2024
Reading the palimpsest of cell interactions: What questions may we ask of the data?
Pavlicev M, Wagner G. Reading the palimpsest of cell interactions: What questions may we ask of the data? IScience 2024, 27: 109670. PMID: 38665209, PMCID: PMC11043885, DOI: 10.1016/j.isci.2024.109670.Peer-Reviewed Original ResearchCompartmentalization of cellular processesStructure of interaction networksCell interactionsMulticellular organismsIntegrity of cellsCellular processesInteraction networkLevels of structural organizationBiological functionsBiological interpretationCell communicationInteraction dataStructural organizationWealth of dataCellsCoordination of functionsOrganizationHigher levels of structural organizationCompartmentalizationInteractionA common allele increases endometrial Wnt4 expression, with antagonistic implications for pregnancy, reproductive cancers, and endometriosis
Pavličev M, McDonough-Goldstein C, Zupan A, Muglia L, Hu Y, Kong F, Monangi N, Dagdas G, Zupančič N, Maziarz J, Sinner D, Zhang G, Wagner G, Muglia L. A common allele increases endometrial Wnt4 expression, with antagonistic implications for pregnancy, reproductive cancers, and endometriosis. Nature Communications 2024, 15: 1152. PMID: 38346980, PMCID: PMC10861470, DOI: 10.1038/s41467-024-45338-4.Peer-Reviewed Original ResearchConceptsFrequency of deleterious allelesAssociated with multiple phenotypesResistance to invasionWnt4 locusAlpha binding sitesPleiotropic mutationsDeleterious allelesPleiotropic SNPsMouse genomeMultiple phenotypesWnt4 transcriptionPopulation frequencyMolecular mechanismsPreovulatory estrogen peakRs3820282Estrogen-responsive tissuesWnt4 expressionCRISPR/Cas 9AllelesTranscriptionEndometriotic fociEndometrial stromaMutationsEpithelial proliferationEstrogen peak
2023
Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts
Dighe A, Maziarz J, Ibrahim-Hashim A, Gatenby R, Kshitiz, Levchenko A, Wagner G. Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts. IScience 2023, 27: 108593. PMID: 38174318, PMCID: PMC10762354, DOI: 10.1016/j.isci.2023.108593.Peer-Reviewed Original ResearchGene expression changesGene expression evolutionEndometrial stromal fibroblastsExpression evolutionExpression changesCell typesGene expressionSimilar gene expression changesSubstantial gene expression changesGene expression profilesSkin fibroblastsMultiple cell typesEvolutionary correlationPhylogenetic evidenceEvolutionary changeDermal skin fibroblastsMammalian speciesExpression profilesPlacental invasivenessComparative datasetCancer growthCultured skin fibroblastsStromal fibroblastsFibroblastsMouse strainsNormalizing 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 ResearchStress, harshness, and evolutionary history
Love A, Wagner G. Stress, harshness, and evolutionary history. Trends In Ecology & Evolution 2023, 38: 903-904. PMID: 37301667, DOI: 10.1016/j.tree.2023.05.013.Peer-Reviewed Original Research
2022
The hierarchical basis of serial homology and evolutionary novelty
DiFrisco J, Love A, Wagner G. The hierarchical basis of serial homology and evolutionary novelty. Journal Of Morphology 2022, 284: e21531. PMID: 36317664, DOI: 10.1002/jmor.21531.Peer-Reviewed Original ResearchConceptsSerial homologyWing serial homologsTree of lifeExtent of homologyParalogous genesEvolutionary noveltyPhylogenetic historyPhylogenetic conceptsGene sequencesSerial homologsEvolutionary precursorPhylogenetic interpretationMost biologistsHomologyCell typesBiological phenomenaGenetic contributionEpidermal appendagesWidespread overlapGenesNew charactersHomologLineagesAppendagesFecundityPhenotypic Plasticity & Evolution: Causes, Consequences, Controversies David W. Pfennig (ed). xxxi + 404 pp., index. Evolutionary Cell Biology. Boca Raton, FL: CRC Press, Taylor & Francis Group, 2021. $230 (hardback); Open Access (pdf).
