Featured Publications
Automated time-lapse data segmentation reveals in vivo cell state dynamics
Genuth M, Kojima Y, Jülich D, Kiryu H, Holley S. Automated time-lapse data segmentation reveals in vivo cell state dynamics. Science Advances 2023, 9: eadf1814. PMID: 37267354, PMCID: PMC10413672, DOI: 10.1126/sciadv.adf1814.Peer-Reviewed Original ResearchConceptsCell statesSingle-cell RNA sequencing dataCell state dynamicsCell behaviorEmbryonic development proceedsCell state transitionsRNA sequencing dataCollective cell behaviorIndividual cell behaviorsZebrafish tailbudLeft-right asymmetryCell tracking dataCollective cell motionGene expressionSequencing dataMolecular processesIndividual embryosDevelopment proceedsEmbryosCell motionParallel identificationBilateral symmetryReproducible patternTailbudState transitions
2005
beamter/deltaC and the role of Notch ligands in the zebrafish somite segmentation, hindbrain neurogenesis and hypochord differentiation
Jülich D, Lim C, Round J, Nicolaije C, Schroeder J, Davies A, Geisler R, Lewis J, Jiang Y, Holley S, Consortium T. beamter/deltaC and the role of Notch ligands in the zebrafish somite segmentation, hindbrain neurogenesis and hypochord differentiation. Developmental Biology 2005, 286: 391-404. PMID: 16125692, DOI: 10.1016/j.ydbio.2005.06.040.Peer-Reviewed Original ResearchConceptsPresomitic mesodermSomite segmentationZebrafish genetic screenEGF repeatsGenetic screenOscillating expressionOscillating genesSegmentation clockDouble mutantDSL domainSubcellular localizationAntimorphic effectsStrong defectsGene expressionNotch pathwayNotch ligandsNew allelesIndividual cellsDeltaCTriple fluorescentCoordinated oscillationsGenesAllelesExpressionLigand functions
2000
Control of her1 expression during zebrafish somitogenesis by a Delta-dependent oscillator and an independent wave-front activity
Holley S, Geisler R, Nüsslein-Volhard C. Control of her1 expression during zebrafish somitogenesis by a Delta-dependent oscillator and an independent wave-front activity. Genes & Development 2000, 14: 1678-1690. PMID: 10887161, PMCID: PMC316735, DOI: 10.1101/gad.14.13.1678.Peer-Reviewed Original ResearchConceptsAnterior presomitic mesodermPresomitic mesodermGene expressionNotch pathwayHER1 expressionZebrafish genesZebrafish somitogenesisEmbryos mutantSomite morphogenesisMolecular clockExpression patternsExpression de novoExpression oscillatesNotch ligandsPathway upstreamSomitogenesisBorder formationConsecutive somitesDe novoSomitesExpressionWave-front modelPathwayClockHER1