2023
Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models
Han Z, Yu G, Yang Y. Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models. 2023, 00: 542-547. DOI: 10.1109/bibm58861.2023.10385593.Peer-Reviewed Original ResearchProtein-protein interaction networkProtein-protein interactionsCancer gene predictionCancer genesGene predictionCancer cell line datasetsGene interaction relationshipsCell line datasetsCancer driver genesMulti-omics dataPan-cancer datasetProtein-proteinPPI networkGene associationsGene representationMulti-OmicsDriver genesGenesGraph neural networksCancer researchGraph transformer networkState-of-the-art performanceCancerState-of-the-artGraph transformation model
2020
The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma
Campbell BR, Chen Z, Faden DL, Agrawal N, Li RJ, Hanna GJ, Iyer NG, Boot A, Rozen SG, Vettore AL, Panda B, Krishnan NM, Pickering CR, Myers JN, Guo X, Kuhs K. The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma. Cancer 2020, 127: 544-553. PMID: 33146897, PMCID: PMC7891879, DOI: 10.1002/cncr.33309.Peer-Reviewed Original ResearchConceptsOral tongue squamous cell carcinomaTongue squamous cell carcinomaSquamous cell carcinomaTongue cancerYounger patientsCell carcinomaTobacco useDriver genesOral tongue cancerPatient-related factorsCancer driver genesTongue cancer specimensAge of onsetMutational landscapeSomatic mutationsMutation signaturesYounger birth cohortsSomatic mutational burdenOlder patientsCancer Genome AtlasSmoking ratesMutational burdenCancer specimensMulticenter consortiumBirth cohort
2016
Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer
Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature Communications 2016, 7: 10982. PMID: 26975529, PMCID: PMC4796315, DOI: 10.1038/ncomms10982.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaBlotting, WesternCell FractionationCell ProliferationChromatin ImmunoprecipitationGene Expression Regulation, NeoplasticGene Regulatory NetworksHCT116 CellsHumansIn Situ Hybridization, FluorescenceMaleMicroRNAsPolycomb Repressive Complex 2Prostatic NeoplasmsPTEN PhosphohydrolaseReverse Transcriptase Polymerase Chain ReactionRNA TransportRNA, Long NoncodingConceptsRegulatory networksPolycomb repressive complex 2Protein-coding genesProtein-coding transcriptsRepressive complex 2Cancer driver genesGene expression profilesTumor suppressive functionTranscriptional regulationSponge lncRNAsCytoplasmic localizationExpression profilesIntegrative analysisSequence featuresDriver genesLncRNAsPTEN expressionFunctional significanceRegulationGenesRNAExpressionComplexes 2Important roleMicroRNAsGenomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma.
Bi X, Zhao S, Adeniran A, Kluger H, Xie Z, Nawaf C, Merino M, Valera V, Pantuck A, Said J, Belldegrun A, Lifton R, Shuch B. Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma. Journal Of Clinical Oncology 2016, 34: 509-509. DOI: 10.1200/jco.2016.34.2_suppl.509.Peer-Reviewed Original ResearchDriver genesCancer driver genesSomatic mutationsProtein traffickingIllumina sequencingSomatic cellsGenomic characterizationCell differentiationCell adhesionLoss of heterozygosityClear cell renal cell carcinomaGenesMutational signaturesCell renal cell carcinomaClonal divergenceGenetic alterationsMutationsTP53 mutationsRepair deficiencySarcomatoid transformationSubset of tumorsCcRCCHypermutationRenal cell carcinomaBAP1
2013
Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes
Evans P, Avey S, Kong Y, Krauthammer M. Adjusting for Background Mutation Frequency Biases Improves the Identification of Cancer Driver Genes. IEEE Transactions On NanoBioscience 2013, 12: 150-157. PMID: 23694700, PMCID: PMC3989533, DOI: 10.1109/tnb.2013.2263391.Peer-Reviewed Original ResearchConceptsMore non-synonymous mutationsMutation frequencyTumor sequencing projectsGene-specific mannerCancer driver genesNon-synonymous mutationsSynonymous mutation ratioMutation biasSequencing projectsBackground mutation frequencyGene expressionDriver genesGenesTumor developmentMutation burdenMutation ratioHigher non-synonymous mutation burdenMutationsMutation countsExpressionBackground frequencyFrequency biasesIdentification
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