Inference of gene regulatory networks using Bayesian nonparametric regression and topology information
Summary: Gene regulatory networks (GRNs) play an important role in cellular systems and are important for understanding biological processes. Many algorithms have been developed to infer the GRNs. However, most algorithms only pay attention to the gene expression data but do not consider the topology information in their inference process, while incorporating this information can partially compensate for the lack of reliable expression data. Here we develop a Bayesian group lasso with spike and slab priors to perform gene selection and estimation for nonparametric models. B-spline basis functions are used to capture the nonlinear relationships flexibly and penalties are used to avoid overfitting. Further, we incorporate the topology information into the Bayesian method as a prior. We present the application of our method on DREAM3 and DREAM4 datasets and two real biological datasets. The results show that our method performs better than existing methods and the topology information prior can improve the result.
- Bayesian nonlinear model selection for gene regulatory networks
- A posterior probability approach for gene regulatory network inference in genetic perturbation data
- Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression
- Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure
- An empirical Bayesian method for estimating biological networks from temporal microarray data
- Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues
- Bayesian nonlinear model selection for gene regulatory networks
- Bayesian variable selection and estimation for group Lasso
- Comparing different ODE modelling approaches for gene regulatory networks
- Fast Bayesian model assessment for nonparametric additive regression
- High-dimensional Bayesian inference in nonparametric additive models
- scientific article; zbMATH DE number 845714 (Why is no real title available?)
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