2018
Effect Sizes of Somatic Mutations in Cancer
Cannataro VL, Gaffney SG, Townsend JP. Effect Sizes of Somatic Mutations in Cancer. Journal Of The National Cancer Institute 2018, 110: 1171-1177. PMID: 30365005, PMCID: PMC6235682, DOI: 10.1093/jnci/djy168.Peer-Reviewed Original ResearchConceptsSelection intensityRecurrent single nucleotide variantsCancer cell lineagesSomatic variantsSingle nucleotide variantsSequence surveysSomatic tissuesReproductive advantageCancer genomesDevelopment of cancerCell lineagesSelective advantageEvolutionary processesDriver genesNucleotide variantsCancer biologyGenetic alterationsSomatic mutationsCancer cellsRelative importanceCancer growthGenesMutationsCancer typesVariants
2016
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
Dornburg A, Fisk JN, Tamagnan J, Townsend JP. PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Ecology And Evolution 2016, 16: 262. PMID: 27905871, PMCID: PMC5134231, DOI: 10.1186/s12862-016-0837-3.Peer-Reviewed Original ResearchConceptsParallel processingOpen-source software packageBayesian posterior distributionLack of softwareOpen-source programPhylogenetic experimental designProbability of resolutionUser hardwareData explorationData visualizationNext-generation sequence datasetsInformation contentSource programNovel visualizationPosterior distributionBayesian settingAdditional sample dataPower usersDataset partitionsBayesian approachSequence data setsSoftware packageDatasetGenomic information contentSoftwarePathScore: a web tool for identifying altered pathways in cancer data
Gaffney SG, Townsend JP. PathScore: a web tool for identifying altered pathways in cancer data. Bioinformatics 2016, 32: 3688-3690. PMID: 27503224, DOI: 10.1093/bioinformatics/btw512.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyHumansInternetMetabolic Networks and PathwaysMutationNeoplasmsSoftware
2015
H-CLAP: hierarchical clustering within a linear array with an application in genetics
Ghosh S, Townsend JP. H-CLAP: hierarchical clustering within a linear array with an application in genetics. Statistical Applications In Genetics And Molecular Biology 2015, 14: 125-141. PMID: 25803088, DOI: 10.1515/sagmb-2013-0076.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBayes TheoremCluster AnalysisComputational BiologyGene Expression ProfilingGeneticsOligonucleotide Array Sequence Analysis
2012
Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology
Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.Peer-Reviewed Original ResearchConceptsF. graminearumOrthologous genesLife historyFusarium graminearumF. verticillioidesGene expressionSexual developmentStage-specific gene expressionSpecies' life historyDifferent life historiesPrevious morphological analysesMorphological developmentLife cycleSexual sporesCereal pathogensUnclassified proteinsFunctional assignmentTranscriptional programsTranscriptome analysisTranscriptional analysisType genesEcological characteristicsApoptotic processFusarium speciesGraminearum
2011
Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods
Mathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. Methods In Molecular Biology 2011, 722: 61-77. PMID: 21590413, DOI: 10.1007/978-1-61779-040-9_5.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsExpensive softwareData generationMultiple platformsGenomic data generationEfficient waySuch dataPossible informationGenome sequencing technologiesKind of analysisData analysisFungal dataUsersDifferent environmentsMicroarray dataBioinformaticistsCostExperimental costSoftwareProtocolBottleneckPlatformTaskTechnologyDataAcademia
2010
LOX: inferring Level Of eXpression from diverse methods of census sequencing
Zhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26: 1918-1919. PMID: 20538728, PMCID: PMC2905554, DOI: 10.1093/bioinformatics/btq303.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyExpressed Sequence TagsGene Expression ProfilingGene Expression Regulation, FungalOligonucleotide Array Sequence AnalysisSoftwareConceptsTranscriptomic sequencing data
2009
The filamentous fungal gene expression database (FFGED)
Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics And Biology 2009, 47: 199-204. PMID: 20025988, PMCID: PMC2822089, DOI: 10.1016/j.fgb.2009.12.001.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsChromosome MappingComputational BiologyComputer GraphicsDatabase Management SystemsDatabases, GeneticGene ExpressionGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalGenome, FungalInternetModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeSequence AlignmentSoftwareSystems IntegrationUser-Computer InterfaceConceptsEfficient web interfaceExpression databaseUser-friendly managementCollection of toolsGene expression databaseDifferent usersData sharingWeb interfaceCollaborative platformExperimental metadataFree databaseRaw dataData submissionUsersMultiple experimentsGene expression dataSharingDatabaseEssential informationAjaxMetadataExpression dataDifferent experimentsRetrievalRelated experimentsMaximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
Zhang Z, Townsend JP. Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences. PLOS Computational Biology 2009, 5: e1000421. PMID: 19557160, PMCID: PMC2695770, DOI: 10.1371/journal.pcbi.1000421.Peer-Reviewed Original ResearchConceptsInformation criterionModel averagingBayesian information criterionMaximum likelihood methodModel likelihoodModel uncertaintyModel selectionDescription of clustersLevel of clusteringPrecision of estimationAkaike information criterionParameter rangeCluster countsLikelihood methodComputational biologyCluster sizeGood accuracyConquer strategyAveragingClusteringModelHierarchical clusteringClustersStatisticsEstimation
2008
Bringing Web 2.0 to bioinformatics
Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings In Bioinformatics 2008, 10: 1-10. PMID: 18842678, PMCID: PMC2638627, DOI: 10.1093/bib/bbn041.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsData exchangeWeb 2.0Data integrationHeterogeneous data sourcesHarness collective intelligenceSharing of dataWeb 2.0 technologiesIntegration of dataMajor bioinformatics challengeWeb servicesData warehousingData creationData sharingCollaborative platformCollective intelligenceAutomatic analysisCommunication modelInformation technologyBioinformatics researchUsersData sourcesSharingMultiple sourcesBioinformatics challengesPlatform