Modeling delayed dynamics in biological regulatory networks from time series data
Summary: Background: The modeling of Biological Regulatory Networks (BRNs) relies on background knowledge, deriving either from literature and/or the analysis of biological observations. However, with the development of high-throughput data, there is a growing need for methods that automatically generate admissible models. Methods: Our research aim is to provide a logical approach to infer BRNs based on given time series data and known influences among genes. Results: We propose a new methodology for models expressed through a timed extension of the automata networks (well suited for biological systems). The main purpose is to have a resulting network as consistent as possible with the observed datasets. Conclusion: The originality of our work is three-fold: (i) identifying the sign of the interaction; (ii) the direct integration of quantitative time delays in the learning approach; and (iii) the identification of the qualitative discrete levels that lead to the systems' dynamics. We show the benefits of such an automatic approach on dynamical biological models, the DREAM4 (in silico) and DREAM8 (breast cancer) datasets, popular reverse-engineering challenges, in order to discuss the precision and the computational performances of our modeling method.
- Inference of delayed biological regulatory networks from time series data
- Inferring gene regulatory networks from temporal expression profiles under time-delay and noise
- Modeling genetic regulatory networks: a delay discrete dynamical model approach
- Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure
- Investigate data dependency for dynamic gene regulatory network identification through high-dimensional differential equation approach
- Completing networks using observed data
- Dynamic network functional comparison via approximate-bisimulation
- Encoding Higher Level Extensions of Petri Nets in Answer Set Programming
- Goal-oriented reduction of automata networks
- Identification of biological regulatory networks from process hitting models
- Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model.
- Inference of delayed biological regulatory networks from time series data
- Knowledge Representation, Reasoning and Declarative Problem Solving
- Refining dynamics of gene regulatory networks in a stochastic -calculus framework
- Synchronization of Boolean networks with time delays
- Synthesis of biological models from mutation experiments
- Temporal Boolean network models of genetic networks and their inference from gene expression time series.
- Temporal constraints in the logical analysis of regulatory networks
- Inference of delayed biological regulatory networks from time series data
- Learning explanations for biological feedback with delays using an event calculus
- Learning equations from biological data with limited time samples
- Modeling genetic regulatory networks: a delay discrete dynamical model approach
- Integrating Time-Series Data in Large-Scale Discrete Cell-Based Models
- STATE-SPACE MODEL WITH TIME DELAYS FOR GENE REGULATORY NETWORKS
- Inferring dynamical models from time-series biological data using an interpretable machine learning method based on weighted expression trees
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