2018
Cancer subtype identification using somatic mutation data
Kuijjer M, Paulson J, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal Of Cancer 2018, 118: 1492-1501. PMID: 29765148, PMCID: PMC5988673, DOI: 10.1038/s41416-018-0109-7.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorComputational BiologyData CurationDatabases, GeneticFemaleGene Regulatory NetworksHumansMutationNeoplasmsPrincipal Component AnalysisPrognosisConceptsSomatic mutation dataAssociated with mutationsNext-generation sequencing technologiesMutation dataBiological pathwaysSets of mutationsSignal transduction pathwaysCancer typesPan-cancer subtypesSequencing technologiesPhenotypic dataCancer Genome AtlasCancer subtype identificationTransduction pathwaysMutational driversSomatic mutationsSubgroup of patientsTargeted treatment optionsMutationsMutation patternsGenome AtlasClassification of patientsMutation profilesPrimary tumorPrognostic subtypes
2017
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson J, Chen C, Lopes-Ramos C, Kuijjer M, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics 2017, 18: 437. PMID: 28974199, PMCID: PMC5627434, DOI: 10.1186/s12859-017-1847-x.Peer-Reviewed Original ResearchConceptsRNA-seq data setsRNA-seqGenotype-Tissue ExpressionRNA-seq processingGenome-wide transcriptional profilingRNA-seq studiesRNA-seq dataGene filteringDownstream analysisRNA sequencingTranscriptional profilesDiverse tissuesAnalytical pipelineR packageQuality controlSignificant analytical challengeSoftware pipelineGenesRNAMulti-group studyNormalization stepAnalytical challengesResultsWeTissueExpression