scholarly journals Genetic Algorithms and Their Application to In Silico Evolution of Genetic Regulatory Networks

2010 ◽  
pp. 297-321 ◽  
Author(s):  
Johannes F. Knabe ◽  
Katja Wegner ◽  
Chrystopher L. Nehaniv ◽  
Maria J. Schilstra
Keyword(s):  
Genetic Algorithms ◽  
In Silico ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
In Silico Evolution

Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Chi-Kan Chen
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
In Silico ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
E Coli ◽  
Reference Methods ◽  
Automatic Relevance Determination ◽  
Gene Expression Time Series ◽  
Expression Time

Abstract The inference of genetic regulatory networks (GRNs) reveals how genes interact with each other. A few genes can regulate many genes as targets to control cell functions. We present new methods based on the order-1 vector autoregression (VAR1) for inferring GRNs from gene expression time series. The methods use the automatic relevance determination (ARD) to incorporate the regulatory hub structure into the estimation of VAR1 in a Bayesian framework. Several sparse approximation schemes are applied to the estimated regression weights or VAR1 model to generate the sparse weighted adjacency matrices representing the inferred GRNs. We apply the proposed and several widespread reference methods to infer GRNs with up to 100 genes using simulated, DREAM4 in silico and experimental E. coli gene expression time series. We show that the proposed methods are efficient on simulated hub GRNs and scale-free GRNs using short time series simulated by VAR1s and outperform reference methods on small-scale DREAM4 in silico GRNs and E. coli GRNs. They can utilize the known major regulatory hubs to improve the performance on larger DREAM4 in silico GRNs and E. coli GRNs. The impact of nonlinear time series data on the performance of proposed methods is discussed.

Modeling Genetic Regulatory Networks Using First-Order Probabilistic Logic

2013 ◽  
Author(s):  
Nand Kishore ◽  
Radhakrishnan Balu ◽  
Shashi P. Karna
Keyword(s):  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Probabilistic Logic ◽  
First Order

scholarly journals Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pooja Singh ◽  
Ehsan Pashay Ahi ◽  
Christian Sturmbauer
Keyword(s):  
In Silico ◽  
Regulatory Networks ◽  
Evolutionary Significance ◽  
Cichlid Species ◽  
Cichlid Fishes ◽  
Gene Coexpression ◽  
Modular Evolution ◽  
Jaw Apparatus ◽  
Coexpression Networks ◽  
Pharyngeal Jaw

Abstract Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Stability and bifurcation of delay-coupled genetic regulatory networks with hub structure

2019 ◽  
Vol 356 (5) ◽  
pp. 2847-2869 ◽  
Author(s):  
Dandan Yue ◽  
Zhi-Hong Guan ◽  
Juan Li ◽  
Feng Liu ◽  
Jiang-Wen Xiao ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Stability And Bifurcation
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