Shan Dong, PhD

Title(s)Postdoctoral Scholar, Psychiatry
SchoolSchool of Medicine
Address401 Parnassus Ave.
San Francisco CA 94143
Phone415-502-2505
ORCID ORCID Icon0000-0001-9130-0225 Additional info
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Brief Bioinform. 2021 Jul 20; 22(4). Dong SS, He WM, Ji JJ, Zhang C, Guo Y, Yang TL. PMID: 33126247.
      View in: PubMed   Mentions: 5     Fields:    
    2. Exome sequencing of fetuses with congenital diaphragmatic hernia supports a causal role for NR2F2, PTPN11, and WT1 variants. Am J Surg. 2021 Jul 20. Schwab ME, Dong S, Lianoglou BR, Aguilar Lucero AF, Schwartz GB, Norton ME, MacKenzie TC, Sanders SJ. PMID: 34315577.
      View in: PubMed   Mentions:
    3. DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment. Comput Struct Biotechnol J. 2021; 19:3650-3657. Rong Y, Dong SS, Hu WX, Guo Y, Chen YX, Chen JB, Zhu DL, Chen H, Yang TL. PMID: 34257842.
      View in: PubMed   Mentions:
    4. An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression. Diabetes. 2021 May 25. Dong SS, Zhu DL, Zhou XR, Rong Y, Zeng M, Chen JB, Jiang F, Tuo XM, Feng Z, Yang TL, Guo Y. PMID: 34035043.
      View in: PubMed   Mentions:    Fields:    
    5. Prenatal exposure to paternal smoking and likelihood for autism spectrum disorder. Autism. 2021 Apr 20; 13623613211007319. Kim B, Ha M, Kim YS, Koh YJ, Dong S, Kwon HJ, Kim YS, Lim MH, Paik KC, Yoo SJ, Kim H, Hong PS, Sanders SJ, Leventhal BL. PMID: 33878952.
      View in: PubMed   Mentions:    Fields:    
    6. Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study. Genome Med. 2021 Mar 26; 13(1):48. Dong SS, Zhang K, Guo Y, Ding JM, Rong Y, Feng JC, Yao S, Hao RH, Jiang F, Chen JB, Wu H, Chen XF, Yang TL. PMID: 33771188.
      View in: PubMed   Mentions: 1     Fields:    
    7. Transcriptome-wide association study identifies multiple genes associated with childhood body mass index. Int J Obes (Lond). 2021 May; 45(5):1105-1113. Yao S, Wu H, Ding JM, Wang ZX, Ullah T, Dong SS, Chen H, Guo Y. PMID: 33627773.
      View in: PubMed   Mentions:    Fields:    
    8. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput Struct Biotechnol J. 2020; 18:2826-2835. Chen YX, Rong Y, Jiang F, Chen JB, Duan YY, Dong SS, Zhu DL, Chen H, Yang TL, Dai Z, Guo Y. PMID: 33133424.
      View in: PubMed   Mentions:
    9. Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. Bioinformatics. 2020 09 15; 36(18):4739-4748. Chen JB, Dong SS, Yao S, Duan YY, Hu WX, Chen H, Wang NN, Chen XF, Hao RH, Thynn HN, Guo MR, Zhang YJ, Rong Y, Chen YX, Zhou FL, Guo Y, Yang TL. PMID: 32539144.
      View in: PubMed   Mentions:    Fields:    
    10. Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs. JCI Insight. 2020 09 03; 5(17). Chen XF, Guo MR, Duan YY, Jiang F, Wu H, Dong SS, Zhou XR, Thynn HN, Liu CC, Zhang L, Guo Y, Yang TL. PMID: 32879140.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    11. RTN4B-mediated suppression of Sirtuin 2 activity ameliorates ß-amyloid pathology and cognitive impairment in Alzheimer's disease mouse model. Aging Cell. 2020 08; 19(8):e13194. Wang Y, Yang JQ, Hong TT, Sun YH, Huang HL, Chen F, Chen XJ, Chen HY, Dong SS, Cui LL, Yang TL. PMID: 32700357.
      View in: PubMed   Mentions: 4     Fields:    
    12. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. Cell Rep. 2020 04 07; 31(1):107489. Werling DM, Pochareddy S, Choi J, An JY, Sheppard B, Peng M, Li Z, Dastmalchi C, Santpere G, Sousa AMM, Tebbenkamp ATN, Kaur N, Gulden FO, Breen MS, Liang L, Gilson MC, Zhao X, Dong S, Klei L, Cicek AE, Buxbaum JD, Adle-Biassette H, Thomas JL, Aldinger KA, O'Day DR, Glass IA, Zaitlen NA, Talkowski ME, Roeder K, State MW, Devlin B, Sanders SJ, Sestan N. PMID: 32268104.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    13. Transcription Factor Enrichment Analysis in Enhancers Identifies EZH2 as a Susceptibility Gene for Osteoporosis. J Clin Endocrinol Metab. 2020 04 01; 105(4). Li M, Yao S, Duan YY, Zhang YJ, Guo Y, Niu HM, Dong SS, Qiu YS, Yang TL. PMID: 31833556.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. The hornwort genome and early land plant evolution. Nat Plants. 2020 02; 6(2):107-118. Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. PMID: 32042158.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    15. A road map for understanding molecular and genetic determinants of osteoporosis. Nat Rev Endocrinol. 2020 02; 16(2):91-103. Yang TL, Shen H, Liu A, Dong SS, Zhang L, Deng FY, Zhao Q, Deng HW. PMID: 31792439.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    16. An Allele-Specific Functional SNP Associated with Two Systemic Autoimmune Diseases Modulates IRF5 Expression by Long-Range Chromatin Loop Formation. J Invest Dermatol. 2020 02; 140(2):348-360.e11. Thynn HN, Chen XF, Hu WX, Duan YY, Zhu DL, Chen H, Wang NN, Chen HH, Rong Y, Lu BJ, Yang M, Jiang F, Dong SS, Guo Y, Yang TL. PMID: 31421124.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    17. Sex-specific SNP-SNP interaction analyses within topologically associated domains reveals ANGPT1 as a novel tumor suppressor gene for lung cancer. Genes Chromosomes Cancer. 2019 Aug 05. Yao S, Dong SS, Ding JM, Rong Y, Zhang YJ, Chen H, Chen JB, Chen YX, Yan H, Dai Z, Guo Y. PMID: 31385379.