Love A, Wagner G. Phenotypic Plasticity & Evolution: Causes, Consequences, Controversies David W. Pfennig (ed). xxxi + 404 pp., index. Evolutionary Cell Biology. Boca Raton, FL: CRC Press, Taylor & Francis Group, 2021. $230 (hardback); Open Access (pdf). Evolution & Development 2022, 24: 173-176. DOI: 10.1111/ede.12420.Peer-Reviewed Original ResearchOrgasm
Pavličev M, Wagner G. Orgasm. 2022, 4843-4850. DOI: 10.1007/978-3-319-55065-7_293.Peer-Reviewed Original ResearchBody Plan Identity: A Mechanistic Model
DiFrisco J, Wagner G. Body Plan Identity: A Mechanistic Model. Evolutionary Biology 2022, 49: 123-141. DOI: 10.1007/s11692-022-09567-z.Peer-Reviewed Original ResearchBody planBody plan evolutionMajor taxonomic groupsSegment polarity networkTransient embryonic structureAbstract Mechanistic modelsAnimal cladesPhylotypic stageMajor cladesPolarity networkTaxonomic groupsEvolutionary changeEvolutionary phenomenaDevelopmental complexityEmbryonic structuresDevelopmental mechanismsEnvironmental perturbationsMechanistic modelMechanistic architectureCladeArthropodsBiological causesGround planChordatesVertebrates
2021
Single-cell analysis of prostaglandin E2-induced human decidual cell in vitro differentiation: a minimal ancestral deciduogenic signal†
Stadtmauer DJ, Wagner G. Single-cell analysis of prostaglandin E2-induced human decidual cell in vitro differentiation: a minimal ancestral deciduogenic signal†. Biology Of Reproduction 2021, 106: 155-172. PMID: 34591094, PMCID: PMC8757638, DOI: 10.1093/biolre/ioab183.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell Line, TransformedCells, CulturedCyclic AMPCyclic AMP-Dependent Protein KinasesDeciduaDinoprostoneEndometriumFemaleFibroblastsGene ExpressionGenome-Wide Association StudyHumansMedroxyprogesterone AcetatePregnancyReceptors, Prostaglandin E, EP2 SubtypeSequence Analysis, RNASingle-Cell AnalysisConceptsPlacental mammalsCore gene regulatory networkCyclic AMP/protein kinase A (cAMP/PKA) pathwayProtein kinase A (PKA) pathwaySenescence-associated genesProgesterone-dependent activationGenome-wide studiesSingle-cell transcriptomicsGene regulatory networksProgesterone-dependent inductionMembrane-permeable cAMPKinase A PathwaySingle-cell analysisUse of PGE2Outgroup taxaCellular statesRegulatory networksPKA axisGene expressionDecidual genesPKA activationPGE2 receptor 2Progestin-dependent inductionA PathwayAdenylyl cyclase activationDevo-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 ResearchTranscriptomic responses to hypoxia in endometrial and decidual stromal cells
Rytkönen KT, Heinosalo T, Mahmoudian M, Ma X, Perheentupa A, Elo LL, Poutanen M, Wagner G. Transcriptomic responses to hypoxia in endometrial and decidual stromal cells. Reproduction 2020, 160: 39-51. PMID: 32272449, DOI: 10.1530/rep-19-0615.Peer-Reviewed Original ResearchConceptsDecidual stromal cellsEndometrial stromal fibroblastsEndometriotic stromal cellsStromal cellsInflammatory transcription factorsEpithelial-mesenchymal transitionExpression of JunDCEBP transcription factorsCell typesHealthy endometriumEndometriosis lesionsProgesterone receptorDecidualization processUterine endometriumStromal fibroblastsMesenchymal transitionProgesterone signalingEndometriumHypoxiaHypoxia pathwayTranscription factorsHuman reproductive successDistinct transcriptional statesExpression of genesJun/Fos
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
2018
The inflammatory origin of mammalian implantation
Wagner G. The inflammatory origin of mammalian implantation. Journal Of Reproductive Immunology 2018, 128: 48. DOI: 10.1016/j.jri.2018.06.022.Peer-Reviewed Original ResearchThe uterine decidual stromal cell: A stabilized stress response?
Wagner G, Erkenbrack E, Maziarz J, Chavan A. The uterine decidual stromal cell: A stabilized stress response? Journal Of Reproductive Immunology 2018, 128: 48. DOI: 10.1016/j.jri.2018.06.023.Peer-Reviewed Original ResearchOrgasm
Pavličev M, Wagner G. Orgasm. 2018, 1-7. DOI: 10.1007/978-3-319-47829-6_293-1.Peer-Reviewed Original ResearchOrgasm
Pavličev M, Wagner G. Orgasm. 2018, 232-237. DOI: 10.1016/b978-0-12-801238-3.64714-1.Peer-Reviewed Original ResearchComparative Placentation-Mammals
Wagner G. Comparative Placentation-Mammals. 2018, 455-461. DOI: 10.1016/b978-0-12-801238-3.64668-8.Peer-Reviewed Original Research
2016
Utero-placental cell interactions revealed by single cell transcriptomics
Pavlicev M, Jones H, Owens K, Chavan A, Wagner G, Muglia L. Utero-placental cell interactions revealed by single cell transcriptomics. Placenta 2016, 45: 64. DOI: 10.1016/j.placenta.2016.06.015.Peer-Reviewed Original Research