Thanh Thanh L. Nguyen, PhD
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Biography
I am a functional genomicist interested in elucidating genetic drivers of disease and translating findings into new diagnostics and targeted treatments. My PhD thesis integrated transcriptomic, genomic and epigenomic approaches to characterize environment-dependent genetic risk variants across autoimmunity, metabolism, mood disorders, osteoporosis and cancer (Nucleic Acids Research 2022, Molecular Psychiatry 2021). Currently as a co-mentored computational and experimental biologist, I am leveraging state-of-the-art massively parallel reporter assays, CRISPR screens and human stem cell technologies to (1) explore the genetic architecture driving functional variation of all human trait-associated genetic variants in the UK Biobank (Nature, under review), and (2) functionally characterize all brain non-coding somatic mosaic variants discovered to date, resolving their causal roles in schizophrenia (Science 2024) and autism spectrum disorder. My postdoc is funded by the NIMH Ruth L. Kirschstein National Research Service Award (NRSA) T32 and F32.
Since joining Yale I have mentored eight trainees from diverse nationalities and backgrounds, and supervised a masters thesis and an undergraduate senior thesis (Boell Prize Award 2025).
Last Updated on March 06, 2026.
Departments & Organizations
- All Institutions
Education & Training
- PhD
- Mayo Clinic, Molecular Pharmacology (2022)
- BA
- Green Mountain College, Self-design in Biology, Math & Philosophy (2017)
Research
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Overview
Public Health Interests
Genetics, Genomics, Epigenetics
ORCID
0000-0002-2281-6540- View Lab Website
Brennand Lab; Reilly Lab
Research at a Glance
Yale Co-Authors
Frequent collaborators of Thanh Thanh L. Nguyen's published research.
Publications Timeline
A big-picture view of Thanh Thanh L. Nguyen's research output by year.
Steven Reilly, PhD
Abhijeet Singh Barath, MBBS, PhD
Alexej Abyzov, PhD
Kristen Brennand, PhD
21Publications
732Citations
Publications
Featured Publications
Glucocorticoids unmask silent non-coding genetic risk variants for common diseases
Nguyen T, Gao H, Liu D, Philips T, Ye Z, Lee J, Shi G, Copenhaver K, Zhang L, Wei L, Yu J, Zhang H, Barath A, Luong M, Zhang C, Gaspar-Maia A, Li H, Wang L, Ordog T, Weinshilboum R. Glucocorticoids unmask silent non-coding genetic risk variants for common diseases. Nucleic Acids Research 2022, 50: 11635-11653. PMID: 36399508, PMCID: PMC9723631, DOI: 10.1093/nar/gkac1045.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGene expressionGenomic sequence variantsNon-coding variantsCis-regulatory elementsLigand-dependent associationBreast cancer risk genesInfluence gene expressionCancer risk genesGenetic risk variantsGene-by-environment interactionsEpigenomic approachesSequence variantsAffected genesRisk variantsAssociated with clinical phenotypesRisk genesVariant functionDisease phenotypeDrug responseGenesDisease riskMechanistic frameworkMAST4Clinical phenotypeRisk factorsMachine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cellsSomatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Maury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsTranscription Factor Binding SitesWhole-genome sequencingOpen chromatinMutational processesSomatic mutationsFactor binding sitesSchizophrenia casesSchizophrenia risk genesSomatic mosaicismSomatic variantsRisk genesG mutationGene expressionGermline mutationsBinding sitesGenesMutationsIncreased somatic mutationsChromatinMosaic somatic mutationsPrenatal neurogenesisContext of schizophreniaBrain neuronsSchizophrenia brainVariants
2026
Functional dissection of complex trait variants at single-nucleotide resolution
