2020
Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals
Xu K, Li B, McGinnis KA, Vickers-Smith R, Dao C, Sun N, Kember RL, Zhou H, Becker WC, Gelernter J, Kranzler HR, Zhao H, Justice AC. Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals. Nature Communications 2020, 11: 5302. PMID: 33082346, PMCID: PMC7598939, DOI: 10.1038/s41467-020-18489-3.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesLarge genome-wide association studiesMillion Veteran ProgramAssociation studiesExpression quantitative trait lociQuantitative trait lociChromatin interactionsComplex traitsFunctional annotationTrait lociSequencing ConsortiumDozen genesSignificant lociSmoking phenotypesLociMultiple populationsNew insightsPhenotypeVeteran ProgramGenetic vulnerabilityGenesTraitsAnnotationEuropean AmericansConsortiumStatistical Methods in Genome-Wide Association Studies
Sun N, Zhao H. Statistical Methods in Genome-Wide Association Studies. Annual Review Of Biomedical Data Science 2020, 3: 1-24. DOI: 10.1146/annurev-biodatasci-030320-041026.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesTraits of interestGenetic architectureIdentification of variantsGWAS dataStatistical methodologyStatistical challengesGenetic risk prediction modelsGenetic markersStatistical methodsHuman diseasesPhenotype informationGenetic variantsTraitsGenotype informationScientific goalsRecent progressGenesVariantsTens of thousandsHundreds of thousandsPrediction modelPathwayThousandsGenotyping Array Design and Data Quality Control in the Million Veteran Program
Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji SG, Sun N, Webster T, Liem A, Hsieh P, Devineni P, Karnam P, Gong X, Radhakrishnan L, Schmidt J, Assimes TL, Huang J, Pan C, Humphries D, Brophy M, Moser J, Muralidhar S, Huang GD, Przygodzki R, Concato J, Gaziano JM, Gelernter J, O’Donnell C, Hauser ER, Zhao H, O’Leary T, Program V, Tsao PS, Pyarajan S. Genotyping Array Design and Data Quality Control in the Million Veteran Program. American Journal Of Human Genetics 2020, 106: 535-548. PMID: 32243820, PMCID: PMC7118558, DOI: 10.1016/j.ajhg.2020.03.004.Peer-Reviewed Original ResearchConceptsMillion Veteran ProgramGenome-wide association studiesGenome-wide scanHigh-quality genotypesArray-based genotypingWhole-genome sequencingNon-European individualsAssociation studiesGenetic markersOmics assaysAxiom arrayDownstream analysisVeteran ProgramCommon variantsGenetic associationAfrican American ancestryAmerican ancestryMVP cohortRare variantsSingle assayDiversityFurther data releasesLarge biobanksPromising resourceQuality control
2019
Genome‐wide association study of cognitive performance in U.S. veterans with schizophrenia or bipolar disorder
Harvey PD, Sun N, Bigdeli TB, Fanous AH, Aslan M, Malhotra AK, Lu Q, Hu Y, Li B, Chen Q, Mane S, Miller P, Rajeevan N, Sayward F, Cheung K, Li Y, Greenwood TA, Gur RE, Braff DL, on the Genetics of Schizophrenia C, Brophy M, Pyarajan S, O'Leary TJ, Gleason T, Przygodszki R, Muralidhar S, Gaziano JM, Concato J, Zhao H, Siever LJ. Genome‐wide association study of cognitive performance in U.S. veterans with schizophrenia or bipolar disorder. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2019, 183: 181-194. PMID: 31872970, DOI: 10.1002/ajmg.b.32775.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAllelesBipolar DisorderCognitionCognition DisordersFemaleGenome-Wide Association StudyGenotypeHumansMaleMiddle AgedNeuropsychological TestsOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSchizophreniaUnited StatesUnited States Department of Veterans AffairsVeteransGENOMICS OF SUICIDAL IDEATION AND BEHAVIOR IN VETERANS WITH SEVERE MENTAL ILLNESS
Harvey P, Bigdeli T, Fanous A, Aslan M, Sun N, Zhao H. GENOMICS OF SUICIDAL IDEATION AND BEHAVIOR IN VETERANS WITH SEVERE MENTAL ILLNESS. European Neuropsychopharmacology 2019, 29: s34. DOI: 10.1016/j.euroneuro.2019.07.069.Peer-Reviewed Original ResearchGenome-wide association study of post-traumatic stress disorder reexperiencing symptoms in >165,000 US veterans
