AIMC Topic: Metabolic Networks and Pathways

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Artificial neural network-based exploration of gene-nutrient interactions in folate and xenobiotic metabolic pathways that modulate susceptibility to breast cancer.

Gene Jan 16, 2016
In the current study, an artificial neural network (ANN)-based breast cancer prediction model was developed from the data of folate and xenobiotic pathway genetic polymorphisms along with the nutritional and demographic variables to investigate how m...
Epistasis, Genetic Gene-Environment Interaction Xenobiotics Metabolic Networks and Pathways Folic Acid Disease Susceptibility Food Female Middle Aged Humans Aged Diet Neural Networks, Computer Adult Case-Control Studies Breast Neoplasms Computational Biology
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LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.

Bioinformatics (Oxford, England) Dec 1, 2015
UNLABELLED: Supervised classification based on support vector machines (SVMs) has successfully been used for the prediction of cis-regulatory modules (CRMs). However, no integrated tool using such heterogeneous data as position-specific scoring matri...
Software Animals Mice Support Vector Machine Metabolic Networks and Pathways Systems Integration Gene Expression Regulation Drosophila Molecular Sequence Annotation Computer Graphics
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Application of artificial neural network to investigate the effects of 5-fluorouracil on ribonucleotides and deoxyribonucleotides in HepG2 cells.

Scientific reports Nov 18, 2015
Endogenous ribonucleotides and deoxyribonucleotides are essential metabolites that play important roles in a broad range of key cellular functions. Their intracellular levels could also reflect the action of nucleoside analogues. We investigated the ...
Inhibitory Concentration 50 Adenine Nucleotides Cytosine Nucleotides Deoxyribonucleotides Metabolic Networks and Pathways Models, Biological Fluorouracil Tandem Mass Spectrometry Guanine Nucleotides Ribonucleotides Thymine Nucleotides Uracil Nucleotides Humans Neural Networks, Computer Hep G2 Cells Cell Survival Chromatography, Liquid
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METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text.

BioMed research international Oct 1, 2015
The substrates of a transporter are not only useful for inferring function of the transporter, but also important to discover compound-compound interaction and to reconstruct metabolic pathway. Though plenty of data has been accumulated with the deve...
Vocabulary, Controlled Entropy Machine Learning Metabolic Networks and Pathways Software Data Mining Algorithms Pattern Recognition, Automated Natural Language Processing Membrane Transport Proteins
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The role of regulation in the origin and synthetic modelling of minimal cognition.

Bio Systems Aug 19, 2015
In this paper we address the question of minimal cognition by investigating the origin of some crucial cognitive properties from the very basic organisation of biological systems. More specifically, we propose a theoretical model of how a system can ...
Models, Theoretical Metabolic Networks and Pathways Synthetic Biology Humans Environment Artificial Intelligence Animals Cognition
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Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery.

PLoS neglected tropical diseases Jun 26, 2015
BACKGROUND: Chagas disease is a neglected tropical disease (NTD) caused by the eukaryotic parasite Trypanosoma cruzi. The current clinical and preclinical pipeline for T. cruzi is extremely sparse and lacks drug target diversity.
Female Humans Trypanosoma cruzi Metabolic Networks and Pathways Animals Machine Learning Genome, Protozoan Computational Biology Chagas Disease Drug Discovery Bayes Theorem Trypanocidal Agents Disease Models, Animal Mice High-Throughput Screening Assays Mice, Inbred BALB C Cell Line
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Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses.

BMC genomics Jun 11, 2015
BACKGROUND: Pathway analysis has been widely used to gain insight into essential mechanisms of the response to myocardial infarction (MI). Currently, there exist multiple pathway databases that organize molecular datasets and manually curate pathway ...
Gene Ontology Algorithms Humans Databases, Genetic Metabolic Networks and Pathways Myocardial Infarction
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Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

BMC bioinformatics Feb 14, 2015
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...
Humans Software Algorithms Gene Regulatory Networks Computational Biology Metabolic Networks and Pathways Multigene Family Gene Ontology Saccharomyces cerevisiae Proteins Arabidopsis Proteins Cytochrome P-450 Enzyme System Semantics Vocabulary, Controlled Molecular Sequence Annotation
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Multifactor dimensionality reduction analysis to elucidate the cross-talk between one-carbon and xenobiotic metabolic pathways in multi-disease models.

Molecular biology reports Feb 4, 2015
Putatively functional polymorphisms of one-carbon and xenobiotic metabolic pathways influence susceptibility for wide spectrum of diseases. The current study was aimed to explore gene-gene interactions among these two metabolic pathways in four disea...
Transferases Multifactor Dimensionality Reduction Xenobiotics Datasets as Topic Gene Expression Regulation Female Epistasis, Genetic Breast Neoplasms Oxidoreductases Male Factor Analysis, Statistical Case-Control Studies Lupus Erythematosus, Systemic Coronary Artery Disease Carbon Genetic Predisposition to Disease Sex Factors Parkinson Disease Humans Polymorphism, Single Nucleotide Metabolic Networks and Pathways
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Application of a metabolic network-based graph neural network for the identification of toxicant-induced perturbations.

Toxicological sciences : an official journal of the Society of Toxicology Jul 1, 2025
Transcriptomic analyses have been an effective approach to investigate the biological responses and metabolic perturbations by environmental contaminants in rodent models. However, it is well recognized that metabolic networks are highly connected an...
Neural Networks, Computer Liver Metabolic Networks and Pathways Environmental Pollutants Polychlorinated Dibenzodioxins Animals Graph Neural Networks Gene Expression Profiling Transcriptome Mice
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