Siraj L, Castro R, Dewey H, Kales S, Butts J, Nguyen T, Kanai M, Berenzy D, Mouri K, Wang Q, Fiziev P, Tsuo K, McCaw Z, Gosai S, Aguet F, Cui R, Kassam I, McRae J, Vockley C, Lareau C, Abramov S, Boystov A, Vierstra J, Okada Y, Gusev A, Jones T, Lander E, Sabeti P, Finucane H, Reilly S, Ulirsch J, Tewhey R. Functional dissection of complex trait variants at single-nucleotide resolution. Nature 2026, 1-11. PMID: 41741648, DOI: 10.1038/s41586-026-10121-6.Peer-Reviewed Original ResearchCitationsAltmetricConceptsRegulatory variantsFunctional dissectionTranscription factor binding motifsTrait-associated variantsSingle-nucleotide resolutionTrait-associated lociSingle-nucleotide alterationsSystematic functional characterizationDiverse cell typesRegulatory grammarTrait variantsComplex traitsSaturation mutagenesisBinding motifTranscription factorsFunctional characterizationTranscription processCanonical mechanismHuman traitsCell typesTranscriptionVariantsTraitsDisease riskEpistasisNovel association of NAV3 with dilated cardiomyopathy and its role in cardiac fibrosis
Wang M, Ghazal R, Srinivas A, Nguyen T, Murthy V, McNamara D, Skime M, Batzler A, Jenkins G, Barlera S, Pileggi S, Mestroni L, Merlo M, Pinet F, Krejčí J, Chaloupka A, de Groote P, Weinshilboum R, Tschumperlin D, Liu D, Pereira N. Novel association of NAV3 with dilated cardiomyopathy and its role in cardiac fibrosis. AJP Heart And Circulatory Physiology 2026, 330: h686-h696. PMID: 41609618, DOI: 10.1152/ajpheart.00806.2025.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsGenome-wide association studiesCell cycle arrestModulation of cardiac fibrosisCycle arrestGenetic determinantsUpregulation of cell cycle regulatorsRNA-seq transcriptome dataDilated CardiomyopathyNeuron navigator 3Cardiac fibrosisFunctional roleCell cycle regulationCell cycle signalingFibroblast activationAssociation studiesCardiac fibroblastsMyocardial recoveryTranscriptome dataCycle regulationRNA sequencingTransforming growth factor-b1Omics approachesNoncanonical signalingAdult human heartNAV3
2024
Androgen receptor-mediated pharmacogenomic expression quantitative trait loci: implications for breast cancer response to AR-targeting therapy
Gao H, Wei L, Indulkar S, Nguyen T, Liu D, Ho M, Zhang C, Li H, Weinshilboum R, Ingle J, Wang L. Androgen receptor-mediated pharmacogenomic expression quantitative trait loci: implications for breast cancer response to AR-targeting therapy. Breast Cancer Research 2024, 26: 111. PMID: 38965614, PMCID: PMC11225427, DOI: 10.1186/s13058-024-01861-2.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsMeSH KeywordsAntineoplastic Agents, HormonalBenzamidesBreast NeoplasmsCell Line, TumorDihydrotestosteroneFemaleGene Expression Regulation, NeoplasticGenome-Wide Association StudyGenotypeHumansNitrilesPharmacogeneticsPharmacogenomic VariantsPhenylthiohydantoinPolymorphism, Single NucleotideQuantitative Trait LociReceptors, AndrogenConceptsSingle nucleotide polymorphismsGenome-wide associationDependent gene expressionSNP-gene pairsAromatase inhibitorsGenome-wide studiesAndrogen receptorBreast cancerSex hormone binding globulin levelsAR agonistsEffects of aromatase inhibitorsTop lociEffects of endocrine therapyAssociated with cancer riskMinor allele genotypeAR-targeted drugsAR-targeted therapiesTreatment of breast cancerGenotype-dependent mannerBreast cancer phenotypeNucleotide polymorphismsCell line panelEstrogen receptor aBreast cancer patientsGene expression
2023
Myocardial Recovery in Recent Onset Dilated Cardiomyopathy: Role of CDCP1 and Cardiac Fibrosis
