Miao Liu
Associate Research ScientistAbout
Research
Publications
2026
A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation
Cheng Y, Wang J, Zhang Y, Yadavalli A, Liu M, Jin S, Buddle G, Haberman A, Schatz D, Wang S. A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation. Science 2026, 393: eadw4243. PMID: 42490500, DOI: 10.1126/science.adw4243.Peer-Reviewed Original Research3D multi-omics tumour atlases: from technology to biology and clinical translation
Liu M, Villazon J, Forjaz A, Tian X, Fan R, Wang S, Shi L, Wirtz D, Kiemen A. 3D multi-omics tumour atlases: from technology to biology and clinical translation. Nature Reviews Cancer 2026, 1-28. PMID: 42298141, DOI: 10.1038/s41568-026-00940-0.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsThis study investigates 3D tumour atlases, showing how spatial multi-omics technologies uncover tumour evolution, aiding early cancer detection, risk stratification, and innovative treatment strategies.Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT
Baysoy A, Tian X, Renauer P, Zhang F, Bai Z, Shi H, Yang M, Zhang D, Liu M, Li H, Tao B, Enninful A, Lu Y, Gao F, Wang G, Zhang W, Tran T, Patterson N, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly J, Pruett-Miller S, Wang D, Xu M, Gerstein M, Chi H, Chen S, Fan R. Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT. Nature Biotechnology 2026, 1-14. PMID: 42277225, DOI: 10.1038/s41587-026-03127-y.Peer-Reviewed Original ResearchThis study introduces Perturb-DBiT, a method enabling spatially resolved CRISPR screens and transcriptomics in tissues, uncovering genetic and RNA-level mechanisms driving cancer and immune interactions.
2025
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S. Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution. Cell 2025, 188: 6953-6970.e12. PMID: 41038164, PMCID: PMC12662569, DOI: 10.1016/j.cell.2025.09.006.Peer-Reviewed Original ResearchConceptsSingle-molecule resolutionWhole-genome coverageFluorescence in situ hybridizationCell type-specificProfiles of transcriptsSpatial transcriptomics methodsSpatial transcriptomics technologiesTranscriptome coverageEngineered RNAsCell-cell interactionsDiverse cellular identitiesMouse genesSubcellular localizationTranscriptomic toolsCRISPR screensCellular identityTranscriptome analysisTranscriptomic methodsTranscriptomic technologiesGene programSpatial transcriptomicsTranscriptomeSingle cellsGenesSpatial organizationTracing the evolution of single-cell 3D genomes in Kras-driven cancers
Liu M, Jin S, Agabiti S, Jensen T, Yang T, Radda J, Ruiz C, Baldissera G, Rajaei M, Li F, Townsend J, Muzumdar M, Wang S. Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. Nature Genetics 2025, 57: 3075-3087. PMID: 40825871, PMCID: PMC12695640, DOI: 10.1038/s41588-025-02297-w.Peer-Reviewed Original ResearchThis study investigates 3D genome changes in Kras-driven cancers, identifying structural bottlenecks in early progression and potential diagnostic and therapeutic biomarkers.
2023
An integrated platform for high-throughput nanoscopy
Barentine A, Lin Y, Courvan E, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace M, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer K, Bewersdorf J, Baddeley D. An integrated platform for high-throughput nanoscopy. Nature Biotechnology 2023, 41: 1549-1556. PMID: 36914886, PMCID: PMC10497732, DOI: 10.1038/s41587-023-01702-1.Peer-Reviewed Original ResearchConceptsLarge data volumesUser-defined extensionsPlugin frameworkData compressionData volumeCamera frameFrame rateAnalysis platformAcquisition taskPlatformIntegrated acquisitionThroughputSingle-molecule localization microscopyTypical throughputHundreds of cellsThree-dimensional fluorescenceFrameworkTens of cellsLocalization microscopyWorkflow
2021
TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations
Cheng Y, Liu M, Hu M, Wang S. TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations. Genome Biology 2021, 22: 309. PMID: 34749781, PMCID: PMC8574027, DOI: 10.1186/s13059-021-02523-8.Peer-Reviewed Original ResearchConceptsInactive X chromosomeActive X chromosomeMajor epigenetic componentsSingle-cell domainsX chromosomeEpigenetic componentsThree-dimensional genome architectureGlobal epigenetic landscapeFemale human cellsLoop extrusion mechanismSame genomic regionGenome architectureChromatin domainsTAD structureChromatin compactionEpigenetic landscapeTAD boundariesChromatin foldingGenomic regionsChromosome copiesGenomic techniquesEpigenetic perturbationsEpigenetic interactionsDistinct cell linesChromosomesSpatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture
Lu Y, Liu M, Yang J, Weissman SM, Pan X, Katz SG, Wang S. Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture. Cell Discovery 2021, 7: 47. PMID: 34183665, PMCID: PMC8238952, DOI: 10.1038/s41421-021-00266-1.Peer-Reviewed Original ResearchWild typeCell typesHSC nicheMultiplexed error-robust fluorescenceStem cell niche architectureFetal liverHematopoietic stem cell nicheStem cell nicheLoss of TET2Endothelial cellsBioinformatic foundationNumber of HSCsNiche architectureTranscriptome profilingSpatial regulationTranscriptional profilesCell nicheArterial endothelial cellsIndividual cellsNicheSitu hybridizationSpatial organizationLiver cell typesMicroenvironment regulationRobust fluorescenceChromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue
Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S. Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Nature Protocols 2021, 16: 2667-2697. PMID: 33903756, PMCID: PMC9007104, DOI: 10.1038/s41596-021-00518-0.Peer-Reviewed Original ResearchConceptsSame single cellNucleome architecturesGene expressionMammalian tissuesChromatin foldingNuclear laminaSingle cellsNumerous RNA speciesDifferent biological processesSingle mammalian cellsDifferent cell typesMultiplexed imagingGenomic organizationGenomic architectureChromatin loopsGenomic regionsRNA speciesIndividual chromosomesMammalian cellsGenomic techniquesBiological processesDetailed protocolCopy numberCell typesNormal development
2020
ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization
Hu M, Yang B, Cheng Y, Radda JSD, Chen Y, Liu M, Wang S. ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. Scientific Reports 2020, 10: 22031. PMID: 33328483, PMCID: PMC7745008, DOI: 10.1038/s41598-020-76439-x.Peer-Reviewed Original ResearchConceptsSingle-molecule RNA FISHSpecific genomic lociSitu hybridizationNucleome architecturesRNA FISHGenomic lociRNA speciesMultiplexed fluorescenceFISH techniqueFishRecent technological advancesMultiplexed imagingHybridizationMultiplexed mannerLociSpeciesFluorescencePowerful methodNotable exampleProbeProbe designTechnological advances