AIMC Topic: Metabolic Networks and Pathways

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

PLoS computational biology Apr 10, 2018
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...
Male Humans Neoplasms Gene Expression Profiling Gene Regulatory Networks Survival Analysis Neural Networks, Computer Proportional Hazards Models Prognosis Kaplan-Meier Estimate Female Databases, Nucleic Acid Computational Biology Sequence Analysis, RNA Metabolic Networks and Pathways High-Throughput Nucleotide Sequencing
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Gas chromatography-mass spectrometry metabolomic study of lipopolysaccharides toxicity on rat basophilic leukemia cells.

Chemico-biological interactions Dec 22, 2017
Lipopolysaccharide (LPS) can lead to uncontrollable cytokine production, fatal sepsis syndrome and depression/multiple organ failure, as pathophysiologic demonstration. Various toxic effects of LPS have been extensively reported, mainly on the toxici...
Principal Component Analysis Metabolic Networks and Pathways Discriminant Analysis Amino Acids Apoptosis Gas Chromatography-Mass Spectrometry Animals Lipopolysaccharides Down-Regulation Cell Line, Tumor Metabolomics Leukemia, Basophilic, Acute Rats Mast Cells
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Data mining and pathway analysis of glucose-6-phosphate dehydrogenase with natural language processing.

Molecular medicine reports Jun 15, 2017
Human glucose-6-phosphate dehydrogenase (G6PD) is a crucial enzyme in the pentose phosphate pathway, and serves an important role in biosynthesis and the redox balance. G6PD deficiency is a major cause of neonatal jaundice and acute hemolyticanemia, ...
Humans Gene Regulatory Networks Signal Transduction Glucosephosphate Dehydrogenase Deficiency MicroRNAs Data Mining Natural Language Processing Gene Ontology Metabolic Networks and Pathways Glucosephosphate Dehydrogenase
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A review of active learning approaches to experimental design for uncovering biological networks.

PLoS computational biology Jun 1, 2017
Various types of biological knowledge describe networks of interactions among elementary entities. For example, transcriptional regulatory networks consist of interactions among proteins and genes. Current knowledge about the exact structure of such ...
Algorithms Research Design Gene Regulatory Networks Computational Biology Metabolic Networks and Pathways Supervised Machine Learning
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ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.

Plant physiology Apr 25, 2017
Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (sto...
Metabolic Networks and Pathways Internet Subcellular Fractions Knowledge Bases Chloroplasts Arabidopsis
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Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.

BMC genomics Mar 14, 2017
BACKGROUND: Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanis...
Survival Analysis Semantics Models, Statistical Metabolic Networks and Pathways Knowledge Bases Humans Prognosis Female Male Neoplasms Models, Genetic Cluster Analysis
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Revealing disease-associated pathways by network integration of untargeted metabolomics.

Nature methods Aug 1, 2016
Uncovering the molecular context of dysregulated metabolites is crucial to understand pathogenic pathways. However, their system-level analysis has been limited owing to challenges in global metabolite identification. Most metabolite features detecte...
Metabolic Networks and Pathways Fatty Acids Sphingolipids Huntington Disease Humans Neural Networks, Computer Machine Learning Steroids Algorithms Metabolomics Databases, Protein
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Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis.

Molecular medicine reports Jul 7, 2016
Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis str...
Metabolic Networks and Pathways Biomarkers Models, Biological Humans Gene Regulatory Networks Diabetes Complications Neural Networks, Computer Signal Transduction Diabetes Mellitus
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Drug target identification using network analysis: Taking active components in Sini decoction as an example.

Scientific reports Apr 20, 2016
Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmac...
Reproducibility of Results Cell Line, Tumor Signal Transduction Metabolomics Drugs, Chinese Herbal Humans Proteins Myocytes, Cardiac Neural Networks, Computer Structure-Activity Relationship Tumor Necrosis Factor-alpha Metabolic Networks and Pathways
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A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

PLoS computational biology Apr 7, 2016
O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing Ga...
Models, Biological Polysaccharides Knowledge Bases Mucins Terminology as Topic Gene Knockout Techniques Humans Glycosyltransferases Computer Simulation Genetic Engineering Protein Processing, Post-Translational CHO Cells Cricetulus Animals Metabolic Networks and Pathways Computational Biology Glycosylation
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