Job title: Professor of Epigenomics

Phone: (+86) 158-2757-8535

Email: XimiaoHe@hust.edu.cn

Academic Areas: Epigenomics and Bioinformatics, Precision Medicine

Research Interests: DNA methylation, Nucleosome, Bioinformatics, Precision Medicine

Our interests lie in genomics and bioinformatics, especially in investigation on the regulation of gene expression from a large amount of genomic, epigenomic, and transcriptomic data using bioinformatic approach; and identification of the role of gene regulation in developmental disorders and diseases. The long-term goal is to identify the correlation of the genomic and epigenomic information with development and disease (especially cancer) and to translate the findings into prognosis, diagnosis and clinical treatment. 

Please also visit our lab at: http://www.openwetware.org/wiki/Hexlab

Academic Degrees

 

  • 2009, PhD in Genomics and Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
  • 2002, BS in Medical Informatics, TJMC, HUST, Wuhan, China

 

Professional Experience

 

  • 09/2016 - present
  • Professor, Tongji Medical College (TJMC), HUST 
  • Director, Centre for Genomic & Proteomic Research, School of Basic Science, TJMC, HUST, Wuhan, China
  • 10/2014 - 09/2016 Research Fellow, National Cancer Institute, NIH, Bethesda, MD 20892
  • 10/2009 - 09/2014 Postdoctoral Visiting Fellow, National Cancer Institute, NIH, Bethesda, MD 20892
  • 07/2006 - 07/2009 Research Assistant, Beijing Institute of Genomics, CAS, Beijing, China
  • 07/2002 - 09/2005 Programmer & Database Group Leader, Bioinformatics Department, Beijing Genomics Institute (BGI), Beijing, China
  • 01/2002 - 06/2002 Research Assistant, Statistics Information Center, Ministry of Health, Beijing, China

Selected Publications

Peer-Reviewed Journals (*first authorship, ^Corresponding authorship); 
 

2017 
 

  1. You L*, Xie R*, Hu H, Gu G, Zheng H, Zhang J, Yang X, He X.^, Cui W^, (2017) High levels of serum β2-microglobulin predict severity of coronary artery disease. 
    BMC Cardiovasc Disord 17(1):71. doi: 10.1186/s12872-017-0502-9 

    2016 

     
  2. Han Y, He X., (2016) Integrating Epigenomics into the Understanding of Biomedical Insight. 
    Bioinform Biol Insights. 10:267-289

     
  3. Syed KS, He X., Tillo D, Wang J, Durell SR, Vinson C., (2016) 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA.
    Biochemistry. 55(49):6940-6948. 

     
  4. Qian Z, Trostel A, Lewis DE, Lee SJ, He X., Stringer AM, Wade JT, Schneider TD, Durfee T, Adhya S.(2016) Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli. 
    Front Mol Biosci. 3:74. 

     
  5. Khund-Sayeed S, He X., Holzberg T, Wang J, Rajagopal D, Upadhyay S, Durell SR, Mukherjee S, Weirauch MT, Rose R, Vinson C. (2016) 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.
    Integr Biol (Camb). 8(9):936-45. doi: 10.1039/c6ib00079g. 

    2015 

     
  6. He X., Tillo D., Vierstra J., Syed K.S., Deng C., Ray G., Stamatoyannopoulos J., Fitzgerald P., Vinson C.^, (2015) Methylated cytosines mutate to transcription factor binding sites that drive tetrapod evolution. 
    Genome Biology and Evolution 7(11):3155-69 

     
  7. Qian Z, Macvanin M, Dimitriadis EK, He X., Zhurkin V, Adhya S^, (2015) A new noncoding RNA arranges bacterial chromosome organization. 
    mBio 6(4):e00998-15 

     
  8. He X., Syed KS, Tillo D., Mann I., Weirauch M.T.^, Vinson C.^, (2015) GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays. 
    G3 (Bethesda), 5:1909-1918 

    2014 

     
  9. He X.*, Chatterjee R.*, Tillo D., Smith A., FitzGerald P., Vinson C.^, (2014) Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes. 
    Epigenetics & Chromatin 7:34 

