2017
Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues
Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP. Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology 2017, 27: 216-232. PMID: 29134709, PMCID: PMC5797489, DOI: 10.1111/mec.14425.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceConserved SequenceEcological and Environmental PhenomenaFungal ProteinsGene Expression Regulation, FungalGene Knockout TechniquesGene Regulatory NetworksGenes, FungalLightModels, BiologicalMultienzyme ComplexesNADH, NADPH OxidoreductasesNeurospora crassaOpsinsOxidation-ReductionOxidative StressPhenotypePhylogenyProtein Structure, SecondaryReproductionUp-RegulationConceptsNOP-1Opsin-like proteinFungal ecologyPlant-associated fungiRapid environmental changeOxidative stress responseKey amino acidsFungal genomesComparative transcriptomicsSexual reproductionOrganismal functionNeurospora crassaEnvironmental cuesGenetic basisSensory rhodopsinStress responseNAD/NADPTransmembrane movementRetinal binding siteGenesAmino acidsFungiEnvironmental changesSexual developmentOpsin
2009
Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
Zhang Z, Townsend JP. Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences. PLOS Computational Biology 2009, 5: e1000421. PMID: 19557160, PMCID: PMC2695770, DOI: 10.1371/journal.pcbi.1000421.Peer-Reviewed Original ResearchConceptsInformation criterionModel averagingBayesian information criterionMaximum likelihood methodModel likelihoodModel uncertaintyModel selectionDescription of clustersLevel of clusteringPrecision of estimationAkaike information criterionParameter rangeCluster countsLikelihood methodComputational biologyCluster sizeGood accuracyConquer strategyAveragingClusteringModelHierarchical clusteringClustersStatisticsEstimation