AIMC Topic: Gene Regulatory Networks

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Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.

PLoS computational biology
Artificial neural networks (ANN) are computing architectures with many interconnections of simple neural-inspired computing elements, and have been applied to biomedical fields such as imaging analysis and diagnosis. We have developed a new ANN frame...

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

BMC systems biology
BACKGROUND: Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, mos...

Prediction and characterization of human ageing-related proteins by using machine learning.

Scientific reports
Ageing has a huge impact on human health and economy, but its molecular basis - regulation and mechanism - is still poorly understood. By today, more than three hundred genes (almost all of them function as protein-coding genes) have been related to ...

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

BMC genomics
BACKGROUND: Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and H...

A Risk Stratification Model for Lung Cancer Based on Gene Coexpression Network and Deep Learning.

BioMed research international
Risk stratification model for lung cancer with gene expression profile is of great interest. Instead of previous models based on individual prognostic genes, we aimed to develop a novel system-level risk stratification model for lung adenocarcinoma b...

Identifying term relations cross different gene ontology categories.

BMC bioinformatics
BACKGROUND: The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecu...

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

BMC bioinformatics
BACKGROUND: Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate om...

Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks.

Molecules (Basel, Switzerland)
The advances in biological technologies make it possible to generate data for multiple conditions simultaneously. Discovering the condition-specific modules in multiple networks has great merit in understanding the underlying molecular mechanisms of ...

Comparative analysis of weighted gene co-expression networks in human and mouse.

PloS one
The application of complex network modeling to analyze large co-expression data sets has gained traction during the last decade. In particular, the use of the weighted gene co-expression network analysis framework has allowed an unbiased and systems-...