     
  10. Chatterjee R.*, He X.*, Huang D., Smith A., FitzGerald P., Vinson C.^, (2014) High resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes. 
    Epigenetics & Chromatin 7:35 

    2013 

     
  11. Deng C.*, He X.*, Hsueh AJ.^, (2013) A single-nucleotide polymorphism of human neuropeptides gene originated from Europe shows decreased bioactivity. 
    PLoS One 8:12 e83009

     
  12. He X.*, Chatterjee R., John S., Bravo H., Sathyanarayana B., Biddie S.C., FitzGerald P.C., Stamatoyannopoulos J.A., Hager G.L., and Vinson C.A.^, (2013) Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding 
    BMC Genomics 14:428

     
  13. Mann I.*, Chatterjee R.*, Zhao J.*, He X.*, Weirauch M., Hughes T.^, Vinson C.^, (2013) CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo, 
    Genome Research 23:6 988-97

     
  14. Caravaca JM, Donahue G, Becker JS, He X., Vinson C, Zaret KS.^, (2013):Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes, 
    Genes Dev., 27251-60

    2012 

     
  15. Chatterjee R., Zhao J., He X., Shlyakhtenko A., Mann I., Waterfall J., Meltzer P., Sathyanarayana B.K., FitzGerald P.C., Vinson C., Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins 
    G3 (Bethesda), 2(2012):1243-56

    2011 

     
  16. Yang L.*, Zhang K.*, Dai W., He X.., Zhao Q., Wang J.^, Sun ZS.^, (2011)Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array 
    BMC Genomics 12:10

    2010 and Before 

     
  17. He X.*, Tao S.*, Jin J., Hu S.^, Yu J.^, (2010) The most redundant sequences in human CpG islands library are derived from mitochondrial genome 
    Genomics, Proteomics & Bioinformatics (GPB) 8:2 81-91

     
  18. Deng C., Cheng C., Ye H., He X., Chen L.^, (2010) Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict, 
    Proc Natl Acad Sci USA 107:50 21593–21598

     
  19. He X.*, Chang S.*, Zhang J.*, Zhao Q*. et al., (2008) MethyCancer: the database of human DNA methylation and cancer, 
    Nucleic Acids Res., 36:D836-41

     
  20. Wang J.*, Xia Q.*, He X.* et al., (2005) SilkDB: a knowledgebase for silkworm biology and genomics, 
    Nucleic Acids Res., 33:D399-402

     
  21. Wang J.*, He X.* et al., (2005) ChickVD: a sequence variation database for the chicken genome, 
    Nucleic Acids Res., 33:D438-41

     
  22. Yu J.*, Wang J.*, Lin W.*, Li S.*, Li H.*, Zhou J.*, Ni P.*,…He X.,…Yang H.^, (2005) The Genomes of Oryza sativa: A History of Duplications, 
    PLoS Biology 3:2 0001-0016

     
  23. Zhao W.*, Wang J.*, He X.*, Huang X*. et al., (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics, 
    Nucleic Acids Res., 32:D377-82

     
  24. Wong, G.K.*, Liu, B.*, Wang J.*, Zhang Y.*, Yang X.*,…He X.,…Yang H.^, (2004) A genetic variation map for chicken with2.8 million single-nucleotide polymorphisms, 
    Nature 432:717-722

     
  25. Wu Q.*, Zhang Y.*, Lu H.*, Wang J.*, He X., et al., (2003) The E Protein Is a Multifunctional Membrane Protein of SARS-CoV, 
    Genomics, Proteomics & Bioinformatics (GPB) 1:2 131-144

     

Book Chapter
 

  1. He X., Wang J., (2007) BGI-RIS V2: Rice Information System at the Beijing Genomics Institute. – Chapter 13 in: Methods in Molecular Biology, vol. 406: 
    Plant Bioinformatics: methods and protocols (Edwards, David ed.) Humana Press Inc., Totawa, NJ. Pp275-300

 

Project

1000 Talents Program for Young Scholars, 2017

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