BioNetGen

swMATH9072MaRDI QIDQ21065FDOQ21065

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Cited In (61)

• Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon
• Symbolic computation of differential equivalences
• Modern methods and software systems of molecular modeling and application of behavior algebra
• Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
• Analysis of Fn14-NF-\(\kappa\)B signaling response dynamics using a mechanistic model
• Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime
• Markov chain aggregation and its applications to combinatorial reaction networks
• Lumpability abstractions of rule-based systems
• A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: development of an integrated mathematical model and computational experiments
• Biochemical Reaction Rules with Constraints
• Chromar, a rule-based language of parameterised objects
• A Syntactic Abstraction for Rule-Based Languages with Binding
• Coarse-graining the dynamics of ideal branched polymers
• Title not available (Why is that?)
• Fragments-based Model Reduction: Some Case Studies
• Proving the absence of unbounded polymers in rule-based models
• Tropical abstraction of biochemical reaction networks with guarantees
• The interplay of double phosphorylation and scaffolding in MAPK pathways
• Formal biochemical space with semantics in Kappa and BNGL
• Mechanistic simulations of inflammation: current state and future prospects
• Reachability analysis via orthogonal sets of patterns
• Comparing chemical reaction networks: a categorical and algorithmic perspective
• A multiscale multicellular spatiotemporal model of local influenza infection and immune response
• Formal Reduction for Rule-based Models
• Nonlinear pattern matching in rule-based modeling languages
• Quantitative Abstractions for Collective Adaptive Systems
• Computational Software
• A predictive mathematical model of the DNA damage G2 checkpoint
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Data-driven analysis of a mechanistic model of CAR T cell signaling predicts effects of cell-to-cell heterogeneity
• Generalizing Gillespie's direct method to enable network-free simulations
• Algebra, Coalgebra, and Minimization in Polynomial Differential Equations
• A unified framework for differential aggregations in Markovian process algebra
• Chromar, a language of parameterised agents
• Verification of spatial and temporal modalities in biochemical systems
• Executable biochemical space for specification and analysis of biochemical systems
• A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity
• Retroactivity effects dependency on the transcription factors binding mechanisms
• Stochastic effects and bistability in T cell receptor signaling
• Efficient Turing-Universal Computation with DNA Polymers
• A collective interpretation semantics for reversing Petri nets
• Computational modelling of the kinetic tile assembly model using a rule-based approach
• Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration
• Symbolic computation of differential equivalences
• An algebraic approach for inferring and using symmetries in rule-based models
• Rigid geometric constraints for Kappa models
• Combining Model Reductions
• The inverse problem in mathematical biology
• Incremental Update for Graph Rewriting
• MobsPy: a meta-species language for chemical reaction networks
• Modelling patterns of gene regulation in the bond-calculus
• SBML to bond graphs: from conversion to composition
• Labelled port graph -- a formal structure for models and computations
• Mathematical models for immunology: current state of the art and future research directions
• eBCSgen 2.0: modelling and analysis of regulated rule-based systems
• A process algebra framework for multi-scale modelling of biological systems
• Semantics and Efficient Simulation Algorithms of an Expressive Multilevel Modeling Language
• Computational modeling of synergistic interaction between \(\alpha\)V\(\beta\)3 integrin and VEGFR2 in endothelial cells: implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides
• Thermodynamic graph-rewriting
• Lifted Bayesian Filtering in Multiset Rewriting Systems
• Containment in Rule-Based Models

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