      View in: PubMed   Mentions: 5     Fields:    
    18. Addressing the Missing Heritability Problem With the Help of Regulatory Features. Evol Bioinform Online. 2019; 15:1176934319860861. Dong SS, Guo Y, Yang TL. PMID: 31320792.
      View in: PubMed   Mentions:
    19. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019 05 15; 35(10):1786-1788. Zhang C, Dong SS, Xu JY, He WM, Yang TL. PMID: 30321304.
      View in: PubMed   Mentions: 86     Fields:    
    20. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. Transl Psychiatry. 2019 01 31; 9(1):56. Niu HM, Yang P, Chen HH, Hao RH, Dong SS, Yao S, Chen XF, Yan H, Zhang YJ, Chen YX, Jiang F, Yang TL, Guo Y. PMID: 30705251.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    21. Integrating regulatory features data for prediction of functional disease-associated SNPs. Brief Bioinform. 2019 01 18; 20(1):26-32. Dong SS, Guo Y, Yao S, Chen YX, He MN, Zhang YJ, Chen XF, Chen JB, Yang TL. PMID: 28968709.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    22. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science. 2018 12 14; 362(6420). An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ. PMID: 30545852.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    23. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Rep. 2018 09 25; 24(13):3441-3454.e12. Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Tourette International Collaborative Genetics Study (TIC Genetics) , Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE) , Tourette Association of America International Consortium for Genetics (TAAICG) , Fernandez TV, Buxbaum JD, De Rubeis S, Grice DE, Xing J, Heiman GA, Tischfield JA, Paschou P, Willsey AJ, State MW. PMID: 30257206.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    24. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet. 2018 04 26; 50(5):727-736. 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. PMID: 29700473.
      View in: PubMed   Mentions: 57     Fields:    Translation:Humans
    25. Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci. 2017 12; 20(12):1661-1668. Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Whole Genome Sequencing for Psychiatric Disorders (WGSPD) , 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. PMID: 29184211.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    26. De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron. 2017 May 03; 94(3):486-499.e9. 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, Tourette International Collaborative Genetics (TIC Genetics) , Tourette Syndrome Association International Consortium for Genetics (TSAICG) , Neale BM, Coppola G, Mathews CA, Tischfield JA, Scharf JM, State MW, Heiman GA. PMID: 28472652.
      View in: PubMed   Mentions: 42     Fields:    Translation:Humans
    27. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron. 2015 Sep 23; 87(6):1215-1233. 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, Autism Sequencing Consortium , Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW. PMID: 26402605.
      View in: PubMed   Mentions: 408     Fields:    Translation:Humans
    28. The female protective effect in autism spectrum disorder is not mediated by a single genetic locus. Mol Autism. 2015; 6:25. Gockley J, Willsey AJ, Dong S, Dougherty JD, Constantino JN, Sanders SJ. PMID: 25973162.
      View in: PubMed   Mentions: 22     Fields:    
    29. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014 Nov 13; 515(7526):216-21. 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. PMID: 25363768.
      View in: PubMed   Mentions: 790     Fields:    Translation:Humans
    30. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep. 2014 Oct 09; 9(1):16-23. 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. PMID: 25284784.
      View in: PubMed   Mentions: 62     Fields:    Translation:Humans
    31. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 2013 Nov 21; 155(5):997-1007. 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. PMID: 24267886.
      View in: PubMed   Mentions: 328     Fields:    Translation:HumansAnimalsCells
    32. H2A.Z nucleosome positioning has no impact on genetic variation in Drosophila genome. PLoS One. 2013; 8(3):e58295. Tang Y, Dong S, Cao X, Zhou Q, Ding G, Jiang C. PMID: 23472174.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    33. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 2011 Nov 21; 12(11):R114. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, Jing HC. PMID: 22104744.
      View in: PubMed   Mentions: 104     Fields:    Translation:AnimalsCells
    34. 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. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L. PMID: 21715386.
      View in: PubMed   Mentions: 1033     Fields:    Translation:HumansCells
    35. Molecular genetic studies of gene identification for osteoporosis. Expert Rev Endocrinol Metab. 2008 Mar; 3(2):223-267. Guo Y, Yang TL, Pan F, Xu XH, Dong SS, Deng HW. PMID: 30764094.
      View in: PubMed   Mentions: 1     Fields: