2017
Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
Dornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances In Genetics 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.ChaptersMeSH KeywordsEvolution, MolecularFungiGenome, FungalGenomicsInformation SystemsModels, GeneticPhylogenyPhylogeographyConceptsTree of lifeFungal evolutionary biologyGenomic-scale dataHundreds of lociGenome-scale analysisFungal phylogenomicsFungal treeSpecies delimitationPhenotypic diversificationFirst genomeEvolutionary biologyPhylogenetic treePhylogenetic inferencePhylogenetic analysisEntire genomeTree inferenceReview of considerationsEvolutionary problemsPhylogenomicsGenomeTreesLociCentral roleExperimental designBiodiversityThe ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.Peer-Reviewed Original ResearchConceptsGene expressionFilamentous fungiCommon garden environmentBody developmentWide gene expressionGene expression phenotypesGene deletion studiesGene expression measurementsMulticellular developmentDivergent speciesSexual phenotypeGene familyEvolved increasesDivergent morphologyKnockout phenotypesAncestral levelsWhole genomeGarden environmentExpression phenotypesDeletion studiesRelevant genesPhenotypic analysisDevelopmental stagesExpression measurementsBody morphologyPreface
Townsend JP, Wang Z. Preface. Advances In Genetics 2017, 100: xi-xii. PMID: 29153406, DOI: 10.1016/s0065-2660(17)30059-7.Chapters
2014
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3: Genes, Genomes, Genetics 2014, 4: 1731-1745. PMID: 25053707, PMCID: PMC4169166, DOI: 10.1534/g3.114.012617.Peer-Reviewed Original ResearchConceptsNeurospora crassaRNA-seqFilamentous fungus Neurospora crassaGenome-wide characterizationProtein coding genesFungus Neurospora crassaPrevious microarray studyRibosome biogenesisCoding genesTranscriptional responseRRNA metabolismCellular metabolismMicroarray studiesGenesCrassaSignificant oxidative stressRNA levelsOrganismsMRNA levelsOxidative stressMRNAMetabolismBiogenesisTranscriptsMycelium
2013
Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.Peer-Reviewed Original ResearchConceptsPerithecial developmentNeurospora crassaGene expressionSexual developmentBody developmentFruiting-body developmentMost upregulated genesReverse genetics approachGlobal gene expressionSimilar expression patternsSame developmental stageMulticellular organismsSexual crossingMat AUnclassified proteinsDevelopmental traitsN. crassaKnockout analysisTranscriptomic landscapeType genesUpregulated genesGenetic basisDiverse functionsExpression patternsStage specificitySex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma
Samils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H. Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings Of The Royal Society B 2013, 280: 20130862. PMID: 23782882, PMCID: PMC3712418, DOI: 10.1098/rspb.2013.0862.Peer-Reviewed Original ResearchConceptsMating typesFilamentous ascomycete Neurospora tetraspermaNeurospora tetraspermaMating-type locusGene expression levelsExpression divergenceTranscriptional divergencePhenotypic divergenceFungal AnaloguesRecombinational suppressionMat ASequence divergenceN. tetraspermaMale developmentDivergent regionsFemale developmentMolecular phenotypesGenesSexual dimorphismMale tissuesExpression levelsDivergencePhenotypeAgar mediumGenome
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 experiments
2007
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. Advances In Genetics 2007, 57: 49-96. PMID: 17352902, PMCID: PMC3673015, DOI: 10.1016/s0065-2660(06)57002-6.Peer-Reviewed Original ResearchConceptsFunctional genomics projectsGenomics projectsFilamentous fungiFilamentous fungus NeurosporaFunctional genomic analysisNon-yeast fungiFunctional genomicsNeurospora genomeFungus NeurosporaNovel genesPositional cloningNeurospora crassaAntisense transcriptsGenomic analysisSNP mapAlternative promotersCDNA libraryExpression analysisGene replacementMutant strainSystematic disruptionExpression dataPhenotypic analysisNeurosporaConditions of growth
2006
Ecological and evolutionary genomics of Saccharomyces cerevisiae
LANDRY CR, TOWNSEND JP, HARTL DL, CAVALIERI D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 2006, 15: 575-591. PMID: 16499686, DOI: 10.1111/j.1365-294x.2006.02778.x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary genomic studiesPrime model systemImportant genetic variationPowerful model speciesEvolutionary genomicsEvolutionary geneticsEvolutionary forcesFunctional genomicsYeast genomeNumerous habitatsModel speciesGenomic studiesUnicellular fungiGenetic variationBiology questionsS. cerevisiaeNatural isolatesGenetic levelGenomicsSaccharomycesModel systemYeastEukaryotesGenomeHabitats
2003
Population Genetic Variation in Genome-Wide Gene Expression
Townsend JP, Cavalieri D, Hartl DL. Population Genetic Variation in Genome-Wide Gene Expression. Molecular Biology And Evolution 2003, 20: 955-963. PMID: 12716989, DOI: 10.1093/molbev/msg106.Peer-Reviewed Original ResearchConceptsGene expression levelsGene expressionNatural populationsGenetic variationNatural isolatesExpression levelsGenome-wide gene expressionPopulation genetic variationGenome-wide scaleComparative gene expressionDifferential gene expressionDNA microarray technologyAmino acid metabolismWine yeast SaccharomycesSulfur assimilationEvolutionary biologistsGenomic scaleYeast SaccharomycesNatural selectionS. cerevisiaeProtein degradationSuch traitsDifferential reproductionMicroarray technologyOrganic evolution
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
2000
Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis
Cavalieri D, Townsend J, Hartl D. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 12369-12374. PMID: 11035792, PMCID: PMC17348, DOI: 10.1073/pnas.210395297.Peer-Reviewed Original ResearchConceptsDNA microarray analysisGene expressionNatural populationsSaccharomyces cerevisiaeMicroarray analysisGenome-wide transcriptional profilingAmino acid permeasesAmino acid biosynthesisSuite of traitsGlobal expression analysisSmooth colony phenotypeExtent of heterozygosityGlobal patternsVineyard isolateGene functionEvolutionary biologyNitrogen assimilationAcid biosynthesisSingle geneTranscriptional profilingUnlinked lociColony phenotypeHomothallic strainsS. cerevisiaeDiploid progeny