2017
Birth/birth-death processes and their computable transition probabilities with biological applications
Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. Journal Of Mathematical Biology 2017, 76: 911-944. PMID: 28741177, PMCID: PMC5783825, DOI: 10.1007/s00285-017-1160-3.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBayes TheoremCommunicable DiseasesComputational BiologyComputer SimulationEnglandEpidemicsHistory, 17th CenturyHost-Parasite InteractionsHumansLikelihood FunctionsMarkov ChainsMathematical ConceptsModels, BiologicalMonte Carlo MethodPlagueProbabilityStochastic ProcessesConceptsBirth-death processTransition probabilitiesFinite-time transition probabilitiesSIR modelMonte Carlo approximationJoint posterior distributionLikelihood-based inferenceApproximate Bayesian computationStatistical inferenceMatrix exponentiationPosterior distributionProcess approximationBivariate extensionBayesian computationFraction representationLaplace transformCorrelation structureUnivariate populationsRemoved (SIR) modelSmall systemsBivariate processEfficient algorithmApproximationDirect inferenceFast method
2014
On the distribution of interspecies correlation for Markov models of character evolution on Yule trees
Mulder WH, Crawford FW. On the distribution of interspecies correlation for Markov models of character evolution on Yule trees. Journal Of Theoretical Biology 2014, 364: 275-283. PMID: 25240905, PMCID: PMC4256168, DOI: 10.1016/j.jtbi.2014.09.016.Peer-Reviewed Original ResearchMeSH KeywordsGenetic SpeciationMarkov ChainsModels, GeneticMutationPhenotypePhylogenyPoisson DistributionProbabilitySpecies SpecificityStochastic ProcessesConceptsPhylogenetic treeYule treeProbability distributionPhylogenetic information contentContinuous-time modelPhylogenetic inference methodsOrnstein-Uhlenbeck modelCharacter evolutionPhylogenetic studiesNumber of mutationsTrait patternsRelated organismsStochastic modelNew speciesSimple continuous-time modelBrownian motionYule processEvolutionary processesPhenotypic changesMutation modelInference methodsSite patternsOptimal designSpeciationMutations