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
2011
PhyDesign: an online application for profiling phylogenetic informativeness
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessPhylogenetic studiesPhylogenetic informativeness analysesBroad taxonomic samplingMolecular phylogenetic studiesTree of lifeOrthologous genesPhylogenetic samplingTaxonomic samplingPhylogenetic questionsPhylogenetic purposesEfficiency of sequencingSequence alignmentMarker selectionUltrametric treeDiverse suiteUtility of locusLociTreesUser-friendly toolGenomeGenesSequencingSpeciesDiversity