Suel-Kee Kim
Associate Research Scientist in NeuroscienceCards
About
Research
Publications
2026
NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development
Sonthalia S, Herb B, Adkins R, Orvis J, Li G, Liao X, Yu Q, Blanco X, Casella A, Liu J, Stein-O’Brien G, Caffo B, Hertzano R, Mahurkar A, Xu J, Gillis J, Werner J, Ma S, Kim S, Micali N, Sestan N, Rakic P, Santpere G, Ament S, Colantuoni C. NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development. Nature Neuroscience 2026, 1-14. PMID: 41882195, DOI: 10.1038/s41593-026-02204-4.Peer-Reviewed Original ResearchNeocortical developmentRadial gliaIn vivo developmentTranscriptome dataIn vitro modelVentricular progenitorsExcitatory neuronsNeocortical neurogenesisNeuronal maturationTranscriptomic programsIn vitroPeak expressionProtracted maturationCerebral organoidsTranscriptome dynamicsHuman dataTranscription factorsAdaptive evolution of gene regulatory networks in mammalian neocortex
Li Z, Kaur N, Santpere G, Muchnik S, Sindhu S, Qi C, Shibata M, Clément O, Klarić T, de Martin X, Luria V, Cho H, Li M, Shibata A, Choi S, Kim H, Tebbenkamp A, Ma S, Han W, Kim S, Pochareddy S, Duy P, Xing X, Bao Y, Xu X, Gladwyn-Ng I, Cullen H, Paolino A, Fenlon L, Kozulin P, Suárez R, Risgaard R, Gulden F, Karger A, Suzuki I, Hirata T, Gobeske K, Richards L, Sousa A, Heng J, Sestan N. Adaptive evolution of gene regulatory networks in mammalian neocortex. Nature 2026, 1-11. PMID: 41851468, DOI: 10.1038/s41586-026-10226-y.Peer-Reviewed Original ResearchCis-regulatory elementsAdaptive evolutionEvolution of gene regulatory networksPutative cis-regulatory elementsGene expressionGene regulatory networksLandscape of gene expressionAssociated with genesTarget gene expressionModern reptilesHighest conservationRegulatory networksBinding motifRegulatory nodesPrefrontal cortexEvolutionary adaptationIntellectual disabilityMolecular diversityBrain connectivityExcitatory projection neuronsZBTB18Complex brainsProjection neuronsMammalsBrainHuman-specific features of the cerebellum and ZP2-regulated synapse development
Kim S, Cherskov A, Sindhwani A, Choi S, Kim H, Li M, Zhang M, Mato-Blanco X, Liu Y, Micali N, Young D, Estacion M, Zhang Y, Ruiz-Jiménez J, Nadkarni A, Luria V, Sindhu S, Chatterjee I, Shibata A, Liang D, Cho H, Park S, Spajic A, Kovner R, Glavan M, Chen R, Risgaard R, Li X, Pochareddy S, Karger A, Huttner A, Morozov Y, Daadi E, Colantuoni C, Gobeske K, Ely J, Hof P, Daadi M, Sherwood C, Duque A, Ma S, Sousa A, Waxman S, Rakic P, Santpere G, Sanders S, Sestan N. Human-specific features of the cerebellum and ZP2-regulated synapse development. Cell 2026, 189: 1802-1819.e28. PMID: 41819103, DOI: 10.1016/j.cell.2026.02.014.Peer-Reviewed Original ResearchConceptsHuman granule cellsZona pellucida glycoprotein 2Granule cellsNeuronal electrophysiological activityAdult cerebellar cortexSynapse regulationCognitive functionGlomerular synapsesNon-human primatesCerebellar cortexMotor coordinationMossy fibersGamete interactionGlycoprotein 2Human brainSynapse developmentSynaptic proteinsElectrophysiological activityHuman cerebellumEvolutionary developmentHuman-specific featuresCo-optionCerebellumHuman adaptationChromatin accessibility profiles
2025
Microencapsulation system for scalable differentiation of peripheral motor neurons from human induced pluripotent stem cells
Kim S, Kim C, Moon H, Han J, Choi S, Park S, Kim H, Choi B, Kang J, Kim J, Kim J. Microencapsulation system for scalable differentiation of peripheral motor neurons from human induced pluripotent stem cells. Biomaterials Science 2025, 13: 4717-4729. PMID: 40662269, DOI: 10.1039/d5bm00535c.Peer-Reviewed Original ResearchConceptsPeripheral motor neuronsMotor neuronsScalable differentiationHigh-throughput productionMature motor neuronsMotor neuron markersEncapsulated chipMolecular featuresHigh-throughput drug screeningSpike firingOn-chipUniform microcapsulesAcid residuesNeuronal markersRegenerative therapyAction potentialsFunctional maturationLow immunogenicityClinical translationPost-encapsulationEncapsulated cellsExtended culturePatterning cuesEmbryoid bodiesSize controlEarly developmental origins of cortical disorders modeled in human neural stem cells
Mato-Blanco X, Kim S, Jourdon A, Ma S, Choi S, Giani A, Paredes M, Tebbenkamp A, Liu F, Duque A, Vaccarino F, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early developmental origins of cortical disorders modeled in human neural stem cells. Nature Communications 2025, 16: 6347. PMID: 40634286, PMCID: PMC12241556, DOI: 10.1038/s41467-025-61316-w.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomicsNeural stem cellsNeural stem cell lineage commitmentGene regulatory networksEarly developmental originHuman neural stem cellsRegulatory networksExpression dynamicsRisk genesStem cellsCortical disordersTransition in vitroTelencephalic developmentEarly phaseGene dysfunctionLineage commitmentCell trajectoriesHuman corticogenesisHuman brain dysfunctionGenesNSCs in vitroMultiple diseasesIn vivoBrain dysfunctionCorticogenesis
