2024
Integrative spatial protein profiling with multi-omics
Fan R. Integrative spatial protein profiling with multi-omics. Nature Methods 2024, 21: 2223-2225. PMID: 39643677, DOI: 10.1038/s41592-024-02533-x.Peer-Reviewed Original ResearchReconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids
Bolondi A, Law B, Kretzmer H, Gassaloglu S, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet J, Meissner A, Smith Z, Chan M. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 2024, 59: 1489-1505.e14. PMID: 38579718, PMCID: PMC11187653, DOI: 10.1016/j.devcel.2024.03.024.Peer-Reviewed Original ResearchNeuro-mesodermal progenitorsFate outcomesStem cell-based modelsEmbryonic trunkEnvironmental cuesMorphological phenotypesDownstream lineagesMolecular recordCell-based modelsCell typesTranscriptional signatureComplex tissuesAxial progenitorsLineagesDevelopmental timeNeural lineagesTransient progenitor populationProgenitor populationsDevelopmental windowPhylogenyscENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Duan Z, Xu S, Srinivasan S, Hwang A, Lee C, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings In Bioinformatics 2024, 25: bbae096. PMID: 38493342, PMCID: PMC10944576, DOI: 10.1093/bib/bbae096.Peer-Reviewed Original ResearchConceptsA/B compartmentsEpigenetic dataChromatin interaction frequenciesCell type-specific mannerChromatin conformational changesGenome binsGenomic regionsChromatin conformationEukaryotic DNAChromatin compartmentsDynamic compartmentalizationRepressed stateGenetic blueprintTranscriptional programsTranscriptional changesChromatinConformational changesComplex tissuesInteraction frequencyCompartmentGenomeChromosomeStructural heterogeneityDNAA/B
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 transferExtracellular Vesicles Mediate the Intercellular Exchange of Nanoparticles
Wu X, Tang T, Wei Y, Cummins K, Wood D, Pang H. Extracellular Vesicles Mediate the Intercellular Exchange of Nanoparticles. Advanced Science 2022, 9: 2102441. PMID: 35243822, PMCID: PMC8895114, DOI: 10.1002/advs.202102441.Peer-Reviewed Original ResearchConceptsIntercellular exchangeExtracellular vesiclesComplex tissuesImportance of EVsCell-cell contactTranscellular transport routeDirect cell-cell contactSubcellular transportNP endocytosisExocytosisAccumulative evidenceVesiclesSame receptorCrucial rolePotential mechanismsCellsTransport routesEndocytosisTissueSignificant fractionTransportVitroAssaysVivoReceptors
2020
Resolving Cell Cycle Speed in One Snapshot with a Live-Cell Fluorescent Reporter
Eastman AE, Chen X, Hu X, Hartman AA, Morales A, Yang C, Lu J, Kueh HY, Guo S. Resolving Cell Cycle Speed in One Snapshot with a Live-Cell Fluorescent Reporter. Cell Reports 2020, 31: 107804. PMID: 32579930, PMCID: PMC7418154, DOI: 10.1016/j.celrep.2020.107804.Peer-Reviewed Original ResearchConceptsFluorescent reportersLive-cell fluorescent reporterCell cycle speedFluorescent timer proteinsCell proliferationCell cycle dynamicsRed fluorescent proteinFaster cycling cellsFate transitionsFusion reporterActive lociTimer proteinFluorescent proteinLength heterogeneityComplex tissuesHematopoietic cellsCycling cellsReporterFluorescence ratioCycle dynamicsProteinFunctional heterogeneityMouse strainsSolid tissuesCycle speed
2016
Neural organoids for disease phenotyping, drug screening and developmental biology studies
Hartley B, Brennand K. Neural organoids for disease phenotyping, drug screening and developmental biology studies. Neurochemistry International 2016, 106: 85-93. PMID: 27744003, PMCID: PMC5389930, DOI: 10.1016/j.neuint.2016.10.004.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHuman induced pluripotent stem cellsNeural organoidsCell-extracellular matrix interactionsCell typesDevelopmental biology studiesSpecific physiological functionsCell-cell interactionsInduced pluripotent stem cellsNervous system cell typesCentral nervous system cell typesPluripotent stem cellsCell replacement therapyBiology studiesCurrent biomedical researchDifferentiation protocolsPhysiological functionsComplex tissuesMatrix interactionsNovel technological platformStem cellsDisease mechanismsSpatial organizationUnknown disease mechanismsToxicity assaysHeterogeneous tissues
2009
Nanofibrous biologic laminates replicate the form and function of the annulus fibrosus
Nerurkar NL, Baker BM, Sen S, Wible EE, Elliott DM, Mauck RL. Nanofibrous biologic laminates replicate the form and function of the annulus fibrosus. Nature Materials 2009, 8: 986-992. PMID: 19855383, PMCID: PMC3415301, DOI: 10.1038/nmat2558.Peer-Reviewed Original ResearchConceptsMulti-scale structural hierarchyAnnulus fibrosus tissue engineeringTissue engineering applicationsLoad-bearing tissuesTensile responseEngineering applicationsTissue engineeringLaminatesBiomimetic materialsComplex mechanical functionsNative tissueStructural hierarchySuccessful engineeringEngineeringScaffoldsAnnulus fibrosusGreat interestShearingMechanical functionComplex tissuesDepositionMaterials
2006
LASER MICRODISSECTION OF PLANT TISSUE: What You See Is What You Get
Nelson T, Tausta SL, Gandotra N, Liu T. LASER MICRODISSECTION OF PLANT TISSUE: What You See Is What You Get. Annual Review Of Plant Biology 2006, 57: 181-201. PMID: 16669760, DOI: 10.1146/annurev.arplant.56.032604.144138.Peer-Reviewed Original ResearchConceptsLaser microdissectionCell typesComplex tissuesStable cell wallCell-specific DNAMost cell typesSpecific cell typesPlant cellsPlant tissuesDNA modificationsCell wallCell-specific propertiesTissue organizationMetabolite profilingSpecific cellsPlantsCellsMicrodissectionMetabolite studiesTissueRNAProteinDNAIdentificationProfiling
2005
A Digital Atlas to Characterize the Mouse Brain Transcriptome
Carson JP, Ju T, Lu HC, Thaller C, Xu M, Pallas SL, Crair MC, Warren J, Chiu W, Eichele G. A Digital Atlas to Characterize the Mouse Brain Transcriptome. PLOS Computational Biology 2005, 1: e41. PMID: 16184189, PMCID: PMC1215388, DOI: 10.1371/journal.pcbi.0010041.Peer-Reviewed Original ResearchConceptsDigital atlasUser queriesQuery patternsAnnotation methodData modalitiesMassive amountsTypes of dataExpression patternsMouse brain transcriptomeGene expression patternsComputational methodsCommon framePostnatal mouse brainBrain transcriptomeQueriesCandidate genesComplex tissuesCellular resolutionGenes
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