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Shan Dong, PhD

TitlePostdoctoral Scholar
InstitutionUniversity of California San Francisco
DepartmentPsychiatry
Address1550 Fourth St
San Francisco CA 94158
Phone415-502-2505
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    Collapse Biography 
    Collapse Education and Training
    Peking University, Beijing, ChinaPh.D07/2015Bioinformatics
    Yale University, New Haven, U.S.09/2013ASD Genetics, Bioinformatics
    Tongji University, Shanghai, ChinaB.Eng07/2010Bioinformatics

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Dong S, Yao S, Chen YX, Guo Y, Zhang YJ, Niu HM, Hao RH, Shen H, Tian Q, Deng HW, Yang TL. Detecting epistasis within chromatin regulatory circuitry reveals CAND2 as a novel susceptibility gene for obesity. Int J Obes (Lond). 2018 May 01. PMID: 29717274.
      View in: PubMed
    2. Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet. 2018 Apr 26. PMID: 29700473.
      View in: PubMed
    3. Chen XF, Zhu DL, Yang M, Hu WX, Duan YY, Lu BJ, Rong Y, Dong S, Hao RH, Chen JB, Chen YX, Yao S, Thynn HN, Guo Y, Yang TL. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. Am J Hum Genet. 2018 May 03; 102(5):776-793. PMID: 29706346.
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    4. Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Publisher Correction: Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci. 2018 Mar 16. PMID: 29549319.
      View in: PubMed
    5. Zhu DL, Chen XF, Hu WX, Dong S, Lu BJ, Rong Y, Chen YX, Chen H, Thynn HN, Wang NN, Guo Y, Yang TL. Multiple functional variants at 13q14 risk locus for osteoporosis regulate RANKL expression through long-range super-enhancer. J Bone Miner Res. 2018 Mar 12. PMID: 29528523.
      View in: PubMed
    6. Hao RH, Gao JL, Li M, Huang W, Zhu DL, Thynn HN, Dong S, Guo Y. Association between fibroblast growth factor 21 and bone mineral density in adults. Endocrine. 2018 Feb; 59(2):296-303. PMID: 29299795.
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    7. Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci. 2017 Dec; 20(12):1661-1668. PMID: 29184211.
      View in: PubMed
    8. Li JB, Ruan YY, Hu B, Dong S, Bi TN, Lin A, Yan WH. Importance of the plasma soluble HLA-G levels for prognostic stratification with traditional prognosticators in colorectal cancer. Oncotarget. 2017 Jul 25; 8(30):48854-48862. PMID: 28415627.
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    9. Yao S, Guo Y, Dong S, Hao RH, Chen XF, Chen YX, Chen JB, Tian Q, Deng HW, Yang TL. Regulatory element-based prediction identifies new susceptibility regulatory variants for osteoporosis. Hum Genet. 2017 08; 136(8):963-974. PMID: 28634715.
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    10. Willsey AJ, Fernandez TV, Yu D, King RA, Dietrich A, Xing J, Sanders SJ, Mandell JD, Huang AY, Richer P, Smith L, Dong S, Samocha KE. De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron. 2017 May 03; 94(3):486-499.e9. PMID: 28472652.
      View in: PubMed
    11. Zhu DL, Guo Y, Zhang Y, Dong S, Xu W, Hao RH, Chen XF, Yan H, Yang SY, Yang TL. A functional SNP regulated by miR-196a-3p in the 3'UTR of FGF2 is associated with bone mineral density in the Chinese population. Hum Mutat. 2017 Jun; 38(6):725-735. PMID: 28317323.
      View in: PubMed
    12. Dong S, Hu WX, Yang TL, Chen XF, Yan H, Chen XD, Tan LJ, Tian Q, Deng HW, Guo Y. SNP-SNP interactions between WNT4 and WNT5A were associated with obesity related traits in Han Chinese Population. Sci Rep. 2017 Mar 08; 7:43939. PMID: 28272483.
      View in: PubMed
    13. Guo Y, Dong S, Yang TL. Epigenomic data facilitate genetic studies for osteoporosis in post-GWAS era. Ann Transl Med. 2017 Feb; 5(4):93. PMID: 28275638.
      View in: PubMed
    14. Guo Y, Dong S, Chen XF, Jing YA, Yang M, Yan H, Shen H, Chen XD, Tan LJ, Tian Q, Deng HW, Yang TL. Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk. Sci Rep. 2016 07 28; 6:30558. PMID: 27465306.
      View in: PubMed
    15. Hao RH, Guo Y, Dong S, Weng GZ, Yan H, Zhu DL, Chen XF, Chen JB, Yang TL. Associations of Plasma FGF2 Levels and Polymorphisms in the FGF2 Gene with Obesity Phenotypes in Han Chinese Population. Sci Rep. 2016 Feb 16; 6:19868. PMID: 26879180; PMCID: PMC4754629.
    16. Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron. 2015 Sep 23; 87(6):1215-1233. PMID: 26402605; PMCID: PMC4624267.
    17. Gockley J, Willsey AJ, Dong S, Dougherty JD, Constantino JN, Sanders SJ. The female protective effect in autism spectrum disorder is not mediated by a single genetic locus. Mol Autism. 2015; 6:25. PMID: 25973162; PMCID: PMC4429476.
