Alexandre Jourdon, PhD
Associate Research Scientist in the Child Study CenterCards
About
Research
Publications
2025
Engineering human neuronal diversity: Morphogens and stem cell technologies for neurodevelopmental biology
Scuderi S, Khouri-Farah N, Rauthan R, Natu A, Wang H, Nelson A, Jourdon A, Vaccarino F. Engineering human neuronal diversity: Morphogens and stem cell technologies for neurodevelopmental biology. Stem Cell Reports 2025, 20: 102615. PMID: 40930068, PMCID: PMC12447334, DOI: 10.1016/j.stemcr.2025.102615.Peer-Reviewed Original ResearchConceptsNeural tube patterningStem cell technologyTube patterningTranscription factor networksComplex assortmentFactor networksPluripotent stem cellsNeuronal cellsPatterns in vivoCell technologyProgenitor cellsEmbryonic tissuesNeurodevelopmental biologyBrain-on-chipNeuropsychiatric disordersHuman brain developmentStem cellsBrain developmentCellsBrain organoidsPatterning processMorphogenTranscriptionBrainStemEarly 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 dysfunctionCorticogenesisSpecification of human brain regions with orthogonal gradients of WNT and SHH in organoids reveals patterning variations across cell lines
Scuderi S, Kang T, Jourdon A, Nelson A, Yang L, Wu F, Anderson G, Mariani J, Tomasini L, Sarangi V, Abyzov A, Levchenko A, Vaccarino F. Specification of human brain regions with orthogonal gradients of WNT and SHH in organoids reveals patterning variations across cell lines. Cell Stem Cell 2025, 32: 970-989.e11. PMID: 40315847, PMCID: PMC12145255, DOI: 10.1016/j.stem.2025.04.006.Peer-Reviewed Original ResearchConceptsGradient of WntGene expression programsSingle-cell transcriptomicsBrain lineagesMorphogen gradientsEpigenetic variationDorso-ventral axisShh signalingExpression programsMorphogenFetal human brainHuman iPSC linesPluripotent stem cellsCell linesNeuronal lineageNeural tubeShhWntLineagesLine-to-line variationEarly patterningPattern systemPattern variationHuman brain regionsIPSC lines
2024
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
Dai R, Chu T, Zhang M, Wang X, Jourdon A, Wu F, Mariani J, Vaccarino F, Lee D, Fullard J, Hoffman G, Roussos P, Wang Y, Wang X, Pinto D, Wang S, Zhang C, consortium P, Chen C, Liu C. Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data. Science Advances 2024, 10: eadh2588. PMID: 38781336, PMCID: PMC11114236, DOI: 10.1126/sciadv.adh2588.Peer-Reviewed Original ResearchConceptsHuman brain transcriptome dataBrain transcriptomic dataRNA-seqTranscriptome dataCell-type gene expressionGene expressionCell-type proportionsSingle-cell dataMultiple brain disordersBrain cell typesCell deconvolution methodsPostmortem brainsRNA sequencingBrain disordersBrain developmentSchizophreniaEQTLAlzheimer's diseaseCell typesOrganoid samplesBrainBiological applications
2023
Author Correction: Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis
Jourdon A, Wu F, Mariani J, Capauto D, Norton S, Tomasini L, Amiri A, Suvakov M, Schreiner J, Jang Y, Panda A, Nguyen C, Cummings E, Han G, Powell K, Szekely A, McPartland J, Pelphrey K, Chawarska K, Ventola P, Abyzov A, Vaccarino F. Author Correction: Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nature Neuroscience 2023, 26: 2035-2035. PMID: 37674007, DOI: 10.1038/s41593-023-01447-9.Peer-Reviewed Original ResearchModeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis
Jourdon A, Wu F, Mariani J, Capauto D, Norton S, Tomasini L, Amiri A, Suvakov M, Schreiner J, Jang Y, Panda A, Nguyen C, Cummings E, Han G, Powell K, Szekely A, McPartland J, Pelphrey K, Chawarska K, Ventola P, Abyzov A, Vaccarino F. Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nature Neuroscience 2023, 26: 1505-1515. PMID: 37563294, PMCID: PMC10573709, DOI: 10.1038/s41593-023-01399-0.Peer-Reviewed Original ResearchConceptsIdiopathic autism spectrum disorderCortical neuron subtypesAutism spectrum disorderEarly cortical developmentCortical organoidsCortical plateExcitatory neuronsCortical developmentRare formNeuron subtypesUnaffected fatherASD pathogenesisForebrain organoidsEarly neurogenesisRare variantsIdiopathic autismRisk genesTranscriptomic alterationsNeuronsProbandsSingle-cell transcriptomicsForebrain developmentSpectrum disorderTranscriptomic changesAlterationsEarly Neuronal Differentiation/patterning of the Human Pallium, Modeling by in Vitro Systems, and Disruption in Developmental Disorders
