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Xianjun Dong, Ph.D.

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Biography
2010
Chinese Government Award for Outstanding Self-financed Students Abroad;
2000
Liu Yonglin Fellowship, Southeast University
2000
2nd prize in the National Undergraduate Mathematical Contest in Modelling
2000
Honour Student, Southeast University
2001
1st prize (Meritorious) in the international Interdisciplinary Contest in Modelling
2002
Honour Graduate, Southeast University
2002
1st prize in the 2002 National Undergraduate Electronic Design Contest;
2009
Scholarship for “Chromatin Domains and Insulators” workshop
2009
MCB Travel Fellowship, University of Bergen

Overview
Dr. Dong received his Ph.D. degree in Bioinformatics in University of Bergen (supervisor: Boris Lenhard) and a Postdoctoral fellowship in Bioinformatics and Integrative Biology in University of Massachusetts Medical School. Dr. Dong is now an Instructor in Harvard Medical School and acts as the Director of Computational Neuroscience Unit of the Precision Neurology Program in Harvard-affiliated Brigham and Women's Hospital in Boston, leading the Bioinformatics team working on neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease etc. He is interested in developing and applying computational methods to understand transcriptional regulation of the human genome, by integrating genomic, transcriptomic, epigenetic, and clinical data from both healthy subjects and patients with neurological diseases. Dr. Dong has 20+ publications with 9000+ citations and H-index of 19. He has made several web-based tools to facilitate the research of long-range gene regulation. He has expertise in analyzing various NGS data, incl. ChIPseq, RNAseq, RNA-PET, CAGE, and WGS data. He was an active member in the ENCODE consortium. He is particularly interested in the non-coding RNAs (miRNA, eRNA, circRNA etc.) in the brain. Dr. Dong is recently awarded by the American Parkinson Disease Association (APDA). He is also running a weekly Bioinformatics Club in BWH. See his website for more details: http://www.sterding.com.

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Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Mittal S, Bjørnevik K, Im DS, Flierl A, Dong X, Locascio JJ, Abo KM, Long E, Jin M, Xu B, Xiang YK, Rochet JC, Engeland A, Rizzu P, Heutink P, Bartels T, Selkoe DJ, Caldarone BJ, Glicksman MA, Khurana V, Schüle B, Park DS, Riise T, Scherzer CR. ß2-Adrenoreceptor is a regulator of the a-synuclein gene driving risk of Parkinson's disease. Science. 2017 09 01; 357(6354):891-898. PMID: 28860381.
    View in: PubMed
  2. Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PLoS One. 2015; 10(12):e0144398. PMID: 26636336; PMCID: PMC4670094.
  3. Locascio JJ, Eberly S, Liao Z, Liu G, Hoesing AN, Duong K, Trisini-Lipsanopoulos A, Dhima K, Hung AY, Flaherty AW, Schwarzschild MA, Hayes MT, Wills AM, Shivraj Sohur U, Mejia NI, Selkoe DJ, Oakes D, Shoulson I, Dong X, Marek K, Zheng B, Ivinson A, Hyman BT, Growdon JH, Sudarsky LR, Schlossmacher MG, Ravina B, Scherzer CR. Association between a-synuclein blood transcripts and early, neuroimaging-supported Parkinson's disease. Brain. 2015 Sep; 138(Pt 9):2659-71. PMID: 26220939; PMCID: PMC4643625.
  4. Bai G, Cheung I, Shulha HP, Coelho JE, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers RH, Weng Z, Akbarian S, Chen JF. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Hum Mol Genet. 2015 Mar 01; 24(5):1441-56. PMID: 25480889; PMCID: PMC4321450.
  5. Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, Macdonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. PLoS Genet. 2014 Feb; 10(2):e1004188. PMID: 24586208; PMCID: PMC3937267.
  6. Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WFJ, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 2014 Mar 20; 507(7492):381-385. PMID: 24531765; PMCID: PMC4820030.
  7. Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 2013 Apr; 5(2):113-6. PMID: 23566087; PMCID: PMC4230708.
  8. Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell. 2013 Apr 11; 50(1):67-81. PMID: 23523368; PMCID: PMC3671569.
  9. Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan; 41(Database issue):D171-6. PMID: 23203885; PMCID: PMC3531197.
  10. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
    View in: PubMed
  11. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep; 22(9):1798-812. PMID: 22955990; PMCID: PMC3431495.
  12. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep; 22(9):1658-67. PMID: 22955978; PMCID: PMC3431483.
  13. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Jun 13; 13(9):R53. PMID: 22950368; PMCID: PMC3491397.
  14. Fredman D, Dong X, Lenhard B. Making enhancers from spare parts of the genome. Genome Biol. 2011 Dec 29; 12(12):138. PMID: 22206586; PMCID: PMC3334608.
  15. Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 2011 Dec 23; 147(7):1498-510. PMID: 22196727; PMCID: PMC3252821.
  16. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
    View in: PubMed
  17. Dong X, Akalin A, Sharma Y, Lenhard B. Translog, a web browser for studying the expression divergence of homologous genes. BMC Bioinformatics. 2010 Jan 18; 11 Suppl 1:S59. PMID: 20122234; PMCID: PMC3009532.
  18. Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res. 2010 Mar; 38(4):1071-85. PMID: 19969543; PMCID: PMC2831330.
  19. Dong X, Fredman D, Lenhard B. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 2009; 10(8):R86. PMID: 19698106; PMCID: PMC2745767.
  20. Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B. Transcriptional features of genomic regulatory blocks. Genome Biol. 2009; 10(4):R38. PMID: 19374772; PMCID: PMC2688929.
  21. Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A, Chourrout D. Differential evolution of the 13 Atlantic salmon Hox clusters. Mol Biol Evol. 2008 Jul; 25(7):1333-43. PMID: 18424774.
    View in: PubMed
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