Featured Publications
Molecular Biology and Evolution of Cancer: From Discovery to Action
Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk J, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Molecular Biology And Evolution 2019, 37: 320-326. PMID: 31642480, PMCID: PMC6993850, DOI: 10.1093/molbev/msz242.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary processesMolecular evolutionary processesEvolution of cancerCancer cell populationsEcological nichesNew therapeutic modesCancer evolutionEcological theoryMolecular biologyCancer biologyCancer progressionSuite of conceptsCell populationsBiologyNicheEvolutionCirculatory systemDeeper understandingDiscoveryCancer
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 metastasesMigrationEvolutionCellsHybridsVariationA phylogenetic approach to study the evolution of somatic mutational processes in cancer
Miura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology 2022, 5: 617. PMID: 35732905, PMCID: PMC9217972, DOI: 10.1038/s42003-022-03560-0.Peer-Reviewed Original ResearchConceptsMutational processesPattern of conservationFalse-positive discovery rateCollection of mutationsSomatic mutational processesPhylogenetic approachGenomic variationSomatic variationCell lineagesMutational signaturesTumor evolutionMutation signaturesPhylogenyCancer cellsDiscovery rateMutationsComputer-simulated datasetsRelative activityLineagesComputational methodsSignaturesConservationDivergenceEvolutionJoint analysis
2018
Neutral Theory and the Somatic Evolution of Cancer
Cannataro VL, Townsend JP. Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology And Evolution 2018, 35: 1308-1315. PMID: 29684198, PMCID: PMC5967571, DOI: 10.1093/molbev/msy079.Peer-Reviewed Original Research
2015
Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects
Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Ecology And Evolution 2015, 15: 86. PMID: 25968460, PMCID: PMC4429678, DOI: 10.1186/s12862-015-0364-7.Peer-Reviewed Original ResearchConceptsGeneralized signalCorrect treeAnalytical predictionsNoise analysisDifferent inference methodsBayesian approachLength spaceInference methodsQuartet treesMaximum likelihoodSimulation studyBranch lengthsInferenceModel treePhylogenetic inferenceUtility of charactersAsymmetrical topologyLong-branch effectsConvergenceTopologyPredictionSpaceSignalsEvolution
2009
Evolving gene expression: from G to E to G×E
Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to G×E. Trends In Ecology & Evolution 2009, 24: 649-658. PMID: 19699549, PMCID: PMC2805859, DOI: 10.1016/j.tree.2009.06.011.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene expressionMode of evolutionGene expression data setsTerms of geneticsExpression data setsGenetic variationBreadth of conclusionsEnvironmental responsesGxE interactionsMultiple individualsGeneticsExpressionSingle strainEnvironmental controlEvolutionEnvironmental effectsKey componentSpeciesG×EInteractionStrains