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
2016
PhyloOncology: Understanding cancer through phylogenetic analysis
Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica Et Biophysica Acta (BBA) - Reviews On Cancer 2016, 1867: 101-108. PMID: 27810337, PMCID: PMC9583457, DOI: 10.1016/j.bbcan.2016.10.006.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAdaptation, PhysiologicalAlgorithmsAnimalsBiomarkers, TumorCell Transformation, NeoplasticEvolution, MolecularGene Expression Regulation, NeoplasticGenetic FitnessGenetic Predisposition to DiseaseGenomicsHeredityHumansModels, GeneticMutationNeoplasmsPedigreePhenotypePhylogenySignal TransductionSystems BiologyTime FactorsConceptsDr. Robert A. GatenbyGenome-scale dataSystems biology approachPowerful systems biology approachUse of phylogeneticsPhylogenetic analysisBiology approachPhylogenetic applicationsSubclonal evolutionCancer biologyCancer progressionSuite of algorithmsPhylogeneticsCancer data setsCancer samplesImproved therapeutic interventionRobust approachDecades of researchFundamental insightsNew toolBiologyDiverse fieldsGatenbyData setsTherapeutic interventions
2014
The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise
Su Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.Peer-Reviewed Original ResearchPhylogenetic inferencePhylogenetic signalRate of evolutionMolecular evolutionary modelsAccurate phylogenetic inferenceFour-taxon treesYeast genus CandidaMolecular evolutionConsensus treeNucleotide substitutionsPrediction of signalsDistribution of signalsEvolutionary modelsModel choiceGenus CandidaUnrealistic modelsCorrect modelInferenceTreesRPB1PhylogenyCladePhylogeneticsRPB2Markov model
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