2021
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Research 2021, 50: d1340-d1347. PMID: 34554251, PMCID: PMC8728274, DOI: 10.1093/nar/gkab851.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingDatabases, GeneticGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansNeoplasmsRNA SplicingSoftwareConceptsAlternative splicingCancer-specific splicing eventsDifferential alternative splicingHuman cancersTCGA tumor samplesSplicing differencesSplicing eventsProtein complexityAdjacent normal samplesSplicingGene expressionSplicing dataNormal samplesAbnormal splicingIntegrative viewMRNA levelsDifferential analysisTumor samplesTranscripts
2018
Predict effective drug combination by deep belief network and ontology fingerprints
Chen G, Tsoi A, Xu H, Zheng W. Predict effective drug combination by deep belief network and ontology fingerprints. Journal Of Biomedical Informatics 2018, 85: 149-154. PMID: 30081101, DOI: 10.1016/j.jbi.2018.07.024.Peer-Reviewed Original Research
2017
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer
Wang H, Luo J, Liu C, Niu H, Wang J, Liu Q, Zhao Z, Xu H, Ding Y, Sun J, Zhang Q. Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinformatics 2017, 18: 388. PMID: 28865443, PMCID: PMC5581471, DOI: 10.1186/s12859-017-1796-4.Peer-Reviewed Original Research
2016
Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology
Hart T, Dider S, Han W, Xu H, Zhao Z, Xie L. Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Scientific Reports 2016, 6: 20441. PMID: 26841718, PMCID: PMC4740793, DOI: 10.1038/srep20441.Peer-Reviewed Original ResearchConceptsPrecision anti-cancer therapyMolecular basisAnti-cancer therapyStructural systems pharmacologyProtein-protein interactionsDrug target identificationNetwork biology analysisMolecular targetsInteractomic dataGenetic interactionsStructural proteomeGenetic networksKey molecular targetsPhenotypic responsesKinase targetsBiology analysisCancer mutationsPleiotropic effectsAnti-cancer effectsNetwork biomarkersTarget identificationGenetic biomarkersSystems pharmacology approachKey nodesTarget
2015
Oncogenes and tumor suppressor genes: comparative genomics and network perspectives
Zhu K, Liu Q, Zhou Y, Tao C, Zhao Z, Sun J, Xu H. Oncogenes and tumor suppressor genes: comparative genomics and network perspectives. BMC Genomics 2015, 16: s8. PMID: 26099335, PMCID: PMC4474543, DOI: 10.1186/1471-2164-16-s7-s8.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, GeneticGene Regulatory NetworksGenes, EssentialGenes, Tumor SuppressorGenomicsHumansMutationNeoplasmsOncogenesProtein Interaction MapsConceptsTumor suppressor geneEssential genesTSG proteinsEssential proteinsHuman protein-protein interaction networkCancer drug target proteinsSuppressor geneWhole human interactomeProtein-protein interaction networkCancer developmentMutation frequencyDirect interactionDrug target identificationCancer drug targetSomatic mutationsDrug target proteinsDrug target genesComparative genomicsLow mutation frequencyCellular functionsHuman interactomeMutation patternsGenetic variationGene setsHigh mutation frequency
2012
Advances in systems biology: computational algorithms and applications
Huang Y, Zhao Z, Xu H, Shyr Y, Zhang B. Advances in systems biology: computational algorithms and applications. BMC Systems Biology 2012, 6: s1. PMID: 23281622, PMCID: PMC3524016, DOI: 10.1186/1752-0509-6-s3-s1.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBiomedical ResearchComputational BiologyGene Regulatory NetworksGenetic Association StudiesGenomicsHumansModels, AnimalSystems BiologyNetwork‐Assisted Investigation of Antipsychotic Drugs and Their Targets
Sun J, Xu H, Zhao Z. Network‐Assisted Investigation of Antipsychotic Drugs and Their Targets. Chemistry & Biodiversity 2012, 9: 900-910. PMID: 22589091, DOI: 10.1002/cbdv.201100356.Peer-Reviewed Original ResearchMeSH KeywordsAntipsychotic AgentsClopenthixolDatabases, FactualDrug InteractionsGene Regulatory NetworksHumansPiperazinesSchizophreniaThiazolesThiothixeneConceptsAdverse drug interactionsAntipsychotic drugsDrug interactionsDrug actionAtypical antipsychotic drugsTreatment of schizophreniaSevere mental disordersMolecular mechanismsPsychiatric medicationsReceptor profileMental disordersAntipsychoticsDrug-gene networkDrugsMolecular actionsDifferent molecular mechanismsDrugBank database