Scuderi S, Jourdon A, Vaccarino F. Early Neuronal Differentiation/patterning of the Human Pallium, Modeling by in Vitro Systems, and Disruption in Developmental Disorders. 2023, 423-442. DOI: 10.1002/9781119860914.ch20.Peer-Reviewed Original ResearchCentral nervous systemDorsal-anterior partHuman cortexCortical developmentInhibitory neuronsSingle-cell omicsAnimal modelsNervous systemCortical layersMammalian brainBrain regionsCortical formationPopulations of excitatoryTangential migrationAltered developmentCortical structuresAnterior partCortical patterningPrecursor cellsEarly neuronal differentiationIncoming afferentsCortexNeuronal differentiationNeuronsHuman specificity
2022
Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability
Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban A, Leckman J, Weinberger D, Vaccarino F, Abyzov A, Walsh C, Park P, Sestan N, Weinberger D, Moran J, Gage F, Vaccarino F, Gleeson J, Mathern G, Courchesne E, Roy S, Chess A, Akbarian S, Bizzotto S, Coulter M, Dias C, D’Gama A, Ganz J, Hill R, Huang A, Khoshkhoo S, Kim S, Lee A, Lodato M, Maury E, Miller M, Borges-Monroy R, Rodin R, Zhou Z, Bohrson C, Chu C, Cortes-Ciriano I, Dou Y, Galor A, Gulhan D, Kwon M, Luquette J, Sherman M, Viswanadham V, Jones A, Rosenbluh C, Cho S, Langmead B, Thorpe J, Erwin J, Jaffe A, McConnell M, Narurkar R, Paquola A, Shin J, Straub R, Abyzov A, Bae T, Jang Y, Wang Y, Molitor C, Peters M, Linker S, Reed P, Wang M, Urban A, Zhou B, Zhu X, Pattni R, Serres Amero A, Juan D, Lobon I, Marques-Bonet T, Solis Moruno M, Garcia Perez R, Povolotskaya I, Soriano E, Antaki D, Averbuj D, Ball L, Breuss M, Yang X, Chung C, Emery S, Flasch D, Kidd J, Kopera H, Kwan K, Mills R, Moldovan J, Sun C, Zhao X, Zhou W, Frisbie T, Cherskov A, Fasching L, Jourdon A, Pochareddy S, Scuderi S. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022, 377: 511-517. PMID: 35901164, PMCID: PMC9420557, DOI: 10.1126/science.abm6222.Peer-Reviewed Original ResearchConceptsTranscription factorsSomatic mutationsPutative transcription factorEnhancer-like regionSingle nucleotide mutationsWhole-genome sequencingGene regulationSomatic duplicationGenome sequencingDamaging mutationsBackground mutagenesisMutationsHypermutabilityClonal expansionMotifDiseased brainPotential linkVivo clonal expansionMutagenesisGenesDuplicationSequencingRegulation
2020
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020, 21: 521. PMID: 33183232, PMCID: PMC7663899, DOI: 10.1186/s12859-020-03858-y.Peer-Reviewed Original ResearchConceptsMultiple displacement amplificationShallow sequencingSingle-cell platformsSingle-cell sequencingCoverage sequencing dataSingle cellsHuman neuronal cellsMosaic mutationsAmount of DNAAmplification qualityCell sequencingCoverage sequencingHigh-coverage dataSequencing dataHaplotype informationPhi29 polymeraseDNA damageIndividual cellsNeuronal cellsSequencingAmplification biasAllelic imbalancePresence of sitesMutationsFragment lengthChapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders
Jourdon A, Mariani J, Scuderi S, Amiri A, Wu F, Yuen E, Abyzov A, Vaccarino F. Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders. 2020, 99-127. DOI: 10.1016/b978-0-12-814409-1.00005-7.ChaptersPluripotent stem cellsStem cellsStudy of speciesHuman neurodevelopmental disordersEpigenome analysisGene regulationIPSC fieldGenomic variationGene expressionGenetic backgroundDisease modelingStudies of neurodevelopmentIPSCsExperimental approachNeurodevelopmental disordersTranscriptomeGenomeCellsCell phenotypingSpeciesExperimental design issuesPhenotypeRegulationExpressionPhenotyping
News
News
- May 01, 2025Source: Yale News
How Molecular Traffic Cops Guide Development of the Human Brain
- September 03, 2023Source: New Haven Register
Yale autism study’s findings could help scientists develop treatment options
- August 10, 2023Source: Yale News
Yale Scientists Reveal Two Paths to Autism in the Developing Brain
- May 04, 2023
April 2023 YCSC Faculty Development Fund Awardees Announced