AIMC Topic: Gene Regulatory Networks

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Reachable Set Estimation for Markovian Jump Neural Networks With Time-Varying Delays.

IEEE transactions on cybernetics
In this paper, the reachable set estimation problem is investigated for Markovian jump neural networks (NNs) with time-varying delays and bounded peak disturbances. Our goal is to find a set as small as possible which bounds all the state trajectorie...

State Estimation for Delayed Genetic Regulatory Networks With Reaction-Diffusion Terms.

IEEE transactions on neural networks and learning systems
This paper addresses the problem of state estimation for delayed genetic regulatory networks (DGRNs) with reaction-diffusion terms using Dirichlet boundary conditions. The nonlinear regulation function of DGRNs is assumed to exhibit the Hill form. Th...

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method.

BMC bioinformatics
BACKGROUND: Prior knowledge networks (PKNs) provide a framework for the development of computational biological models, including Boolean models of regulatory networks which are the focus of this work. PKNs are created by a painstaking process of lit...

Brief isoflurane anaesthesia affects differential gene expression, gene ontology and gene networks in rat brain.

Behavioural brain research
Much is still unknown about the mechanisms of effects of even brief anaesthesia on the brain and previous studies have simply compared differential expression profiles with and without anaesthesia. We hypothesised that network analysis, in addition t...

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

BMC genomics
BACKGROUND: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing...

Recurrent neural network based hybrid model for reconstructing gene regulatory network.

Computational biology and chemistry
One of the exciting problems in systems biology research is to decipher how genome controls the development of complex biological system. The gene regulatory networks (GRNs) help in the identification of regulatory interactions between genes and offe...

Identification of informative genes and pathways using an improved penalized support vector machine with a weighting scheme.

Computers in biology and medicine
Incorporation of pathway knowledge into microarray analysis has brought better biological interpretation of the analysis outcome. However, most pathway data are manually curated without specific biological context. Non-informative genes could be incl...

Batch Mode TD($\lambda$ ) for Controlling Partially Observable Gene Regulatory Networks.

IEEE/ACM transactions on computational biology and bioinformatics
External control of gene regulatory networks (GRNs) has received much attention in recent years. The aim is to find a series of actions to apply to a gene regulation system making it avoid its diseased states. In this work, we propose a novel method ...

Protein-protein interaction network construction for cancer using a new L1/2-penalized Net-SVM model.

Genetics and molecular research : GMR
Identifying biomarker genes and characterizing interaction pathways with high-dimensional and low-sample size microarray data is a major challenge in computational biology. In this field, the construction of protein-protein interaction (PPI) networks...

Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method.

BioMed research international
The number of gene-related databases has been growing largely along with the research on genes of bioinformatics. Those databases are filled with various gene functions, pathways, interactions, and so forth, while much biomedical knowledge about huma...