2013
Nonlinear intrinsic variables and state reconstruction in multiscale simulations
Dsilva CJ, Talmon R, Rabin N, Coifman RR, Kevrekidis IG. Nonlinear intrinsic variables and state reconstruction in multiscale simulations. The Journal Of Chemical Physics 2013, 139: 184109. PMID: 24320256, DOI: 10.1063/1.4828457.Peer-Reviewed Original ResearchHigh-dimensional simulation dataLow-dimensional descriptionSimulation dataEnzyme reaction networksSlow time scaleStochastic simulationMeasurement noisePartial observationsPhysical phenomenaMultiscale simulationsReaction networksIntrinsic variablesSimulation ensemblesAlanine dipeptideSimulationsState reconstructionEnsembleProcess variabilityTime scalesAtomistic simulationsVariablesNoiseApproachSimple features
2009
The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 2009, 58: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.Peer-Reviewed Original ResearchConceptsCharacter state reconstructionCommon ancestorAncestral character state reconstructionPhylogenetic informativeness analysesSexual reproductive structuresAscus dehiscenceMaximum likelihood phylogenyPhylogenetic informativenessEcological traitsFungal systematicsAncestral reconstructionNutritional modesRibosomal genesLargest phylumMorphological traitsRelated speciesReproductive structuresProtein geneAscomycota TreePezizomycotinaMultiple originsState reconstructionSporocarpsGene assessmentGenesMore is better: the uses of developmental genetic data to reconstruct perianth evolution
Hileman LC, Irish VF. More is better: the uses of developmental genetic data to reconstruct perianth evolution. American Journal Of Botany 2009, 96: 83-95. PMID: 21628177, DOI: 10.3732/ajb.0800066.Peer-Reviewed Original ResearchDevelopmental genetic dataGenetic dataPerianth evolutionState reconstructionCharacter state reconstructionAncestral state reconstructionAngiosperm cladesAngiosperm evolutionExtant speciesEvolutionary historyPhylogenetic reconstructionDifferentiated perianthMorphological dataCharacter statesExpression dataDistinct organsMaximum likelihood frameworkPerianthNew insightsFunctional dataMultiple linesLikelihood frameworkAngiospermsCladeSepals
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