2022
Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models
Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers 2022, 14: 4326. PMID: 36077861, PMCID: PMC9454754, DOI: 10.3390/cancers14174326.Peer-Reviewed Original ResearchDynamic evolutionary historyMolecular phylogenetic analysisMolecular evolutionary analysisTumor cell migrationEvolutionary historyEvolutionary analysisPhylogenetic analysisDispersal routesCell migrationTumor evolutionTumor genetic heterogeneityGenetic heterogeneityMetastatic cellsClonesTumor migrationMigration historyGeneral patternPhylogeneticsFundamental questionsEvolution of metastasesMigrationEvolutionCellsHybridsVariation
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
2019
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum
Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio 2019, 10: 10.1128/mbio.02119-19. PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mbio.02119-19.Peer-Reviewed Original ResearchConceptsGene expressionMating lociFungal diversityResponsive genesSexual developmentSecondary metabolism gene clustersGenome-wide gene expressionMating-type genesRich fungal diversitySecondary metabolism pathwaysModel filamentous fungusSecondary metabolic pathwaysWide gene expressionNumerous secondary metabolitesGene expression responsesHistidine kinaseLife cycleSexual reproductionHomothallic speciesDevelopmental genesEvolutionary biologistsHeterokaryon incompatibilityAsexual reproductionDistinct morphological stagesEvolutionary history
2016
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum R, Berv J, Dornburg A, Field D, Townsend J, Lemmon E, Lemmon A. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2016, 534: s7-s8. DOI: 10.1038/nature19417.Peer-Reviewed Original ResearchMajor avian lineagesAvian lineagesSister groupSequence dataLiving birdsCretaceous–Palaeogene mass extinctionIdentical phylogenetic treesDivergence time analysesGenomic sequence dataSuccessive sister groupsMaximum likelihood analysisNext-generation DNA sequencingHybrid enrichmentNuclear lociAvian phylogenyCrown birdsComprehensive phylogenyMajor cladesEvolutionary historyMajor radiationPhylogenetic treeCladePhylogenyLikelihood analysisDNA sequencing
2015
Inferring the Origin of Metastases from Cancer Phylogenies
Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research 2015, 75: 4021-4025. PMID: 26260528, PMCID: PMC4833389, DOI: 10.1158/0008-5472.can-15-1889.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsComplete phylogenyEvolutionary historyPhylogeny-based testsFuture phylogenetic studiesMolecular evolutionary modelsMetastatic subclonesMonophyletic cladePhylogenetic reconstructionCancer lineagesPhylogenetic studiesNatural selectionPhylogenyCancer phylogeniesOrigin of metastasesCancer biologyMetastatic cascadeSubclonesTargeted sequencingEvolutionary modelsDriver mutationsUltra-deep sequencingSequencingRecent studiesMonophylyClade