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profileXianjun Dong, Ph.D.

TitleInstructor in Neurology
InstitutionBrigham and Women's Hospital
DepartmentNeurology
AddressBrigham and Women
Neurology
60 Fenwood Rd
Boston MA 02115
Phone857/307-5423
Fax857/307-5476
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Collapse Biography 
Collapse awards and honors
2010Chinese Government Award for Outstanding Self-financed Students Abroad;
2000Liu Yonglin Fellowship, Southeast University
20002nd prize in the National Undergraduate Mathematical Contest in Modelling
2000Honour Student, Southeast University
20011st prize (Meritorious) in the international Interdisciplinary Contest in Modelling
2002Honour Graduate, Southeast University
20021st prize in the 2002 National Undergraduate Electronic Design Contest;
2009Scholarship for “Chromatin Domains and Insulators” workshop
2009MCB Travel Fellowship, University of Bergen

Collapse Overview 
Collapse overview
Dr. Dong is a computational biologist with more than 10 years of research experience. His research interests include developing and applying computational algorithms to integrate and analyze genomics and next-generation sequencing (NGS) data in order to provide better understanding of molecular mechanisms and biological processes that underlie development and diseases. Before his PhD, he was trained in Biomedical Engineering in both Bachelor and Master. He took his PhD with Dr. Lenhard Boris by studying transcriptional gene regulation in vertebrate genomes. He discovered a list of novel regulatory elements (i.e. enhancers) coupled in coding exons, by using the methods of comparative genomics and epigenomics. Later he did a postdoctoral research with Prof. Weng Zhiping in UMass Medical School, where he has exclusively involved in the scale-up phase of the ENCODE Project, specifically by modeling gene expression with various genomic and epigenomics features (e.g. H3K4me3, H3K36, H3K79 etc.) in various cellular context. He has also had fun in the world of small RNA, esp. piRNA and miRNA, in studying their roles in development and in neuronal disease. Recently he moved to Brigham and Women's Hospital and Harvard Medical School and worked as a bioinformatics lead in Dr. Scherzer Clemens's neurogenomics lab. The main interest of Dr. Dong's research is to understand both the structure and the function of brain genome of patients with Parkinson's disease, by analyzing NGS data like RNA-seq, genotyping, genome sequencing etc..


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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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 2013 Apr; 5(2):113-6. PMID: 23566087; PMCID: PMC4230708.
  7. 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.
  8. 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.
  9. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222; PMCID: PMC3079585.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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