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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. Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. Bioinformatics. 2020 Jun 15. 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:    
    2. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. Cell Rep. 2020 Apr 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:    Fields:    
    3. 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: 1     Fields:    
    4. 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:    Fields:    Translation:Humans
    5. An Allele-Specific Functional SNP Associated with Two Systemic Autoimmune Diseases Modulates IRF5 Expression by Long-Range Chromatin Loop Formation. J Invest Dermatol. 2020 Feb; 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: 1     Fields:    
    6. 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: 1     Fields:    
    7. 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:
    8. 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: 5     Fields:    
    9. 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:    Fields:    Translation:HumansCells
    10. 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:    Fields:    Translation:HumansCells
    11. 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: 14     Fields:    Translation:HumansCells
    12. 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, 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: 4     Fields:    Translation:Humans
    13. 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: 15     Fields:    Translation:Humans
    14. 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, 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: 7     Fields:    Translation:Humans
    15. 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, Neale BM, Coppola G, Mathews CA, Tischfield JA, Scharf JM, State MW, Heiman GA. PMID: 28472652.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    16. 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, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW. PMID: 26402605.
      View in: PubMed   Mentions: 212     Fields:    Translation:Humans
    17. 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: 16     Fields:    
    18. 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: 499     Fields:    Translation:Humans
    19. 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: 47     Fields:    Translation:Humans
    20. 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: 234     Fields:    Translation:HumansAnimalsCells
    21. 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
    22. 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: 514     Fields:    Translation:HumansCells
    23. 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:    
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