    18. Guo Y, Yang TL, Dong S, Yan H, Hao RH, Chen XF, Chen JB, Tian Q, Li J, Shen H, Deng HW. Genetic analysis identifies DDR2 as a novel gene affecting bone mineral density and osteoporotic fractures in Chinese population. PLoS One. 2015; 10(2):e0117102. PMID: 25658585; PMCID: PMC4319719.
    19. Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014 Nov 13; 515(7526):216-21. PMID: 25363768; PMCID: PMC4313871.
    20. Dong S, Yang TL, Yan H, Rong ZQ, Chen JB, Hao RH, Chen XF, Guo Y. Association analyses of FGFR2 gene polymorphisms with femoral neck bone mineral density in Chinese Han population. Mol Genet Genomics. 2015 Apr; 290(2):485-91. PMID: 25300516.
      View in: PubMed
    21. Dong S, Walker MF, Carriero NJ, DiCola M, Willsey AJ, Ye AY, Waqar Z, Gonzalez LE, Overton JD, Frahm S, Keaney JF, Teran NA, Dea J, Mandell JD, Hus Bal V, Sullivan CA, DiLullo NM, Khalil RO, Gockley J, Yuksel Z, Sertel SM, Ercan-Sencicek AG, Gupta AR, Mane SM, Sheldon M, Brooks AI, Roeder K, Devlin B, State MW, Wei L, Sanders SJ. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep. 2014 Oct 09; 9(1):16-23. PMID: 25284784.
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    22. Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 2013 Nov 21; 155(5):997-1007. PMID: 24267886; PMCID: PMC3995413.
    23. Tang Y, Dong S, Cao X, Zhou Q, Ding G, Jiang C. H2A.Z nucleosome positioning has no impact on genetic variation in Drosophila genome. PLoS One. 2013; 8(3):e58295. PMID: 23472174; PMCID: PMC3589275.
    24. Zhou TH, Dong S, Li S, Zhao GF. Genetic structure within and among populations of Saruma henryi, an endangered plant endemic to China. Biochem Genet. 2012 Feb; 50(1-2):146-58. PMID: 22210543.
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    25. Lei SF, Shen H, Yang TL, Guo Y, Dong S, Xu XH, Deng FY, Tian Q, Liu YJ, Liu YZ, Li J, Deng HW. Genome-wide association study identifies HMGN3 locus for spine bone size variation in Chinese. Hum Genet. 2012 Mar; 131(3):463-9. PMID: 21947420; PMCID: PMC4450081.
    26. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W316-22. PMID: 21715386; PMCID: PMC3125809.
    27. Pan F, Liu XG, Guo YF, Chen Y, Dong S, Qiu C, Zhang ZX, Zhou Q, Yang TL, Guo Y, Zhu XZ, Deng HW. The regulation-of-autophagy pathway may influence Chinese stature variation: evidence from elder adults. J Hum Genet. 2010 Jul; 55(7):441-7. PMID: 20448653; PMCID: PMC2923432.
    28. Xu XH, Dong S, Guo Y, Yang TL, Lei SF, Papasian CJ, Zhao M, Deng HW. Molecular genetic studies of gene identification for osteoporosis: the 2009 update. Endocr Rev. 2010 Aug; 31(4):447-505. PMID: 20357209; PMCID: PMC3365849.
    29. Guo Y, Tan LJ, Lei SF, Yang TL, Chen XD, Zhang F, Chen Y, Pan F, Yan H, Liu X, Tian Q, Zhang ZX, Zhou Q, Qiu C, Dong S, Xu XH, Guo YF, Zhu XZ, Liu SL, Wang XL, Li X, Luo Y, Zhang LS, Li M, Wang JT, Wen T, Drees B, Hamilton J, Papasian CJ, Recker RR, Song XP, Cheng J, Deng HW. Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. PLoS Genet. 2010 Jan 08; 6(1):e1000806. PMID: 20072603; PMCID: PMC2794362.
    30. Dong S, Liu XG, Chen Y, Guo Y, Wang L, Zhao J, Xiong DH, Xu XH, Recker RR, Deng HW. Association analyses of RANKL/RANK/OPG gene polymorphisms with femoral neck compression strength index variation in Caucasians. Calcif Tissue Int. 2009 Aug; 85(2):104-12. PMID: 19458885; PMCID: PMC2916082.
    31. Sha BY, Yang TL, Zhao LJ, Chen XD, Guo Y, Chen Y, Pan F, Zhang ZX, Dong S, Xu XH, Deng HW. Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population. J Hum Genet. 2009 Apr; 54(4):199-202. PMID: 19229253.
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    32. Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, Pan F, Chen Y, Zhang ZX, Dong S, Xu XH, Yan H, Liu X, Qiu C, Zhu XZ, Chen T, Li M, Zhang H, Zhang L, Drees BM, Hamilton JJ, Papasian CJ, Recker RR, Song XP, Cheng J, Deng HW. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet. 2008 Dec; 83(6):663-74. PMID: 18992858; PMCID: PMC2667994.