2022
Benchmarking automated cell type annotation tools for single-cell ATAC-seq data
Wang Y, Sun X, Zhao H. Benchmarking automated cell type annotation tools for single-cell ATAC-seq data. Frontiers In Genetics 2022, 13: 1063233. PMID: 36583014, PMCID: PMC9792779, DOI: 10.3389/fgene.2022.1063233.Peer-Reviewed Original ResearchCell type annotationScATAC-seq dataScRNA-seq dataScATAC-seqCell typesSingle-cell ATAC-seq dataAvailable single-cell datasetsRegulatory genomic regionsScRNA-seq data setsSingle-cell datasetsATAC-seq dataNovel cell typesSimilar cell typesSeurat v3Genomic regionsSequencing depthComplex tissuesDeep annotationAnnotationCellular compositionHuman tissuesType annotationsAnnotation toolAnnotation methodLabel transfer
2020
Evolution of Embryo Implantation Was Enabled by the Origin of Decidual Stromal Cells in Eutherian Mammals
Chavan AR, Griffith OW, Stadtmauer D, Maziarz J, Pavlicev M, Fishman R, Koren L, Romero R, Wagner GP. Evolution of Embryo Implantation Was Enabled by the Origin of Decidual Stromal Cells in Eutherian Mammals. Molecular Biology And Evolution 2020, 38: 1060-1074. PMID: 33185661, PMCID: PMC7947829, DOI: 10.1093/molbev/msaa274.Peer-Reviewed Original ResearchConceptsEutherian mammalsEutherian lineagesDecidual stromal cellsNovel cell typesStromal cellsInflammatory responseStem lineageEutherian pregnancyCommon ancestorEvolutionary mechanismsExtended gestationMost marsupialsEmbryo attachmentEmbryo implantationMarsupialsLineagesCell typesMammalsMechanistic understandingEutheriansHelper T cellsFetal-maternal interfaceMammalian pregnancyMaternal tissuesNeutrophil recruitment
2018
The mammalian decidual cell evolved from a cellular stress response
Erkenbrack EM, Maziarz JD, Griffith OW, Liang C, Chavan AR, Nnamani MC, Wagner GP. The mammalian decidual cell evolved from a cellular stress response. PLOS Biology 2018, 16: e2005594. PMID: 30142145, PMCID: PMC6108454, DOI: 10.1371/journal.pbio.2005594.Peer-Reviewed Original ResearchConceptsCellular stress responseNovel cell typesStress responseEndometrial stromal fibroblastsCell typesCell type diversityDecidual stromal cellsCore regulatory genesOxidative stress responseDecidual cell typesEvolutionary noveltyPrecursor cell typesEffector genesRegulatory genesEutherian mammalsTranscription factorsOpossum Monodelphis domesticaOrganismal structureType diversityMolecular mechanismsAnimal speciesMonodelphis domesticaGenesStromal cellsSpecies
2017
Invited Talk: Developing Deep Multi-Source Intelligent Learning that Facilitates the Advancement of Single Cell Genomics Research
Yang W, Weissman S, Guan R, Zhang J, Canaan A, Yang M. Invited Talk: Developing Deep Multi-Source Intelligent Learning that Facilitates the Advancement of Single Cell Genomics Research. 2017, 750-753. DOI: 10.1109/bibm.2017.8217749.Peer-Reviewed Original Research
2016
Cellular Innate Immunity: An Old Game with New Players
Gasteiger G, D'Osualdo A, Schubert DA, Weber A, Bruscia EM, Hartl D. Cellular Innate Immunity: An Old Game with New Players. Journal Of Innate Immunity 2016, 9: 111-125. PMID: 28006777, PMCID: PMC6738785, DOI: 10.1159/000453397.Peer-Reviewed Original ResearchConceptsInnate immunityMyeloid-derived suppressor cellsInnate lymphoid cellsInnate immune cellsAdaptive immune responsesNovel therapeutic opportunitiesCell typesSuppressor cellsImmune cellsImmune responseLymphoid cellsTherapeutic opportunitiesInfectious diseasesCurrent conceptsMolecular pathwaysImmunityCellsNovel cell typesInflammasomeDisease
2015
The statistical geometry of transcriptome divergence in cell-type evolution and cancer
Liang C, Forrest A, Wagner G. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature Communications 2015, 6: 6066. PMID: 25585899, DOI: 10.1038/ncomms7066.Peer-Reviewed Original ResearchConceptsCell typesCell type modelCell type evolutionAncestral cell typeSister cell typesNovel cell typesGene expression profilesTranscriptome divergenceOrganismal complexityTranscriptomic dataExpression profilesCancer cell linesTranscriptomeCancer cellsCell linesNormal cellsKey predictionsStatistical geometryFANTOM5Statistical modelCellsEncodesTree structureLittle understandingDivergence
1994
Circulating Fibrocytes Define a New Leukocyte Subpopulation That Mediates Tissue Repair
Bucala R, Spiegel L, Chesney J, Hogan M, Cerami A. Circulating Fibrocytes Define a New Leukocyte Subpopulation That Mediates Tissue Repair. Molecular Medicine 1994, 1: 71-81. PMID: 8790603, PMCID: PMC2229929, DOI: 10.1007/bf03403533.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBone MarrowBone Marrow CellsCD4 AntigensCell AdhesionCells, CulturedCentrifugationChimeraCollagenConnective TissueCytoskeletonDNA-Binding ProteinsDose-Response Relationship, RadiationFemaleFibroblastsFlow CytometryFluorescent Antibody TechniqueHumansImmunohistochemistryLeukocytesMaleMiceMice, Inbred BALB CMicroscopy, ElectronMolecular Sequence DataNuclear ProteinsPhenotypeSex-Determining Region Y ProteinTime FactorsTranscription FactorsTransplantation, HeterologousVimentinWound HealingConceptsTissue injuryLeukocyte subpopulationsScar formationLong-term remodelingFibroblast-like propertiesNormal wound repairConnective tissue scarConnective tissue elementsCell typesFibrotic responseTissue scarWound chambersPathological fibrotic responsesHost responseInjuryConnective tissueFibrocytesWound repairFibroblast propertiesTissue repairTissue elementsDistinctive phenotypeSubpopulationsTissueNovel cell types
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