Reactive models for biological regulatory networks
In ``Reactive Models for Biological Regulatory Networks the authors compare and contrast reactive models to Boolean networks and piecewise linear models for the inference of gene regulatory networks. Following a brief overview of the state-of-the-art (with an example), the authors describe in detail, including several examples, approaches based on ordinary differential equations and piecewise linear models and subsequently Boolean networks. The examples are carefully chosen to underline the characteristics of the models. Next, the switch graphs and reactive frames are introduced. A further extension is represented by reactive Boolean networks for which recovering attractors and bisimulation and minimisation are presented from a computational/mathematical angle. For the entire collection see [Zbl 1425.92004].
- The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model
- A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
- A survey of models for inference of gene regulatory networks
- Attractors in Boolean networks: a tutorial
- Boolean networks for modeling gene regulation
- Modeling the dynamic behavior of biochemical regulatory networks
- Introducing fuzzy reactive graphs: a simple application on biology
- Correspondence of Trap Spaces in Different Models of Bioregulatory Networks
- Relation-changing models meet paraconsistency
- Multifaceted formal methods and their interdisciplinary role -- from the cathedral of `components as coalgebras' to the HCI context and the open source software bazaar
- Graded relation updates in modal logic
- Labeled fuzzy reactive graphs
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