0000000000807243

AUTHOR

Michiel E. Adriaens

0000-0002-4472-7119

showing 2 related works from this author

Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets

2012

PLoS one 7(11), e49831 (2012). doi:10.1371/journal.pone.0049831

MaleEXPRESSIONMicroarrayMicroarraysPopulationlcsh:MedicineBiologyMETABOLISMMalignancyBioinformaticsMetastasisMolecular GeneticsProstate cancerGeneticsCancer GeneticsBiomarkers TumormedicineHumansEpithelial–mesenchymal transitioneducationProstate carcinogenesislcsh:ScienceBiologyCANCER CELLSSIGNATURESOligonucleotide Array Sequence Analysiseducation.field_of_studyMultidisciplinarySystems BiologyProstate CancerCHOLESTEROLlcsh:RComputational BiologyCancers and NeoplasmsProstatic NeoplasmsGenomicsmedicine.diseaseEPITHELIAL-MESENCHYMAL TRANSITIONGene Expression Regulation NeoplasticMODELGenitourinary Tract TumorsCell Transformation NeoplasticOncologyCancer cellBIOLOGICAL PATHWAYSMedicinelcsh:QMetabolic Networks and PathwaysResearch Article
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EFMviz

2020

Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…

0301 basic medicineComputer scienceEndocrinology Diabetes and Metabolismgenome-scale metabolic modelslcsh:QR1-502computer.software_genreBiochemistryData typelcsh:MicrobiologySBML03 medical and health sciences0302 clinical medicineData visualizationGraph drawingProtocolACETATEdata visualizationCELLSBMLCYTOSCAPEMolecular BiologyGENE-EXPRESSIONSoftware visualizationbusiness.industryPATHWAY ANALYSISnetwork visualizationelementary flux modesToolboxVisualization030104 developmental biologyWorkflowDEFINITIONESCHERICHIA-COLIGROWTHData miningbusinesscomputerSET030217 neurology & neurosurgeryMetabolites
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