Inferring biologically relevant models: nested canalyzing functions
From MaRDI portal
Abstract: Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast.
Recommendations
- Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions
- The number of multistate nested canalyzing functions
- Boolean nested canalizing functions: a comprehensive analysis
- Nested canalyzing depth and network stability
- Nested canalyzing, unate cascade, and polynomial functions
Cites work
- scientific article; zbMATH DE number 638938 (Why is no real title available?)
- scientific article; zbMATH DE number 5494031 (Why is no real title available?)
- A computational algebra approach to the reverse engineering of gene regulatory networks
- Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions
- Nested canalyzing, unate cascade, and polynomial functions
- Reverse-engineering of polynomial dynamical systems
- SINGULAR
- The number of multistate nested canalyzing functions
Cited in
(10)- Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions
- The number of multistate nested canalyzing functions
- Structural properties of continuous representations of Boolean functions for gene network modelling
- Context-Specific Nested Effects Models
- Average sensitivity of nested canalizing multivalued functions
- Stratification and enumeration of Boolean functions by canalizing depth
- Reconstructing Chain Functions in Genetic Networks
- A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets
- Regulatory patterns in molecular interaction networks
- Algebraic Models and Their Use in Systems Biology
This page was built for publication: Inferring biologically relevant models: nested canalyzing functions
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q355920)
