2016
Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Cho H, Berger B, Peng J. Compact Integration of Multi-Network Topology for Functional Analysis of Genes. Cell Systems 2016, 3: 540-548.e5. PMID: 27889536, PMCID: PMC5225290, DOI: 10.1016/j.cels.2016.10.017.Peer-Reviewed Original ResearchMultiple heterogeneous networksBiological network dataLow-dimensional vectorsProtein function predictionMashup frameworkShelf machineArt performanceHeterogeneous networksNetwork dataScience domainMashupsIndividual networksInference tasksTopological landscapeNetwork integrationInteraction predictionNetworkFunction predictionUnsolved challengeMore accurate inferencesPresent toolsAccurate inferenceFunctional interaction networkTopological contextTopological patterns
2015
Exploiting ontology graph for predicting sparsely annotated gene function
Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics 2015, 31: i357-i364. PMID: 26072504, PMCID: PMC4542782, DOI: 10.1093/bioinformatics/btv260.Peer-Reviewed Original ResearchConceptsFunction prediction algorithmsPrediction algorithmVariety of algorithmsFunctional labelsOntology graphCross-validation experimentsOverfitting problemGraph structurePrevious stateGene functionAlgorithmAnnotation catalogsTens of thousandsMolecular interaction networksFunction predictionOntology databasePoor predictive performanceAnnotationLabelsPredictive performanceGene Ontology databaseInformationLarge numberGO termsInteraction networks