HeX Lab:Publications

HeX Laboratory

Tongji Medical College(TJMC),HUST

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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