2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomology
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
2010
Multi-targeted priming for genome-wide gene expression assays
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.Peer-Reviewed Original ResearchMeSH KeywordsDNA PrimersGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalMetabolic Networks and PathwaysMyceliumNeurospora crassaNitrogenOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionReverse TranscriptionRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSequence Analysis, RNAConceptsGene expressionGene expression assaysNeurospora crassaRibosomal RNAExpression assaysMost protein-coding genesEarly sexual developmentGenome-wide gene expressionTransfer RNA genesProtein-coding genesNitrogen starvation responseGenome of SaccharomycesPreponderance of genesGlobal gene expressionResponse of SaccharomycesCommon sequence motifsSexual developmentDetailed expression profilesReverse transcriptionRNA genesStarvation responseTag sequencingSequence motifsTransfer RNATranscriptomic assays
2005
Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii
Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics 2005, 171: 109-117. PMID: 15965255, PMCID: PMC1456504, DOI: 10.1534/genetics.105.040923.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, FungalCoccidioidesCoccidioidomycosisDNA, FungalEvolution, MolecularGene ConversionGenetic VariationHumansMembrane GlycoproteinsMutationPhylogenyPolymorphism, GeneticRecombination, GeneticRepetitive Sequences, Nucleic AcidSequence Analysis, DNASpecies SpecificityTandem Repeat SequencesConceptsPathogenic fungus Coccidioides immitisConcerted evolutionProtein-coding genesC. posadasiiGenetic distance analysisPoint mutation rateHost-pathogen interactionsCell surface proteinsGenome dynamicsPathogen's benefitMultigene familyUnequal crossingGeographic rangeFungus Coccidioides immitisRepetitive domainEntire geneMutation rateRepetitive arraysSurface proteinsDistance analysisGenesHost immune systemImmune systemImmunodominant proteinsParasitic phase