2024
Effect of loops on the mean-square displacement of Rouse-model chromatin
Yuan T, Yan H, Bailey M, Williams J, Surovtsev I, King M, Mochrie S. Effect of loops on the mean-square displacement of Rouse-model chromatin. Physical Review E 2024, 109: 044502. PMID: 38755928, DOI: 10.1103/physreve.109.044502.Peer-Reviewed Original ResearchConceptsStretching exponentConsistent with recent experimentsTopologically associating domainsMean square displacementRecent experimentsLoop extrusionExponent valuesTAD formationTree of lifeDynamics of chromatinExponentEffects of loopChromatin lociChromatin dynamicsRouse modelChromatin organizationChromatin mobilityGene locusContact mapsDynamicsChromatinLoopPolymer dynamicsLociPolymer simulations
2016
Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction
Zhao Y, Schreiner SM, Koo PK, Colombi P, King MC, Mochrie SG. Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction. Biophysical Journal 2016, 111: 19-24. PMID: 27410730, PMCID: PMC4945324, DOI: 10.1016/j.bpj.2016.05.036.Peer-Reviewed Original ResearchConceptsChromatin biologyLac operator arraysMembrane marker proteinsNuclear positionBroad practical utilityNuclear volumeNuclear peripheryOrganelle shapeChromatin markersTranscriptional regulationSubnuclear positionLacI-GFPDNA repairIndividual lociNuclear compartmentPopulation of cellsNuclear envelopeLocus positionParticular locusMarker proteinsImage analysis pipelineLociCell populationsAnalysis pipelineBiological accuracy