2022
A 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
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 sequencingFuture Perspectives and Challenges of Fungal Systematics in the Age of Big Data
Wang Z, Nilsson R, James T, Dai Y, Townsend J. Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. Fungal Biology 2016, 25-46. DOI: 10.1007/978-3-319-29137-6_3.ChaptersFungal systematicsMolecular phylogenyEnvironmental DNA surveysHigh-throughput sequencingSequence-based classificationFungal treeFungal evolutionPhylogenetic informativenessFungal genomesIntegrative taxonomyDNA surveysFungal researchEvolutionary biologyPhylogenetic inferenceComparative biologyTaxonomic ranksEcological charactersFungal classificationInformative experimental designGenetic markersMycological researchPhylogenySanger sequencingSystematicsBiology
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 ResearchInferring 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
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
2010
Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny
Ohenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 2010, 102: 1089-1095. PMID: 20943508, DOI: 10.3852/09-317.Peer-Reviewed Original Research