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 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
2011
PhyDesign: an online application for profiling phylogenetic informativeness
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessPhylogenetic studiesPhylogenetic informativeness analysesBroad taxonomic samplingMolecular phylogenetic studiesTree of lifeOrthologous genesPhylogenetic samplingTaxonomic samplingPhylogenetic questionsPhylogenetic purposesEfficiency of sequencingSequence alignmentMarker selectionUltrametric treeDiverse suiteUtility of locusLociTreesUser-friendly toolGenomeGenesSequencingSpeciesDiversityGetting 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 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 experimentsEvolution 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
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
2002
Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks
Grosu P, Townsend JP, Hartl DL, Cavalieri D. Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks. Genome Research 2002, 12: 1121-1126. PMID: 12097350, PMCID: PMC186628, DOI: 10.1101/gr.226602.Peer-Reviewed Original Research