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Xianjun Dong, Ph.D.

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Biography
2019 - 2020
American Parkinson's Disease Association Research Award
2019
Advanced Center for Parkinson’s Disease Research (ACEPD) Seed Award
2018
Research Excellence Award, Brigham and Women's Hospital
2018
BRI NextGen Award, Brigham Research Institute
2017 - 2018
American Parkinson's Disease Association Research Award
2010
Chinese Government Award for Outstanding Self-financed Students Abroad;
2009
MCB Travel Fellowship, University of Bergen
2002
First prize in the 2002 National Undergraduate Electronic Design Contest, China
2001
Meritorious in the international Interdisciplinary Contest in Modelling (ICM), US

Overview
Dr. Dong is an Assistant Professor at Harvard Medical School and leads the Genomics and Bioinformatics Hub at Brigham and Women's Hospital. He received his Ph.D. degree in Bioinformatics at the University of Bergen (supervisor: Boris Lenhard) and a Postdoctoral fellowship in Bioinformatics and Integrative Biology at the University of Massachusetts Medical School. He has been the Director of Computational Neuroscience Unit of the Precision Neurology Program (Director: Clemens Scherzer, MD) at Brigham and Women's Hospital since 2013, 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 the 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 12,000+ citations and an H-index of 21. 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 of 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). See his website for more details: http://www.sterding.com.

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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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. Dong X, Liao Z, Gritsch D, Hadzhiev Y, Bai Y, Locascio JJ, Guennewig B, Liu G, Blauwendraat C, Wang T, Adler CH, Hedreen JC, Faull RLM, Frosch MP, Nelson PT, Rizzu P, Cooper AA, Heutink P, Beach TG, Mattick JS, Müller F, Scherzer CR. Publisher Correction: Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. Nat Neurosci. 2019 Jan; 22(1):144-147. PMID: 30482917.
    Citations:    Fields:    
  2. Dong X, Liao Z, Gritsch D, Hadzhiev Y, Bai Y, Locascio JJ, Guennewig B, Liu G, Blauwendraat C, Wang T, Adler CH, Hedreen JC, Faull RLM, Frosch MP, Nelson PT, Rizzu P, Cooper AA, Heutink P, Beach TG, Mattick JS, Müller F, Scherzer CR. Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. Nat Neurosci. 2018 10; 21(10):1482-1492. PMID: 30224808.
    Citations:    Fields:    
  3. 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.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  4. 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.
    Citations: 11     Fields:    Translation:HumansCells
  5. 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.
    Citations: 16     Fields:    Translation:Humans
  6. 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.
    Citations: 15     Fields:    Translation:HumansCells
  7. 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.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  8. 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.
    Citations: 38     Fields:    Translation:HumansAnimalsCells
  9. Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 2013 Apr; 5(2):113-6. PMID: 23566087.
    Citations: 12     Fields:    Translation:HumansCells
  10. 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.
    Citations: 82     Fields:    Translation:AnimalsCells
  11. 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.
    Citations: 92     Fields:    Translation:HumansCells
  12. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
    Citations: 3893     Fields:    Translation:HumansAnimalsCells
  13. 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.
    Citations: 270     Fields:    Translation:HumansCells
  14. 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.
    Citations: 75     Fields:    Translation:HumansCells
  15. 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.
    Citations: 90     Fields:    Translation:HumansCells
  16. Fredman D, Dong X, Lenhard B. Making enhancers from spare parts of the genome. Genome Biol. 2011 Dec 29; 12(12):138. PMID: 22206586.
    Citations:    Fields:    Translation:HumansAnimalsCells
  17. 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.
    Citations: 186     Fields:    Translation:HumansAnimalsCells
  18. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
    Citations: 591     Fields:    Translation:HumansCells
  19. 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.
    Citations:    Fields:    Translation:Cells
  20. 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.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  21. 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.
    Citations: 12     Fields:    Translation:Animals
  22. 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.
    Citations: 35     Fields:    Translation:HumansCells
  23. 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.
    Citations: 23     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.