HeX Lab:Publications
From OpenWetWare
Jump to navigationJump to search
HeX Laboratory
Tongji Medical College(TJMC),HUST
Peer-Reviewed Journals (*first authorship, ^Corresponding authorship);
2017
- 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 - Han Y, He X., (2016) Integrating Epigenomics into the Understanding of Biomedical Insight.
Bioinform Biol Insights. 10:267-289 - 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. - 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. - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - Wang J.*, Xia Q.*, He X.* et al., (2005) SilkDB: a knowledgebase for silkworm biology and genomics,
Nucleic Acids Res., 33:D399-402 - Wang J.*, He X.* et al., (2005) ChickVD: a sequence variation database for the chicken genome,
Nucleic Acids Res., 33:D438-41 - 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 - 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 - 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 - 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
- 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