Gelernter J, Sun N, Polimanti R, Pietrzak R, Levey DF, Bryois J, Lu Q, Hu Y, Li B, Radhakrishnan K, Aslan M, Cheung KH, Li Y, Rajeevan N, Sayward F, Harrington K, Chen Q, Cho K, Pyarajan S, Sullivan PF, Quaden R, Shi Y, Hunter-Zinck H, Gaziano JM, Concato J, Zhao H, Stein MB. Genome-wide association study of post-traumatic stress disorder reexperiencing symptoms in >165,000 US veterans. Nature Neuroscience 2019, 22: 1394-1401. PMID: 31358989, PMCID: PMC6953633, DOI: 10.1038/s41593-019-0447-7.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesHigh linkage disequilibrium regionLinkage disequilibrium regionWide association studyDisequilibrium regionBioinformatics analysisTranscriptomic profilesMillion Veteran ProgramChromosome 17Genetic risk factorsNew insightsUK Biobank dataReexperiencing of traumaStriatal medium spiny neuronsVeteran ProgramSignificant regionsCAMKVEuropean AmericansBiobank dataMedium spiny neuronsTCF4BiologyKANSL1African American cohortS93. GENOMICS OF SUICIDAL IDEATION AND BEHAVIOR IN VETERANS WITH SCHIZOPHRENIA AND BIPOLAR ILLNESS
Harvey P, Aslan M, Sun N, Zhao H, Concato J. S93. GENOMICS OF SUICIDAL IDEATION AND BEHAVIOR IN VETERANS WITH SCHIZOPHRENIA AND BIPOLAR ILLNESS. Schizophrenia Bulletin 2019, 45: s342-s342. PMCID: PMC6455790, DOI: 10.1093/schbul/sbz020.638.Peer-Reviewed Original ResearchGenome-wide Association Study of Maximum Habitual Alcohol Intake in >140,000 U.S. European and African American Veterans Yields Novel Risk Loci
Gelernter J, Sun N, Polimanti R, Pietrzak RH, Levey DF, Lu Q, Hu Y, Li B, Radhakrishnan K, Aslan M, Cheung KH, Li Y, Rajeevan N, Sayward F, Harrington K, Chen Q, Cho K, Honerlaw J, Pyarajan S, Lencz T, Quaden R, Shi Y, Hunter-Zinck H, Gaziano JM, Kranzler HR, Concato J, Zhao H, Stein MB, Program D, Program M. Genome-wide Association Study of Maximum Habitual Alcohol Intake in >140,000 U.S. European and African American Veterans Yields Novel Risk Loci. Biological Psychiatry 2019, 86: 365-376. PMID: 31151762, PMCID: PMC6919570, DOI: 10.1016/j.biopsych.2019.03.984.Peer-Reviewed Original ResearchConceptsAdditional genome-wide significant lociRisk lociWide association study (GWAS) analysisAssociation studiesGenome-wide significant lociGenome-wide association studiesGenetic correlationsWide association studyNovel risk lociAlcohol-related traitsStrong statistical supportSmoking-related traitsAdditional genomesSignificant lociPancreatic delta cellsChromosome 4Chromosome 11Protein productsChromosome 8Quantitative phenotypesMillion Veteran ProgramVeterans Affairs Million Veteran ProgramLociCell typesChromosome 17M25 GENETICS OF COGNITIVE FUNCTION IN SCHIZOPHRENIA AND BIPOLAR DISORDER
Harvey P, Sun N, Lu Q, Hu Y, Li B, Chen Q, Aslan M, Radhakrishnan K, Cheung K, Li Y, Sayward F, Rajeevan N, Zhao H, Gaziano M, Concato J. M25 GENETICS OF COGNITIVE FUNCTION IN SCHIZOPHRENIA AND BIPOLAR DISORDER. European Neuropsychopharmacology 2019, 29: s967-s968. DOI: 10.1016/j.euroneuro.2017.08.332.Peer-Reviewed Original ResearchSTUDIES ON ALCOHOL DEPENDENCE GENETICS FROM YALE-PENN AND THE MVP
Gelernter J, Sun N, Polimanti R, Zhou H, Levey D, Harrington K, Gaziano M, Pyarajan S, Aslan M, Sayward F, Li B, Farrer L, Zhao H, Concato J, Stein M. STUDIES ON ALCOHOL DEPENDENCE GENETICS FROM YALE-PENN AND THE MVP. European Neuropsychopharmacology 2019, 29: s1035-s1036. DOI: 10.1016/j.euroneuro.2018.07.032.Peer-Reviewed Original ResearchRESULTS FROM THE USVA MVP PTSD COOPERATIVE STUDY GWAS: PCL TRAITS
Gelernter J, Sun N, Polimanti R, Zhou H, Pietrzak R, Levey D, Harrington K, Gaziano M, Pyarajan S, Radhakrishnan K, Hu Y, Li B, Zhao H, Concato J, Stein M. RESULTS FROM THE USVA MVP PTSD COOPERATIVE STUDY GWAS: PCL TRAITS. European Neuropsychopharmacology 2019, 29: s1055-s1056. DOI: 10.1016/j.euroneuro.2018.07.071.Peer-Reviewed Original Research