Liu D, Wang M, Murthy V, McNamara D, Nguyen T, Philips T, Vyas H, Gao H, Sahni J, Starling R, Cooper L, Skime M, Batzler A, Jenkins G, Barlera S, Pileggi S, Mestroni L, Merlo M, Sinagra G, Pinet F, Krejčí J, Chaloupka A, Miller J, de Groote P, Tschumperlin D, Weinshilboum R, Pereira N. Myocardial Recovery in Recent Onset Dilated Cardiomyopathy: Role of CDCP1 and Cardiac Fibrosis. Circulation Research 2023, 133: 810-825. PMID: 37800334, PMCID: PMC10746262, DOI: 10.1161/circresaha.123.323200.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenome-wide association studiesAssociation studiesRecent-onset dilated cardiomyopathyGenome-wide association study signalsLeft ventricular ejection fractionVentricular ejection fractionDilated CardiomyopathyHuman cardiac fibroblastsCardiac fibrosisMyocardial recoveryEjection fractionHeart failureAssociated with improved cardiac functionTranscriptome profilingCDCP1 expressionStandard drug therapyMolecular mechanismsVariant allelesAttenuated cardiac fibrosisHeart failure patientsCellular modelKnockdownDecreased AktStudy signalsCDCP1
2022
Pharmacological targeting of androgen receptor elicits context-specific effects in estrogen receptor-positive breast cancer
Wei L, Gao H, Yu J, Zhang H, Nguyen T, Gu Y, Passow M, Carter J, Qin B, Boughey J, Goetz M, Weinshilboum R, Ingle J, Wang L. Pharmacological targeting of androgen receptor elicits context-specific effects in estrogen receptor-positive breast cancer. Cancer Research 2022, 83: 456-470. PMID: 36469363, PMCID: PMC9896025, DOI: 10.1158/0008-5472.can-22-1016.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsER+ breast cancerAR-targeted therapiesBreast cancer modelAndrogen receptorBreast cancerAR agonistsCancer modelsAR/ER ratioEstrogen receptor-positive breast cancerReceptor-positive breast cancerAssociated with improved prognosisAR-targeted drugsAlterations of global gene expressionRelationship of ARBinding of ARER+ tumorsAR expressionCell growth inhibitionAR signalingImprove prognosisEstrogen receptorER levelsTumor growthTreatment strategiesEnz treatmentGlucocorticoids mediate transcriptome‐wide alternative polyadenylation: Potential mechanistic and clinical implications
Nguyen T, Liu D, Gao H, Ye Z, Lee J, Wei L, Yu J, Zhang L, Wang L, Ordog T, Weinshilboum R. Glucocorticoids mediate transcriptome‐wide alternative polyadenylation: Potential mechanistic and clinical implications. Clinical And Translational Science 2022, 15: 2758-2771. PMID: 36128656, PMCID: PMC9652440, DOI: 10.1111/cts.13402.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsAlternative polyadenylationTranscriptome-wide alternative polyadenylationAssociated with multiple biological processesRegulating alternative polyadenylationGenetic regulatory mechanismsRNA-binding proteinsTranslation-related pathwaysGlucocorticoid-mediated expressionInvestigated transcriptome-wideMultiple biological processesCell type-specificHuman B lymphoblastoid cell lineTranscriptome-widePotential functional mechanismsRNA transcriptsGenetic variantsB-lymphoblastoid cell linesGene expressionRegulatory mechanismsBiological processesAntiviral inhibitorsImpact of glucocorticoidsDisease phenotypeGenesFunctional consequencesProteomic Biomarkers of Sacubitril/Valsartan Treatment Response in Heart Failure With Preserved Ejection Fraction: Molecular Insights Into Sex Differences
Nguyen T, Wang M, Liu D, Iyer S, Bonilla H, Acker N, Murthy V, Shrivastava S, Desai V, Burnett J, Redfield M, Bailey K, Weinshilboum R, Pereira N. Proteomic Biomarkers of Sacubitril/Valsartan Treatment Response in Heart Failure With Preserved Ejection Fraction: Molecular Insights Into Sex Differences. Circulation Heart Failure 2022, 15: e009629. PMID: 35656806, PMCID: PMC9489635, DOI: 10.1161/circheartfailure.122.009629.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
Academic Achievements & Community Involvement
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Honors
honor Keystone Scholarship
02/24/2025International AwardKeystone SymposiaDetailsUnited Stateshonor Reviewer’s Choice Abstract (top 10%)
10/01/2022National AwardAmerican Society of Human Geneticshonor Presidential Trainee Award
03/01/2022, 03/01/2021National AwardAmerican Society for Clinical Pharmacology & Therapeutics
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