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Xianjun Dong, Ph.D.

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Biography
awards and honors
2021 - 2022
American Parkinson's Disease Association Research Award
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
overview
Xianjun Dong is an Assistant Professor in the Department of Neurology at Harvard Medical School, a Faculty member of the HMS Initiative for RNA Medicine, and an Associate Member of the Broad Institute. Since 2020, Dr. Dong has been appointed to direct this Genomics and Bioinformatics Hub at Brigham and Women’s Hospital (BWH) and also run his own research lab as an independent PI. Before taking this position, Dr. Dong has been serving as the Director of the Computational Neuroscience Unit of the Precision Neurology Program at BWH and an Instructor at Harvard Medical School for 7 years. He specialized 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. He is particularly interested in the non-coding RNAs (eRNA, circRNA, miRNA, etc.) in the human brain. He has expertise in analyzing various NGS data, incl. ChIPseq, RNAseq, RNA-PET, CAGE, and WGS data.

Dr. Dong received his PhD 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 (supervisor: Zhiping Weng). He was an active member of the ENCODE consortium. He has 40+ publications with 20,000+ citations and an H-index of 24. He is recently awarded by the American Parkinson’s Disease Association (APDA), Aligning Science Across Parkinson’s (ASAP), and NIH (two R01, U01, R41, U19). In his spare time, he raises three kids and 15 chickens. See his website for more details: http://sterding.github.io.
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webpage

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. U19 1U19NS130617 (Dong) Dec 1, 2022 - Nov 30, 2027
    NIH
    Human PRECISION Human Pain Center - Data Core
    Role Description: The goal of this core is to act as a data center for large-scale multiomics datasets generated by the U19 Center by building infrastructure, providing data management, coordination, analysis and sharing.
    Role: PI
  2. R01 AG078948-01 (Dong, Sun) Jul 1, 2022 - Jun 30, 2027
    NIH/NINDS
    Regulation mechanism and functional genomics of LINE1 RNA in TDP-43 linked neurodegeneration
    Role Description: The goal of this project is to study the regulation mechanism and functional genomics of LINE1 RNA in TDP-43 linked neurodegeneration.
    Role: PI
  3. R01 NS124916-01 (Lee, Dong) Dec 1, 2021 - Nov 30, 2026
    NIH/NINDS
    Systematic study of extracellular vesicles and their integrative analysis with Parkinson's organoids MAP
    Role Description: The goal of this study is to develop a new 3D mini-brain microphysiological analysis platform (MAP) to recapitulate the dopamine neurons’ interconnectivity and study molecular neurodegeneration systematically.
    Role: PI
  4. R41AG076098 (CHEN, YUCHAO) Sep 30, 2021 - Mar 29, 2022
    NIH
    EXODUS-enabled High-throughput Multi-omics Profiling of Extracellular Vesicles for Diagnosis of Preclinical Alzheimer's Disease
    Role Description: The goal is to develop a collaborative hub providing genomics and bioinformatics service hub to the Neurology research community at Brigham and Women’s Hospital.
    Role: PI
  5. (Xianjun Dong) Sep 1, 2021 - Aug 31, 2021
    APDA
    Developing RNA biomarkers of early PD pathology from brain organoids and extracellular vesicles
    Role: PI