2018
159. GWAS of PTSD Re-experiencing Symptoms in the VA Million Veteran Program
Stein M, Gelernter J, Zhao H, Sun N, Pietrzak R, Harrington K, Cho K, Honerlaw J, Quaden R, Gaziano J, Concato J, MVP M. 159. GWAS of PTSD Re-experiencing Symptoms in the VA Million Veteran Program. Biological Psychiatry 2018, 83: s64-s65. DOI: 10.1016/j.biopsych.2018.02.177.Peer-Reviewed Original Research
2016
Arabidopsis SAURs are critical for differential light regulation of the development of various organs
Sun N, Wang J, Gao Z, Dong J, He H, Terzaghi W, Wei N, Deng XW, Chen H. Arabidopsis SAURs are critical for differential light regulation of the development of various organs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 6071-6076. PMID: 27118848, PMCID: PMC4889401, DOI: 10.1073/pnas.1604782113.Peer-Reviewed Original ResearchConceptsPhytochrome-interacting factorsAuxin levelsType 2C protein phosphatasesElongation of hypocotylsExpansion of cotyledonsSmall auxinArabidopsis seedlingsProtein phosphataseRNA genesHypocotyl elongationCotyledon expansionTranscriptomic analysisLight regulationDifferential regulationCell enlargementHypocotylsSAURPhosphatase activityCotyledonsDifferential growthGenesMutation analysisExpressionRegulationDeetiolation
2014
Putting things in order
Sun N, Zhao H. Putting things in order. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 16236-16237. PMID: 25380598, PMCID: PMC4246324, DOI: 10.1073/pnas.1418862111.Peer-Reviewed Original Research
2010
Bayesian Methods in Genomics and Proteomics Studies
Sun N, Zhao H. Bayesian Methods in Genomics and Proteomics Studies. 2010, 125-136. DOI: 10.1002/9780470669716.ch6.Peer-Reviewed Original ResearchTrends and Statistical Challenges in Genomewide Association Studies
Sun N, Zhao H. Trends and Statistical Challenges in Genomewide Association Studies. 2010, 283-308. DOI: 10.1002/9780470567647.ch12.Peer-Reviewed Original Research
2009
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies
Jiao Y, Lori Tausta S, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nature Genetics 2009, 41: 258-263. PMID: 19122662, DOI: 10.1038/ng.282.Peer-Reviewed Original Research
2008
The promise of systems biology for deciphering the control of C 4 leaf development: transcriptome profiling of leaf cell types
Nelson T, Tausta S, Gandotra N, Liu T, Ceserani T, Chen M, Jiao Y, Ma L, Deng X, Sun N, Holfold M, Li N, Zhao H. The promise of systems biology for deciphering the control of C 4 leaf development: transcriptome profiling of leaf cell types. 2008, 317-332. DOI: 10.1142/9789812709523_0018.Peer-Reviewed Original Research
2007
Identifying Stage-Specific Genes by Combining Information from Two Different Types of Oligonucleotide Arrays
Liu Y, Sun N, Liu J, Chen L, McIntosh M, Zheng L, Zhao H. Identifying Stage-Specific Genes by Combining Information from Two Different Types of Oligonucleotide Arrays. 2007, 59-74. DOI: 10.1007/978-0-387-34569-7_5.Peer-Reviewed Original Research
2006
Bayesian error analysis model for reconstructing transcriptional regulatory networks
Sun N, Carroll RJ, Zhao H. Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 7988-7993. PMID: 16702552, PMCID: PMC1472417, DOI: 10.1073/pnas.0600164103.Peer-Reviewed Original ResearchConceptsTranscriptional regulatory networksGene expression dataTranscription regulationRegulatory networksExpression dataProtein-DNA binding dataDNA sequence dataFundamental biological processesYeast cell cycleHigh-throughput technologiesMicroarray gene expression dataBiological experimentsSequence dataGenomic dataBiological processesCell cycleClear biological interpretationThroughput technologiesBiological interpretationMarkov chain Monte CarloBayesian hierarchical model frameworkBiochemical reactionsRegulationLinear system modelHierarchical model framework