Ximiao HE

Personal Information

Title: Professor

Department: Department of Physiology

Email: XimiaoHe@hust.edu.cn

Clinical Focus: Genomics, Epigenomics, Bioinformatics, Precision Medicine

Research Focus/Interests: His research 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. It includes: 1. DNA methylation in cell differentiation and cancer, cardiovascular diseases 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

Biography

Dr. He is a professor at School of Basic Medicine, Tongji Medical College (TJMC), Huazhong University of Science and Technology (HUST), Wuhan in China. Prior to joining TJMC, he was a Research Fellow at National Cancer Institute (NCI), National Institutes of Health (NIH), USA. He earned his Ph.D. in Genomics and Bioinformatics at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) in 2009. During his Ph.D. study, Dr. He has participated in rice, chicken and silkworm genome projects. He also identified the human CGI on the whole human genome, and developed a public database (MethyCancer) to integrate human DNA methylation and cancer (NAR in 2008).  He completed his postdoctoral training in the laboratory of Dr. Charles Vinson at NCI, NIH, USA. In Dr. Vinson’s lab, he and his colleagues revealed the nucleosome-mediated collaboration between TFs in a whole genome-wide in vivo (BMC Genomics in 2013). They first reported that DNA methylation enhanced binding for CEBPA and CEBPB TFs by DNA arrays (in vitro) and WGBS (in vivo), which is ground-breaking, as traditionally methylation was thought to only inhibit gene expression (Genome Research in 2013). He discovered that nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) on whole genome-wide level, which provides a link between epigenetic modifications, chromatin structure, and regulatory function (Epigenetics & Chromatin in 2014). He also discovered that CpG methylation can function as the mutator to form new TFBSs to drive vertebrate evolution (Genome Biology and Evolution in 2015). Recently, his lab showed that the stable intronic sequence RNAs (sisRNA) are selected regions in introns with distinct properties (BMC Genomics in 2020). In another collaboration work, he and his colleagues reported the upregulation of retrotransposon in SARS-CoV-2 infected cells, the chimeric transcripts of retrotransposon and SARS-CoV-2 RNA for potential human genome invasion of viral fragments (Front Cell Infect Microbiol in 2021). At present, he has published 33 peer-reviewed papers in leading scientific journals, including Nature, PNAS, PLoS Biology, NAR, Genome Research, Genome Biology and Evolution, Genes & Development, GPB, Epigenetics & Chromatin, Aging. His works have been heavily cited over 2,600 times by scientists worldwide.

Education

2009   Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China, PhD in Genomics
2002   Tongji Medical College (TJMC), Huazhong University of Science and Technology (HUST), Wuhan, China, BS in Medical Informatics

Boards, Advisory Committees, Professional Organizations

Associate Editor, Evolutionary Bioinformatics (2016-present)
Editorial Board Member, Current Medical Science (2020-present)
Member, International Society for Computational Biology (ISCB)
Member, Human Genome Organization (HUGO)
Member, Chinese Association of Physiological Sciences
Member, The Physiology Association of Hubei Provinces
Member, The Physiology Association of Wuhan

Publications

FIRST AUTHORSHIP (*) OR CORRESPONDING AUTHORSHIP (^)
1.	Gao C*, Pu H*, Zhou Q*, Tao T, Liu H, Sun X, He X^, Xiao J^. (2021) Two reactive behaviors of chondrocytes in an IL-1β-induced inflammatory environment revealed by the single-cell RNA sequencing. Aging (Albany NY). doi: 10.18632/aging.202857.
2.	Yin Y, Liu XZ, He X^, Zhou LQ^, (2021) Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells. Front Cell Infect Microbiol. 11:609160.
3.	Fan Y., Hang X., He X^, (2020) The impact factors of 3D genome organization. Sci Sin Vitae 50: 465–483
4.	Jin J.*, He X.^, Silva E.^, (2020) The stable intronic sequence RNAs (sisRNA) are selected regions in introns with distinct properties. BMC Genomics 21(1):287
5.	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
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.	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 
8.	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 
9.	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 
10.	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 (
11.	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  
12.	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 
13.	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
14.	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 
15.	Wang J.*, Xia Q.*, He X.* et al., (2005)  SilkDB: a knowledgebase for silkworm biology and genomics, Nucleic Acids Res., 33:D399-402 
16.	Wang J.*, He X.* et al., (2005) ChickVD: a sequence variation database for the chicken genome, Nucleic Acids Res., 33:D438-41 
17.	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 

CO-AUTHORS
1.	Wu J, Wu Z, He A, Zhang T, Zhang P, Jin J, Li S, Li G, Li X, Liang S, Pei L, Liu R, Tian Q, He X, Lu Y, Tang Z^, Li H^. (2021) Genome-Wide Screen and Validation of Microglia Pro-Inflammatory Mediators in Stroke. Aging Dis.;12(3):786-800
2.	Cai Y, Zhang Y, Ke X, Guo Y, Yao C, Tang N, Pang P, Xie G, Fang L, Zhang Z, Li J, Fan Y, He X, Wen R, Pei L, Lu Y. (2019) Transcriptome Sequencing Unravels Potential Biomarkers at Different Stages of Cerebral Ischemic Stroke. Front Genet. 10:814.
3.	Tillo D, Ray S, Syed KS, Gaylor MR, He X., Wang J, Assad N, Durell S, Porollo A, Weirauch MT, Vinson C, (2017) The Epstein-Barr virus B-ZIP protein Zta recognizes specific DNA sequences containing 5-methylcytosine and 5-hydroxymethylcytosine. Biochemistry 56(47):6200-6210
4.	Han YX., He X., (2016) Integrating Epigenomics into the Understanding of Biomedical Insight, Bioinformatics and Biology Insights. (Invited Review, in press)
5.	Syed K.S., He X., Tillo D., Wang J., Durell SR., Vinson C.^, (2016) 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) increase CREB1 binding to the C/EBP half-site tetramer GCAA, Biochemistry. (In Press, IF = 2.876)
6.	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., Frontiers in Molecular Biosciences, 3:74 
7.	Syed K.S., He X., Holzberg T., Wang J., Rajagopal D., Upadhyay S., Durell SR., Sathyanarayana BK., 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, Integrative Biology. (IF = 4.309).
8.	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)
9.	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)
10.	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) 
11.	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)
12.	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)
13.	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)
14.	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)
15.	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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Ximiao HE

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