User:Ximiao He

I am a new member of OpenWetWare!

Contact Info

Ximiao He (an artistic interpretation)

• Ximiao He
• Tongji Medical College (TJMC), Huazhong University of Science and Technology (HUST)
• School of Basic Medicine, Building No. 2, Room 1427
• 13 Hangkong Road
• Wuhan, Hubei, China 430030
• Tel: (+86)158-2757-8535.
• Email: XimiaoHe AT hust.edu.cn
• Email me through OpenWetWare
• Lab homepage

I work in the Department of Medical Genetics at HUST University. I learned about OpenWetWare from Dr. Wei Li from BCM., and I've joined because I want to set up my own lab pages and share my research with the community on OWW.

EDUCATION

• 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

ACADEMIC POSITIONS

• 09/2016 - present Professor, School of Basic Medicine, TJMC, HUST, Wuhan, China 430030
• 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

RESEARCH INTERESTS

1. DNA methylation in cell differentiation and cancer
2. Effects of nucleosome occupancy and methylation on gene regulation
3. Alternative splicing in disease and development
4. Evolution of new genes and comparative genomics
5. Tools and web services for analysis of genomic/epigenomic data

PUBLISHIONS

• FIRST AUTHOR OR JOINT FIRST AUTHOR OR CORRESPONDING AUTHOR (*first authorship, ^Corresponding authorship)

1. 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 (IF = 4.529)
2. 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 (IF = 3.508)
3. 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 (IF = 5.333)
4. 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 (IF = 5.333)
5. 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 (IF = 3.702)
6. 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 (IF = 4.360)
7. 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 (IF = 15.567)
8. 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
9. 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 (IF = 9.112)
10. Wang J.*, Xia Q.*, He X.* et al., (2005) SilkDB: a knowledgebase for silkworm biology and genomics, Nucleic Acids Res., 33:D399-402 (IF=9.112)
11. Wang J.*, He X.* et al., (2005) ChickVD: a sequence variation database for the chicken genome, Nucleic Acids Res., 33:D438-41 (IF = 9.112)
12. 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 (IF = 9.112)

• CO-AUTHORS

1. Syed K.S., He X., Holzberg T., Wang J., Rajagopal D., Durell SR., Sathyanarayana BK., Mukherjee S., Weirauch MT., Rose R., Vinson C.^, (2016) 5-hydroxymethyl cytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA binding of B-HLH transcription factor TCF4 but not USF1, Integrative Biology. (IF = 4.309, Accepted).
2. 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 (IF = 6.781)
3. 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 (IF = 12.305)
4. 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 (IF = 3.508)
5. 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 (IF = 4.360)
6. 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 (IF = 10.563)
7. 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 (IF = 11.896)
8. 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 (IF = 41.456)
9. 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 CHAPTERS

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

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