Bibliographic
selected publications
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, Liu C, Dozmorov M. Review of multi-omics data resources and integrative analysis for human brain disorders. Brief Funct Genomics. 2021 07 17; 20(4):223-234. PMID: 33969380; PMCID: PMC8287916.
    Citations: 6     Fields:    Translation:HumansCells
  2. Dong X, Li X, Chang TW, Scherzer CR, Weiss ST, Qiu W. powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. Bioinformatics. 2021 May 19. PMID: 34009297; PMCID: PMC9492284.
    Citations: 7     Fields:    
  3. Iwaki H, Leonard HL, Makarious MB, Bookman M, Landin B, Vismer D, Casey B, Gibbs JR, Hernandez DG, Blauwendraat C, Vitale D, Song Y, Kumar D, Dalgard CL, Sadeghi M, Dong X, Misquitta L, Scholz SW, Scherzer CR, Nalls MA, Biswas S, Singleton AB. Accelerating Medicines Partnership: Parkinson's Disease. Genetic Resource. Mov Disord. 2021 08; 36(8):1795-1804. PMID: 33960523; PMCID: PMC8453903.
    Citations: 11     Fields:    Translation:Humans
  4. Liu G, Peng J, Liao Z, Locascio JJ, Corvol JC, Zhu F, Dong X, Maple-Grødem J, Campbell MC, Elbaz A, Lesage S, Brice A, Mangone G, Growdon JH, Hung AY, Schwarzschild MA, Hayes MT, Wills AM, Herrington TM, Ravina B, Shoulson I, Taba P, Kõks S, Beach TG, Cormier-Dequaire F, Alves G, Tysnes OB, Perlmutter JS, Heutink P, Amr SS, van Hilten JJ, Kasten M, Mollenhauer B, Trenkwalder C, Klein C, Barker RA, Williams-Gray CH, Marinus J, Scherzer CR. Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson's disease. Nat Genet. 2021 06; 53(6):787-793. PMID: 33958783; PMCID: PMC8459648.
    Citations: 24     Fields:    Translation:HumansCells
  5. Li C, Ou R, Chen Y, Gu X, Wei Q, Cao B, Zhang L, Hou Y, Liu K, Chen X, Song W, Zhao B, Wu Y, Li T, Dong X, Shang H. Genetic Modifiers of Age at Onset for Parkinson's Disease in Asians: A Genome-Wide Association Study. Mov Disord. 2021 09; 36(9):2077-2084. PMID: 33884653.
    Citations: 2     Fields:    Translation:Humans
  6. Chen Y, Zhu Q, Cheng L, Wang Y, Li M, Yang Q, Hu L, Lou D, Li J, Dong X, Lee LP, Liu F. Exosome detection via the ultrafast-isolation system: EXODUS. Nat Methods. 2021 02; 18(2):212-218. PMID: 33432243.
    Citations: 42     Fields:    Translation:HumansCells
  7. Tsuji J, Thomson T, Chan E, Brown CK, Oppenheimer J, Bigelow C, Dong X, Theurkauf WE, Weng Z, Schwartz LM. High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. Physiol Genomics. 2020 10 01; 52(10):492-511. PMID: 32926651.
    Citations: 2     Fields:    Translation:AnimalsCells
  8. 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:    
  9. 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; PMCID: PMC6334654.
    Citations: 34     Fields:    Translation:HumansAnimalsCells
  10. 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: 155     Fields:    Translation:HumansAnimalsCells
  11. 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.
    Citations: 24     Fields:    Translation:HumansCells
  12. 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.
    Citations: 42     Fields:    Translation:Humans
  13. 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.
    Citations: 34     Fields:    Translation:HumansCells
  14. 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: 56     Fields:    Translation:HumansAnimalsCells
  15. 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.
    Citations: 84     Fields:    Translation:HumansAnimalsCells
  16. Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 2013 Apr; 5(2):113-6. PMID: 23566087.
    Citations: 49     Fields:    Translation:HumansCells
  17. 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.
    Citations: 173     Fields:    Translation:AnimalsCells
  18. 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: 176     Fields:    Translation:HumansCells
  19. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
    Citations: 7598     Fields:    Translation:HumansAnimalsCells
  20. 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: 478     Fields:    Translation:HumansCells
  21. 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: 99     Fields:    Translation:HumansCells
  22. 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: 122     Fields:    Translation:HumansCells
  23. 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
  24. 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: 258     Fields:    Translation:HumansAnimalsCells
  25. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
    Citations: 755     Fields:    Translation:HumansCells
  26. 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
  27. 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: 29     Fields:    Translation:HumansAnimalsCells
  28. 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: 15     Fields:    Translation:Animals
  29. 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: 50     Fields:    Translation:HumansCells
  30. 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: 34     Fields:    Translation:AnimalsCells
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