maryam Yousefian; Elisa Tonello; Anna-Simone Frank; Heike Siebert; Susanna Röblitz (CMSB, 2024)

Detection of dynamic communities in temporal networks with sparse data. - Natasa Djurdjevac Conrad; Elisa Tonello; Johannes Zonker; Heike Siebert (Appl. Netw. Sci., 2025)