2023
Normalizing need not be the norm: count-based math for analyzing single-cell data
Church S, Mah J, Wagner G, Dunn C. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory In Biosciences 2023, 143: 45-62. PMID: 37947999, DOI: 10.1007/s12064-023-00408-x.Peer-Reviewed Original Research
2021
Devo-Evo of Cell Types
Wagner G. Devo-Evo of Cell Types. 2021, 511-528. DOI: 10.1007/978-3-319-32979-6_153.Peer-Reviewed Original ResearchEvolutionary developmental biologyCell typesDevelopmental biologyCore gene regulatory networkAncestral cell typeCell type identityTranscription factor proteinsGene regulatory networksGene treesGene duplicationEvolutionary descentRegulatory complexRegulatory networksPopulation of cellsMolecular mechanismsFactor proteinOrganisms increasesEvolutionary perspectiveLineagesBiologyType identityMajor current challengeSpecific setTreesGenes
2020
Character identity mechanisms: a conceptual model for comparative-mechanistic biology
DiFrisco J, Love A, Wagner G. Character identity mechanisms: a conceptual model for comparative-mechanistic biology. Biology & Philosophy 2020, 35: 44. DOI: 10.1007/s10539-020-09762-2.Peer-Reviewed Original Research
2019
Devo-Evo of Cell Types
Wagner G. Devo-Evo of Cell Types. 2019, 1-18. DOI: 10.1007/978-3-319-33038-9_153-1.Peer-Reviewed Original ResearchEvolutionary developmental biologyCell typesDevelopmental biologyCore gene regulatory networkAncestral cell typeCell type identityTranscription factor proteinsGene regulatory networksGene treesGene duplicationEvolutionary descentRegulatory complexRegulatory networksPopulation of cellsMolecular mechanismsFactor proteinOrganisms increasesEvolutionary perspectiveLineagesBiologyType identityMajor current challengeSpecific setTreesGenes
2015
Evolutionary innovations and novelties: Let us get down to business!
Wagner G. Evolutionary innovations and novelties: Let us get down to business! Zoologischer Anzeiger 2015, 256: 75-81. DOI: 10.1016/j.jcz.2015.04.006.Peer-Reviewed Original ResearchCore gene regulatory networkGene regulatory networksRegulatory networksNovel body partsEvolutionary innovationEvolutionary developmental biologyCore regulatory networkBody part identityEvolutionary noveltyEvolutionary biologistsEvolutionary biologyDevelopmental biologyEvolutionary changeBiological processesCell typesImportant unanswered questionsBiologyCritical insightsGenomicsRecent advancesMechanistic aspectsGenesBiologistsUnanswered questionsBody partsHomology in the Age of Developmental Genomics
Wagner G. Homology in the Age of Developmental Genomics. 2015, 25-43. DOI: 10.1007/978-3-7091-1862-7_2.Peer-Reviewed Original ResearchModel organismsEvolutionary biologyHomology conceptRecent common ancestorDevelopmental genomicsPhylogenetic relationshipsCommon ancestorDarwinian traditionHomologySame organOrganismsSpeciesComparative anatomyDifferent animalsBiologistsBiologyFundamental roleRichard OwenImportant roleGenomicsAncestorGenesOrgansHumansRole
2014
Reinventing the Organism: Evolvability and Homology in Post-Dahlem Evolutionary Biology
Wagner G. Reinventing the Organism: Evolvability and Homology in Post-Dahlem Evolutionary Biology. Boston Studies In The Philosophy And History Of Science 2014, 307: 327-342. DOI: 10.1007/978-94-017-9412-1_15.Peer-Reviewed Original ResearchEvolutionary biologyDahlem ConferenceGenotype-phenotype mapStructure of organismsLimited pleiotropyNatural selectionEvolutionary causationPhenotype evolutionOrganism conceptRandom mutationsHomologyOrganismsEvolvabilityBiologyDevelopmental structuresMutationsDevelopmental organizationPleiotropySeedsFitnessSelectionAdaptation
2009
Measuring Morphological Integration Using Eigenvalue Variance
Pavlicev M, Cheverud J, Wagner G. Measuring Morphological Integration Using Eigenvalue Variance. Evolutionary Biology 2009, 36: 157-170. DOI: 10.1007/s11692-008-9042-7.Peer-Reviewed Original Research
2008
The gene regulatory logic of transcription factor evolution
Wagner GP, Lynch VJ. The gene regulatory logic of transcription factor evolution. Trends In Ecology & Evolution 2008, 23: 377-385. PMID: 18501470, DOI: 10.1016/j.tree.2008.03.006.Peer-Reviewed Original ResearchConceptsTranscription factor proteinsDevelopmental evolutionGene regulatory logicMinimal pleiotropic effectsTranscription factor evolutionFactor proteinTranscription factor functionEvolution of developmentTranscription factor genesCis-regulatory elementsFunction of proteinsAdaptive evolutionDevelopmental biologyRegulatory logicNovel functionFactor genesFactor functionProtein changesPleiotropic effectsProteinRecent studiesEvolutionGenesRelative contributionBiologyPleiotropic scaling of gene effects and the ‘cost of complexity’
Wagner GP, Kenney-Hunt JP, Pavlicev M, Peck JR, Waxman D, Cheverud JM. Pleiotropic scaling of gene effects and the ‘cost of complexity’. Nature 2008, 452: 470-472. PMID: 18368117, DOI: 10.1038/nature06756.Peer-Reviewed Original ResearchConceptsQuantitative trait lociEffects of pleiotropyOrganismal complexityGenetic sequence dataHigher organismsEvolutionary biologyTrait lociMouse genomeSequence dataBiology questionsSkeletal traitsGene effectsMost mutationsCost of complexityGenetic mutationsTraitsMutationsMultiple effectsGenomeSkeletal characteristicsPleiotropyLociPleiotropicOrganismsBiology
