2017
Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology And Evolution 2017, 34: 3006-3022. PMID: 28962009, PMCID: PMC5850860, DOI: 10.1093/molbev/msx213.Peer-Reviewed Original ResearchConceptsPoisson random fieldRandom fieldsEnsemble of modelsRandom field frameworkField frameworkClustering modelHistorical demographic trendsAmino acid-altering substitutionsSelection intensityEnsembleHigh powerUniform selectionProtein-coding genesProtein coding genesHeterogeneity of selectionDNA sequence polymorphismsComparison of polymorphisms
2016
PhyloOncology: Understanding cancer through phylogenetic analysis
Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica Et Biophysica Acta (BBA) - Reviews On Cancer 2016, 1867: 101-108. PMID: 27810337, PMCID: PMC9583457, DOI: 10.1016/j.bbcan.2016.10.006.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAdaptation, PhysiologicalAlgorithmsAnimalsBiomarkers, TumorCell Transformation, NeoplasticEvolution, MolecularGene Expression Regulation, NeoplasticGenetic FitnessGenetic Predisposition to DiseaseGenomicsHeredityHumansModels, GeneticMutationNeoplasmsPedigreePhenotypePhylogenySignal TransductionSystems BiologyTime FactorsConceptsDr. Robert A. GatenbyGenome-scale dataSystems biology approachPowerful systems biology approachUse of phylogeneticsPhylogenetic analysisBiology approachPhylogenetic applicationsSubclonal evolutionCancer biologyCancer progressionSuite of algorithmsPhylogeneticsCancer data setsCancer samplesImproved therapeutic interventionRobust approachDecades of researchFundamental insightsNew toolBiologyDiverse fieldsGatenbyData setsTherapeutic interventionsPathScore: 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 Research
2013
AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification
Dai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z. AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics 2013, 29: 1837-1839. PMID: 23732274, PMCID: PMC3702255, DOI: 10.1093/bioinformatics/btt284.Peer-Reviewed Original Research
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 clusteringClustersStatisticsEstimationEvolution of Reproductive Morphology in Leaf Endophytes
Wang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of Reproductive Morphology in Leaf Endophytes. PLOS ONE 2009, 4: e4246. PMID: 19158947, PMCID: PMC2617777, DOI: 10.1371/journal.pone.0004246.Peer-Reviewed Original ResearchConceptsLeaf endophytesEcological roleDead host tissuesCommon developmental pathwayEndophytic lifestyleAsexual developmentSaprobic speciesReproductive structuresReproductive morphologySaprobic fungiFungal tissueFungal classificationDead woodEndophytic fungiDevelopmental pathwaysBody sizeFungal morphologySignificant divergenceLeotiomycetesFungiEndophytesHost tissuesProblematic groupRhytismatalesImportant role
2008
The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
Townsend JP, López-Giráldez F, Friedman R. The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree. Journal Of Molecular Evolution 2008, 67: 437-447. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.Peer-Reviewed Original ResearchConceptsAmino acid sequencePhylogenetic informativenessAcid sequenceVertebrate treeDNA sequencesMolecular evolutionary patternsEarly placental mammalsGenes c-mycDivergence timesMolecular evolutionPhylogenetic conflictEarly vertebratesEvolutionary patternsPlacental mammalsNucleotide sequenceMuroid rodentsFunctional constraintsGenesC-MycSupport valuesSequenceNucleotidesNumber of charactersHigh informativenessTrees
2005
A Bayesian method for analysing spotted microarray data
Meiklejohn CD, Townsend JP. A Bayesian method for analysing spotted microarray data. Briefings In Bioinformatics 2005, 6: 318-330. PMID: 16420731, DOI: 10.1093/bib/6.4.318.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2004
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
Townsend JP. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 2004, 5: 54. PMID: 15128431, PMCID: PMC420235, DOI: 10.1186/1471-2105-5-54.Peer-Reviewed Original Research