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
2021
Cell-to-Cell Adhesion and Neurogenesis in Human Cortical Development: A Study Comparing 2D Monolayers with 3D Organoid Cultures
Scuderi S, Altobelli GG, Cimini V, Coppola G, Vaccarino FM. Cell-to-Cell Adhesion and Neurogenesis in Human Cortical Development: A Study Comparing 2D Monolayers with 3D Organoid Cultures. Stem Cell Reports 2021, 16: 264-280. PMID: 33513360, PMCID: PMC7878838, DOI: 10.1016/j.stemcr.2020.12.019.Peer-Reviewed Original Research
2020
PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids
Jourdon A, Scuderi S, Capauto D, Abyzov A, Vaccarino FM. PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids. Neuropsychopharmacology 2020, 46: 70-85. PMID: 32659782, PMCID: PMC7689467, DOI: 10.1038/s41386-020-0763-3.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRecent single-cell technologiesGene regulatory networksSingle-cell technologiesMulti-omics investigationsPluripotent stem cellsTranscriptional dynamicsBrain developmentCell fateEpigenomic datasetsRegulatory networksElement activityNeural lineagesStem cellsBrain organoidsOrganoidsBiological modelsFetal brainPsychENCODEBrain biologyMajor questionsEpigenomicsFetal tissuesTranscriptomicsLineagesBiology
2018
Comprehensive functional genomic resource and integrative model for the human brain
Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE, Roussos P, Akbarian S, Jaffe A, White K, Weng Z, Sestan N, Geschwind D, Knowles J, Gerstein M, Ashley-Koch A, Crawford G, Garrett M, Song L, Safi A, Johnson G, Wray G, Reddy T, Goes F, Zandi P, Bryois J, Jaffe A, Price A, Ivanov N, Collado-Torres L, Hyde T, Burke E, Kleiman J, Tao R, Shin J, Akbarian S, Girdhar K, Jiang Y, Kundakovic M, Brown L, Kassim B, Park R, Wiseman J, Zharovsky E, Jacobov R, Devillers O, Flatow E, Hoffman G, Lipska B, Lewis D, Haroutunian V, Hahn C, Charney A, Dracheva S, Kozlenkov A, Belmont J, DelValle D, Francoeur N, Hadjimichael E, Pinto D, van Bakel H, Roussos P, Fullard J, Bendl J, Hauberg M, Mangravite L, Peters M, Chae Y, Peng J, Niu M, Wang X, Webster M, Beach T, Chen C, Jiang Y, Dai R, Shieh A, Liu C, Grennan K, Xia Y, Vadukapuram R, Wang Y, Fitzgerald D, Cheng L, Brown M, Brown M, Brunetti T, Goodman T, Alsayed M, Gandal M, Geschwind D, Won H, Polioudakis D, Wamsley B, Yin J, Hadzic T, De La Torre Ubieta L, Swarup V, Sanders S, State M, Werling D, An J, Sheppard B, Willsey A, White K, Ray M, Giase G, Kefi A, Mattei E, Purcaro M, Weng Z, Moore J, Pratt H, Huey J, Borrman T, Sullivan P, Giusti-Rodriguez P, Kim Y, Sullivan P, Szatkiewicz J, Rhie S, Armoskus C, Camarena A, Farnham P, Spitsyna V, Witt H, Schreiner S, Evgrafov O, Knowles J, Gerstein M, Liu S, Wang D, Navarro F, Warrell J, Clarke D, Emani P, Gu M, Shi X, Xu M, Yang Y, Kitchen R, Gürsoy G, Zhang J, Carlyle B, Nairn A, Li M, Pochareddy S, Sestan N, Skarica M, Li Z, Sousa A, Santpere G, Choi J, Zhu Y, Gao T, Miller D, Cherskov A, Yang M, Amiri A, Coppola G, Mariani J, Scuderi S, Szekely A, Vaccarino F, Wu F, Weissman S, Roychowdhury T, Abyzov A. Comprehensive functional genomic resource and integrative model for the human brain. Science 2018, 362 PMID: 30545857, PMCID: PMC6413328, DOI: 10.1126/science.aat8464.Peer-Reviewed Original ResearchConceptsQuantitative trait lociCell type proportionsComprehensive functional genomics resourceExpression quantitative trait lociFunctional genomics resourcesSingle-cell expression profilesGene regulatory networksFurther quantitative trait lociPsychENCODE ConsortiumGenomic resourcesComprehensive online resourceRegulatory networksKey genesCross-population variationExpression profilesMolecular mechanismsCell typesGenesAdult brainPolygenic risk scoresStudy variantsChromatinSplicingGenetic riskInterpretable deep learning modelTranscriptome and epigenome landscape of human cortical development modeled in organoids
Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford G, Sestan N, Abyzov A, Vaccarino F, Akbarian S, An J, Armoskus C, Ashley-Koch A, Beach T, Belmont J, Bendl J, Borrman T, Brown L, Brown M, Brown M, Brunetti T, Bryois J, Burke E, Camarena A, Carlyle B, Chae Y, Charney A, Chen C, Cheng L, Cherskov A, Choi J, Clarke D, Collado-Torres L, Dai R, De La Torre Ubieta L, DelValle D, Devillers O, Dracheva S, Emani P, Evgrafov O, Farnham P, Fitzgerald D, Flatow E, Francoeur N, Fullard J, Gandal M, Gao T, Garrett M, Geschwind D, Giase G, Girdhar K, Giusti-Rodriguez P, Goes F, Goodman T, Grennan K, Gu M, Gürsoy G, Hadjimichael E, Hahn C, Haroutunian V, Hauberg M, Hoffman G, Huey J, Hyde T, Ivanov N, Jacobov R, Jaffe A, Jiang Y, Jiang Y, Johnson G, Kassim B, Kefi A, Kim Y, Kitchen R, Kleiman J, Knowles J, Kozlenkov A, Li M, Li Z, Lipska B, Liu C, Liu S, Mangravite L, Mariani J, Mattei E, Miller D, Moore J, Nairn A, Navarro F, Park R, Peters M, Pinto D, Pochareddy S, Polioudakis D, Pratt H, Price A, Purcaro M, Ray M, Reddy T, Rhie S, Roussos P, Sanders S, Santpere G, Schreiner S, Sheppard B, Shi X, Shieh A, Shin J, Skarica M, Song L, Sousa A, Spitsyna V, State M, Sullivan P, Swarup V, Szatkiewicz J, Szekely A, Tao R, van Bakel H, Wang Y, Wang D, Warrell J, Webster M, Weissman S, Weng Z, Werling D, White K, Willsey J, Wiseman J, Witt H, Won H, Wray G, Xia Y, Xu M, Yang Y, Yang M, Zandi P, Zhang J, Zharovsky E. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 2018, 362 PMID: 30545853, PMCID: PMC6426303, DOI: 10.1126/science.aat6720.Peer-Reviewed Original Research
2015
The PsychENCODE project
Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nature Neuroscience 2015, 18: 1707-1712. PMID: 26605881, PMCID: PMC4675669, DOI: 10.1038/nn.4156.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainChromosome MappingEpigenesis, GeneticGenetic CodeHumansMental DisordersTranscriptome
2014
Transcriptome Analysis of the Human Striatum in Tourette Syndrome
Lennington JB, Coppola G, Kataoka-Sasaki Y, Fernandez TV, Palejev D, Li Y, Huttner A, Pletikos M, Sestan N, Leckman JF, Vaccarino FM. Transcriptome Analysis of the Human Striatum in Tourette Syndrome. Biological Psychiatry 2014, 79: 372-382. PMID: 25199956, PMCID: PMC4305353, DOI: 10.1016/j.biopsych.2014.07.018.Peer-Reviewed Original ResearchConceptsCopy number variantsGenome-wide association studiesGene coexpression modulesNumber variantsGene network analysisCommon genetic variantsCoexpression modulesUpregulated genesMetabolism modulesImmune-related genesNetwork analysisAssociation studiesDifferential expressionUpregulated modulesGenetic variantsGenesPatient's striatumTS individualsTranscriptomeVariantsMetabolic alterationsSame regionGamma-aminobutyric acidergic interneuronsTranscriptsRNA
2012
Modeling human cortical development in vitro using induced pluripotent stem cells
Mariani J, Simonini MV, Palejev D, Tomasini L, Coppola G, Szekely AM, Horvath TL, Vaccarino FM. Modeling human cortical development in vitro using induced pluripotent stem cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12770-12775. PMID: 22761314, PMCID: PMC3411972, DOI: 10.1073/pnas.1202944109.Peer-Reviewed Original ResearchConceptsHuman brain developmentHuman induced pluripotent stem cellsLayer-specific cortical neuronsBrain developmentHuman cerebral cortexHuman cortical developmentStem cellsPluripotent stem cellsCerebral cortexCortical neuronsCortical developmentCNS regionsRadial gliaCortical wallDorsal telencephalonEmbryonic telencephalonGene expression profilesInduced pluripotent stem cellsIntermediate progenitorsTelencephalic developmentTelencephalonExpression profilesTranscriptional programsCellsGlia