2025
spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data
Zhao H, Liu T, Huang T, Ding T, Wu H, Humphrey P, Perincheri S, Schalper K, Ying R, Xu H, Zou J, Mahmood F. spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data. 2025 DOI: 10.21203/rs.3.rs-6941589/v1.Peer-Reviewed Original ResearchInformation retrieval capabilitiesMedical report generationMulti-modal alignmentSingle-modal dataDownstream tasksLanguage modelModel architectureComputer systemsAI systemsSpatial domain identificationData modalitiesHistopathological imagesReport generationEvaluation taskMultimodal representationsTaskMulti-omics dataFoundation modelMulti-omics technologiesDataSpatial biologyMulti-OmicsTissue contextDomain identificationInformation
2023
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo
May D, Yun S, Gonzalez D, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez L, Cockburn K, Greco V. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. ELife 2023, 12: e83444. PMID: 36880644, PMCID: PMC10027315, DOI: 10.7554/elife.83444.Peer-Reviewed Original ResearchConceptsStem cell differentiationCell differentiationStem cell compartmentCompaction changesChromatin compaction statesDynamic transcriptional statesCell compartmentChromatin architectureCell cycle statusChromatin rearrangementNascent RNATranscriptional burstingTranscriptional statesLive imagingTissue contextGene expressionDifferentiating cellsGlobal remodelingIndividual cellsCycle statusStem cellsDifferentiation statusDifferentiationCellsMorphological changes
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