2018
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.Peer-Reviewed Original ResearchConceptsSerovar CopenhageniPublic health relevanceSevere casesSerogroup IcterohaemorrhagiaeSerovar IcterohaemorrhagiaeWorldwide zoonosisHealth relevanceIcterohaemorrhagiaeCopenhageniVirulent strainHigh discriminatory powerSerovarsGlobal isolatesFrameshift mutationDiscriminatory powerFirst studyPathogenic speciesIsolatesHeterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C
Cannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene 2018, 37: 2444-2455. PMID: 29453361, DOI: 10.1038/s41388-017-0105-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAmino Acid SubstitutionAnimalsCase-Control StudiesDisease ProgressionDrug Resistance, NeoplasmFemaleGenetic HeterogeneityHigh-Throughput Nucleotide SequencingHumansMaleMiceMice, Inbred BALB CMice, NudeNeoplasmsOncogenesPoint MutationPolymorphism, Single NucleotideProto-Oncogene Proteins p21(ras)Sequence Analysis, DNAYoung AdultConceptsTime of treatmentTargeted therapyLung tumorsDe novo mutationsNew targeted therapiesPatient-derived xenograftsHighest fitness advantageKRAS G12C variantNovo mutationsEvidence of heterogeneityNovel KRAS mutationPreclinical promiseSuch therapyHigh prevalenceKRAS mutationsTreatment resistanceBRAF V600EKRASTherapyTargeted inhibitorsTumorsAssociated oncogeneRAS genesHuman cancersOncogenic mutationsSomatic evolutionary timings of driver mutations
Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. BMC Cancer 2018, 18: 85. PMID: 29347918, PMCID: PMC5774140, DOI: 10.1186/s12885-017-3977-y.Peer-Reviewed Original ResearchBase SequenceCarcinogenesisClonal EvolutionGenetic HeterogeneityHumansMutationNeoplasmsSequence Analysis, DNA
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
2015
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015, 526: 569-573. PMID: 26444237, DOI: 10.1038/nature15697.Peer-Reviewed Original ResearchSolving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi
Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi. Environmental Microbiology Reports 2015, 7: 658-667. PMID: 26033481, DOI: 10.1111/1758-2229.12303.Peer-Reviewed Original ResearchConceptsPotential plant hostsEnvironmental sequencesDiversity of ecologyEctomycorrhizal fungiEcological roleGenetic divergenceGeographic distributionUnculturable fungiPhylogenetic informativenessPlant hostsEcologyITS phylogenyITS sequencesRoot tipsEnvironmental samplesSpeciesMetagenomic investigationSequence alignmentHost typeHelvellaDiversityFungiDiversity of relationshipsSequenceSoil
2013
Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
2012
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
Townsend JP, Su Z, Tekle YI. Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny. Systematic Biology 2012, 61: 835-849. PMID: 22389443, DOI: 10.1093/sysbio/sys036.Peer-Reviewed Original ResearchConceptsPhylogenetic signalPhylogenetic noisePhylogenetic treeAdditional sequence dataRate of evolutionPhylogenetic researchPhylogenetic experimental designSequence dataImpact of collectionInternodesPower of resolutionFundamental unitTreesPhylogeneticsPhylogenyPolytomyGenesLociPotential signalsSignalsExample data setsData sets
2011
Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference
Townsend JP, Leuenberger C. Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference. Systematic Biology 2011, 60: 358-365. PMID: 21303824, DOI: 10.1093/sysbio/syq097.Peer-Reviewed Original Research
2010
Identification of new molecular markers for assembling the eukaryotic tree of life
Tekle YI, Grant JR, Kovner AM, Townsend JP, Katz LA. Identification of new molecular markers for assembling the eukaryotic tree of life. Molecular Phylogenetics And Evolution 2010, 55: 1177-1182. PMID: 20302952, DOI: 10.1016/j.ympev.2010.03.010.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, ProteinEukaryotaEvolution, MolecularGenetic MarkersPhylogenySequence Analysis, DNAConceptsEukaryotic treePhylogenetic signalMolecular markersKey phylogenetic positionPhylogenetic informativeness profilesAppropriate molecular markersEukaryotic supergroupsUnicellular eukaryotesOrthologous groupsPhylogenomic analysisPhylogenetic positionNew molecular markersMolecular dataMultigene analysisMorphological charactersProtein databaseUniversal degenerate primersDegenerate primersLack of resolutionDeep branchWhole treeTreesEukaryotesDeep relationshipTargeted sampling
2009
Evolution 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
2007
Profiling Phylogenetic Informativeness
Townsend JP. Profiling Phylogenetic Informativeness. Systematic Biology 2007, 56: 222-231. PMID: 17464879, DOI: 10.1080/10635150701311362.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEvolution, MolecularGenes, BRCA1Genes, mycGenes, RAG-1PhylogenyReceptors, SomatotropinRodentiaSequence Analysis, DNAConceptsPhylogenetic informativenessRapid radiationPhylogenetic studiesCharacter samplingBroad phylogenetic studyRapid adaptive radiationGenome-scale dataAddition of charactersAdaptive radiationPhylogenetic signalSoft polytomiesPhylogenetic profilesPhylogenetic hypothesisAncestral lineagePhylogenetic experimentsEarly metazoansPhylogenetic charactersSequence dataMuroid rodentsHistorical radiationPolytomyBase pairsGenesC-MycGenes BRCA1
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