2024
Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells
Kim S, Seo S, Stein-O’Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde T, Kleinman J, Voss T, Fertig E, Shin J, Bürli R, Cross A, Brandon N, Weinberger D, Chenoweth J, Hoeppner D, Sestan N, Colantuoni C, McKay R. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells. Stem Cell Reports 2024, 19: 1336-1350. PMID: 39151428, PMCID: PMC11411333, DOI: 10.1016/j.stemcr.2024.07.004.Peer-Reviewed Original ResearchHuman pluripotent stem cellsEarly mammalian developmentConsequences of variationPluripotent stem cellsTranscriptomic variationMammalian developmentTranscriptomic patternsTranscriptomic traitsReplicate linesMesendodermal lineagesNeural fateAdult tissuesLineagesHindbrain fateTranscriptional signatureTranscriptomic signaturesEarly eventLineage biasHuman pluripotent stem cell linesStem cellsFateIndividual variationAnterior to posterior structuresEpigenetic originCells
2023
Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon
Micali N, Ma S, Li M, Kim S, Mato-Blanco X, Sindhu S, Arellano J, Gao T, Shibata M, Gobeske K, Duque A, Santpere G, Sestan N, Rakic P. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Science 2023, 382: eadf3786. PMID: 37824652, PMCID: PMC10705812, DOI: 10.1126/science.adf3786.Peer-Reviewed Original Research
2022
Cellular recovery after prolonged warm ischaemia of the whole body
Andrijevic D, Vrselja Z, Lysyy T, Zhang S, Skarica M, Spajic A, Dellal D, Thorn SL, Duckrow RB, Ma S, Duy PQ, Isiktas AU, Liang D, Li M, Kim SK, Daniele SG, Banu K, Perincheri S, Menon MC, Huttner A, Sheth KN, Gobeske KT, Tietjen GT, Zaveri HP, Latham SR, Sinusas AJ, Sestan N. Cellular recovery after prolonged warm ischaemia of the whole body. Nature 2022, 608: 405-412. PMID: 35922506, PMCID: PMC9518831, DOI: 10.1038/s41586-022-05016-1.Peer-Reviewed Original ResearchConceptsSingle-nucleus transcriptomic analysesSpecific gene expression patternsCellular recoveryGene expression patternsCellular processesMammalian cellsTranscriptomic analysisLarge mammalsExpression patternsCellular repair processesCell deathComprehensive resourceUnderappreciated potentialPhysiological challengesTissue integrityRepair processSpecific changesPorcine brainMammalsOrgansMultiple organsImpaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus
Duy PQ, Weise SC, Marini C, Li XJ, Liang D, Dahl PJ, Ma S, Spajic A, Dong W, Juusola J, Kiziltug E, Kundishora AJ, Koundal S, Pedram MZ, Torres-Fernández LA, Händler K, De Domenico E, Becker M, Ulas T, Juranek SA, Cuevas E, Hao LT, Jux B, Sousa AMM, Liu F, Kim SK, Li M, Yang Y, Takeo Y, Duque A, Nelson-Williams C, Ha Y, Selvaganesan K, Robert SM, Singh AK, Allington G, Furey CG, Timberlake AT, Reeves BC, Smith H, Dunbar A, DeSpenza T, Goto J, Marlier A, Moreno-De-Luca A, Yu X, Butler WE, Carter BS, Lake EMR, Constable RT, Rakic P, Lin H, Deniz E, Benveniste H, Malvankar NS, Estrada-Veras JI, Walsh CA, Alper SL, Schultze JL, Paeschke K, Doetzlhofer A, Wulczyn FG, Jin SC, Lifton RP, Sestan N, Kolanus W, Kahle KT. Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus. Nature Neuroscience 2022, 25: 458-473. PMID: 35379995, PMCID: PMC9664907, DOI: 10.1038/s41593-022-01043-3.Peer-Reviewed Original ResearchConceptsCongenital hydrocephalusCerebral ventricular dilatationPrimary defectNeuroepithelial cell differentiationRisk genesCerebrospinal fluid homeostasisWhole-exome sequencingNeuroepithelial stem cellsCortical hypoplasiaReduced neurogenesisVentricular dilatationVentricular enlargementCH mutationsPrenatal hydrocephalusDisease heterogeneityBrain surgeryCSF circulationHydrocephalusGenetic subtypesFluid homeostasisNeuroepithelial cellsNovo mutationsBrain transcriptomicsStem cellsCell differentiation
2021
Regulation of prefrontal patterning and connectivity by retinoic acid
Shibata M, Pattabiraman K, Lorente-Galdos B, Andrijevic D, Kim SK, Kaur N, Muchnik SK, Xing X, Santpere G, Sousa AMM, Sestan N. Regulation of prefrontal patterning and connectivity by retinoic acid. Nature 2021, 598: 483-488. PMID: 34599305, PMCID: PMC9018119, DOI: 10.1038/s41586-021-03953-x.Peer-Reviewed Original ResearchConceptsPrefrontal cortexRetinoic acidGranular layer 4Neocortex of humansRetinoic acid signalingCerebral cortexRetinoic acid receptorsMotor cortexMotor areaMediodorsal thalamusFetal developmentCortical expansionAcid receptorsGenetic deletionDendritic spinogenesisLayer 4Synthesizing enzymesCortexAcid signalingNeural developmentMiceCritical roleSignalingThalamusSpinogenesis