Featured Publications
Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma
Fisk JN, Mahal AR, Dornburg A, Gaffney SG, Aneja S, Contessa JN, Rimm D, Yu JB, Townsend JP. Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma. Cancer Letters 2021, 526: 346-351. PMID: 34780851, PMCID: PMC8702484, DOI: 10.1016/j.canlet.2021.11.011.Peer-Reviewed Original ResearchConceptsMutational processesSingle ancestral lineageAncestral lineageProgression of cancerMetastatic lineagesPhylogenetic analysisGenetic resistanceEvolutionary processesExogenous mutational processesCancer evolutionConsolidative therapyMutational signature analysisEGFR-positive non-small cell lung cancerNon-small cell lung cancerKey eventsLineagesCell populationsTherapeutic resistanceLocal consolidative therapyClinical time courseCell lung cancerDisease etiologyTherapeutic decision makingCisplatin therapyLung cancer
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
2021
The somatic molecular evolution of cancer: Mutation, selection, and epistasis
Dasari K, Somarelli JA, Kumar S, Townsend JP. The somatic molecular evolution of cancer: Mutation, selection, and epistasis. Progress In Biophysics And Molecular Biology 2021, 165: 56-65. PMID: 34364910, PMCID: PMC8819680, DOI: 10.1016/j.pbiomolbio.2021.08.003.Peer-Reviewed Original ResearchConceptsCancer evolutionEpistatic interactionsNeutral mutation rateCancer progressionEvolution of neoplasmsSingle nucleotide variantsMolecular evolutionRate of fixationGenetic interactionsEvolutionary biologyPhylogenetic analysisCopy number aberrationsPhylogenetic relationsNeutral mutationsGenomic dataSelective pressureSynonymous mutationsMutation rateChromosomal instabilityPhenotypic changesLoss of heterozygosityFitness landscapeClonal deconvolutionTumor microenvironmentEnvironment interaction
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
2018
Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira
Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 45. PMID: 29600195, PMCID: PMC5863495, DOI: 10.3389/fcimb.2018.00045.Peer-Reviewed Original ResearchConceptsResponse regulatorTwo-component system proteinsDNA-binding response regulatorGlobal transcriptional regulationHybrid histidine kinaseGlobal gene regulationNovel signal pathwayComprehensive genomic analysisPhosphotransfer assaysTCS genesHistidine kinaseGene duplicationTranscriptional regulationGene regulationCorresponding genesPhylogenetic analysisGenomic analysisMolecular basisMutant strainSystem proteinsSignaling systemInfection processGenesBranched pathwayVirulence
2017
Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
Dornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances In Genetics 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.ChaptersConceptsTree of lifeFungal evolutionary biologyGenomic-scale dataHundreds of lociGenome-scale analysisFungal phylogenomicsFungal treeSpecies delimitationPhenotypic diversificationFirst genomeEvolutionary biologyPhylogenetic treePhylogenetic inferencePhylogenetic analysisEntire genomeTree inferenceReview of considerationsEvolutionary problemsPhylogenomicsGenomeTreesLociCentral roleExperimental designBiodiversity
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 interventionsEarly and multiple origins of metastatic lineages within primary tumors
Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2140-2145. PMID: 26858460, PMCID: PMC4776530, DOI: 10.1073/pnas.1525677113.Peer-Reviewed Original ResearchConceptsMetastatic lineagesGenetic changesEarly genetic divergenceMolecular evolutionary modelsSingle genetic changeDivergent lineagesTumor phylogeneticsDivergence timesAncestral stateGenetic divergenceCancer lineagesPhylogenetic analysisEvolutionary processesLineagesCancer evolutionMultiple originsDriver genesCancer biologyCancer progressionSomatic mutationsTumor developmentEvolutionary modelsDriver mutationsChronogramMutations
2013
Phylogenetic and phylogenomic overview of the Polyporales
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013, 105: 1350-1373. PMID: 23935031, DOI: 10.3852/13-003.Peer-Reviewed Original ResearchConceptsSingle-copy genePhylogenetic informativeness analysesResidual polyporoid cladeBayesian phylogenetic analysisPolyporales speciesMajor lineagesPhylogenomic datasetsAvailable genomesCorresponding cladesPhlebioid cladePolyporoid cladeNew genomesGenome dataPhylogenetic analysisSuprageneric taxonomyCertain taxaPhylogenetic systematicsGenomic datasetsIdentical topologiesPolyporalesGenomeCladeSupport valuesGenesLineages
2011
Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data. PLOS ONE 2011, 6: e19039. PMID: 21533038, PMCID: PMC3080880, DOI: 10.1371/journal.pone.0019039.Peer-Reviewed Original ResearchConceptsFungal lineagesSoil fungal diversityNovel fungal lineagesTree estimationITS dataNuclear ribosomal ITS regionEnvironmental samplesRibosomal ITS regionFungal diversityPublic sequence databasesComplex communitiesDivergent taxaBasal classPhylogenetic testsNovel lineageITS phylogenyPhylogenetic analysisEctomycorrhizal isolatesITS sequencesITS regionEnvironmental samplingSequence databasesSATéFocal questionLineages
2005
Horizontal gene transfer, genome innovation and evolution
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 2005, 3: 679-687. PMID: 16138096, DOI: 10.1038/nrmicro1204.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHorizontal gene transferHGT eventsImportance of HGTLife historyConcatenation of genesGene transferTypes of genesGroups of organismsGene historiesReticulation eventsPhylogenetic signalTaxonomic samplingMicrobial evolutionSelective sweepsGenome innovationPhylogenetic reconstructionEvolutionary biologyProkaryotic genomesSuch genesMicrobial communitiesPhylogenetic analysisGene swappingHorizontal transferTaxonomic classificationGenes