2007
The road to modularity
Wagner GP, Pavlicev M, Cheverud JM. The road to modularity. Nature Reviews Genetics 2007, 8: 921-931. PMID: 18007649, DOI: 10.1038/nrg2267.Peer-Reviewed Original ResearchConceptsProtein-protein interaction networkMolecular systems biologyPatterns of evolutionGene duplicationGene regulationEvolutionary biologyNeutral mutationsBiological organizationQuantitative traitsInteraction networksSystems biologyStructure of macromoleculesEnvironmental conditionsBiologyDuplicationTraitsMutationsRegulationSelectionModularityMacromolecules
2005
Natural Selection and the Origin of Modules
Wagner G, Mezey J, Calabretta R. Natural Selection and the Origin of Modules. 2005, 33-50. DOI: 10.7551/mitpress/4734.003.0009.Peer-Reviewed Original ResearchCognitive scienceArtificial lifeEvolutionary biologyHerbert A. SimonScientific revolutionDifferent disciplinary contextsVariety of disciplinesLatest theoriesA. SimonDisciplinary contextsScienceScientific discussionNatural selectionDominant themesDisciplinesSpecialized conceptsArtLifeMathematicsResearch agendaEconomicsPhilosophyConceptComputer scienceBiology
2001
Modeling Genetic Architecture: A Multilinear Theory of Gene Interaction
Hansen T, Wagner G. Modeling Genetic Architecture: A Multilinear Theory of Gene Interaction. Theoretical Population Biology 2001, 59: 61-86. PMID: 11243929, DOI: 10.1006/tpbi.2000.1508.Peer-Reviewed Original ResearchConceptsGenotype-phenotype mapGene interactionsQuantitative genetic variationEffects of epistasisGenetic canalizationGenetic experimentsGenetic variationGene substitutionGenetic backgroundEpistasisTractable modelComplex functionsCentral importanceLociBiologyCanalizationPhenotypeGenotypesInteractionSum of linear
2000
Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1
Wagner G, Chiu C, Laubichler M. Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1. Integrative And Comparative Biology 2000, 40: 819-831. DOI: 10.1668/0003-1569(2000)040[0819:deaams]2.0.co;2.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsDevelopmental evolutionEvolutionary innovationDevelopmental mechanismsFunction of genesEvolutionary geneticsGenetic architectureEvolutionary originEvolutionary biologyAssessment of homologyDevelopmental dynamicsSpecies differencesBiologyGenetic factorsHomologyGenesMechanismGeneticsSpeciesEvolutionRoleElucidationOriginMechanistic scienceCharacterDevelopmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1
Wagner G, Chiu C, Laubichler M. Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1. Integrative And Comparative Biology 2000, 40: 819-831. DOI: 10.1093/icb/40.5.819.Peer-Reviewed Original ResearchDevelopmental evolutionEvolutionary innovationDevelopmental mechanismsFunction of genesEvolutionary geneticsGenetic architectureEvolutionary originEvolutionary biologyAssessment of homologyDevelopmental dynamicsSpecies differencesBiologyGenetic factorsHomologyGenesMechanismGeneticsSpeciesEvolutionRoleElucidationOriginMechanistic scienceCharacterWhat is the promise of developmental evolution? part I: Why is developmental biology necessary to explain evolutionary innovations?
Wagner G. What is the promise of developmental evolution? part I: Why is developmental biology necessary to explain evolutionary innovations? Journal Of Experimental Zoology 2000, 288: 95-98. PMID: 10931493, DOI: 10.1002/1097-010x(20000815)288:2<95::aid-jez1>3.0.co;2-5.Commentaries, Editorials and LettersCharacter identification in evolutionary biology: The role of the organism
Wagner G, Laubichler M. Character identification in evolutionary biology: The role of the organism. Theory In Biosciences 2000, 119: 20-40. DOI: 10.1007/s12064-000-0003-7.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsBiological processesBiological charactersImportant biological charactersHigher-level biological processesAdaptive evolutionEvolutionary biologyMathematical theoryRelevant charactersMathematical modelCharacter decompositionOrganismsBiologyOrganismic perspectiveBiological modelsPhysical sciencesBiological theoryIdentificationTheoryTraitsInheritanceModelAnalytical methodCellsCharacterAppropriate instances
1993
Beyond Digital Naturalism
Fontana W, Wagner G, Buss L. Beyond Digital Naturalism. Artificial Life 1993, 1: 211-227. DOI: 10.1162/artl.1993.1.1_2.211.Commentaries, Editorials and LettersHow can a character be developmentally constrained despite variation in developmental pathways?
Wagner G, Misof B. How can a character be developmentally constrained despite variation in developmental pathways? Journal Of Evolutionary Biology 1993, 6: 449-455. DOI: 10.1046/j.1420-9101.1993.6030449.x.Commentaries, Editorials and LettersDevelopmental constraintsDevelopmental biologyDevelopmental pathwaysEvolutionary developmental biologyComparative developmental biologyDevelopmental variationBody planAdaptive pressuresConservative patternAdult variationFundamental riddleHomologyBiologyBiological basisConservationPathwayAnatomical featuresMorphological patternsHomologuesEarly perturbationsVariationPatternsEarly stagesAdult patternFunction