Hexlab:Publications

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

           2024

  1. Pu H*, Gao C*, Zou Y*, Zhao L, Li G, Liu C, Zhao L, Zheng M, Sheng G, Sun X, Hao X, Wang C^, He X^, Xiao J^. (2024) Single cell transcriptome profiling of infrapatellar fat pad highlights the role of interstitial inflammatory fibroblasts in osteoarthritis.
    Int Immunopharmacol. 131:111888. doi: 10.1016/j.intimp.2024.111888.
  2. Tian Q*, Yin Y*, Tian Y*, Wang Y, Wang YF, Fukunaga R, Fujii T, Liao AH, Li L, Zhang W, He X^, Xiang W^, Zhou LQ^, (2024) Chromatin Modifier EP400 Regulates Oocyte Quality and Zygotic Genome Activation in Mice.
    Adv Sci. e2308018. doi: 10.1002/advs.202308018
  3. Cai Z*, Zhu M*, Xu L*, Wang Y, Xu Y, Yim WY, Cao H, Guo R, Qiu X, He X, Shi J, Qiao W^, Dong N^, (2024) Directed Differentiation of Human Induced Pluripotent Stem Cells to Heart Valve Cells.
    Circulation doi: 10.1161/CIRCULATIONAHA.123.065143.
  4. Huang J, Jin S, Guo R, Wu W, Yang C, Qin Y, Chen Q, He X, Qu J^, Yang Z^. (2024) Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis.
    RNA. 30(4):435-447. doi: 10.1261/rna.079865.123.
  5. Fan Y*, Liu X, Guan F, Hang X, He X^, Jin J^. (2024) Investigating the Potential Shared Molecular Mechanisms between COVID-19 and Alzheimer's Disease via Transcriptomic Analysis.
    Viruses.16(1):100. doi: 10.3390/v16010100

    2023

  6. Wang Y, Sun Z, Ping J, Tang J, He B, Chang T, Zhou Q , Yuan S, Tang Z, Li X, Lu Y, He R, He X , Liu Z^, Yin L^, Wu N^. (2023) Cell volume controlled by LRRC8A-formed volume-regulated anion channels fine-tunes T cell activation and function.
    Nat Commun. 14(1):7075.

  7. Wang HX*, Liu XZ*, He X , Xiao C, Huang DX, Yi SH. (2023) Identification of Mixtures of Two Types of Body Fluids Using the Multiplex Methylation System and Random Forest Models.
    Curr Med Sci. 43(5):908-918.

  8. Zhu M*, Liang H*, Zhang Z, Jiang H, Pu J, Hang X, Zhou Q, Xiang J, He X.^, (2023) Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in embryonic and adult mammalian heart.
    Frontiers of Medicine. ePub doi: 10.1007/s11684-023-0987-9

  9. Liu F*, Zhou Q*, Jiang HF*, Zhang TT, Miao C, Xu XH, Wu JX, Yin SL, Xu SJ, Peng JY, Gao PP, Cao X^, Pan F^, He X^, Chen XQ^, (2023) Piperlongumine conquers temozolomide chemoradiotherapy resistance to achieve immune cure in refractory glioblastoma via boosting oxidative stress-inflamation-CD8+-T cell immunity.
    J Exp Clin Cancer Res 42(1):118. doi: 10.1186/s13046-023-02686-1

  10. Peng P, Chen ZR, Zhang XL, Guo DS, Zhang B, He X., Wan F., (2023) Construction and Verification of an RNA-Binding Protein-Associated Prognostic Model for Gliomas.
    Curr Med Sci. 43(1):156-165. doi: 10.1007/s11596-022-2694-1

  11. Mei NH, Guo SM, Zhou Q, Zhang YR, Liu XZ, Yin Y, He X., Yang J, Yin TL, Zhou LQ^, (2023) H3K4 Methylation Promotes Expression of Mitochondrial Dynamics Regulators to Ensure Oocyte Quality in Mice.
    Adv Sci 10(12):e2204794. doi: 10.1002/advs.202204794

    2022

  12. Yin Y.*, Liu X.*,Tian Q, Fan YX, Ye Z, Meng TQ, Wei GH, Xiong CL, Li HG, He X.^, Zhou LQ.^, (2022) Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-months recovery of COVID-19.
    Front Cell Dev Biol. 10:1001558 doi: 10.3389/fcell.2022.1001558

  13. Li X, Li L, Zhou K, Zhang H, Maalim AA, Chen X, He X., Ding X, Xu C, Wang Y. (2022) Glioma Shapes Blood-Brain Barrier Integrity and Remodels the Tumor Microenvironment: Links with Clinical Features and Prognosise.
    J Clin Med 11(19):5863. doi: 10.3390/jcm11195863

  14. Guo SM*, Liu XP*, Tian Q*, Fei CF, Zhang YR, Li ZM, Yin Y^, He X^, Zhou LQ^. (2022) Regulatory roles of alternative splicing at Ezh2 gene in mouse oocytes.
    Reprod Biol Endocrinol 20(1):99. doi: 10.1186/s12958-022-00962-x

  15. Tian Q, Tian Y, Guo SM,He X., Yin Y^, Zhou LQ^, (2022) APpan is essential for preimplantation development in mice†.
    Biol Reprod 107(3):723-731. doi: 10.1093/biolre/ioac098

  16. Cheng GP*, Guo SM, Yin Y, Li YY, He X., Zhou LQ^, (2022) Aberrant Expression of Mitochondrial SAM Transporter SLC25A26 Impairs Oocyte Maturation and Early Development in Mice.
    Oxid Med Cell Longev 2022:1681623. doi: 10.1155/2022/1681623

  17. Zhu M*, Zhang C*, Zhang Z, Liao X, Ren D, Li R, Liu S, He X.^, Dong N.^, (2022) Changes in transcriptomic landscape in human end-stage heart failure with distinct etiology.
    iScience 25(3):103935. doi: 10.1016/j.isci.2022.103935

  18. Fei CF*, Guo SM*, Yin Y, He X, Zhou LQ., (2022) Exposure of mouse oocytes to N,N-dimethylformamide impairs mitochondrial functions and reduces oocyte quality.
    Environ Toxicol doi: 10.1002/tox.23506

  19. Chen H*, Xue J*, Zhang Z*, Zhang G*, Xu X, Li H, Zhang R, Ullah N, Chen L, Amanullah, Zang Z, Lai S, He X., Li W, Guan M^, Li J^, Chen L^, Deng C.^, (2022) High-speed rail model reveals the gene tandem amplification mediated by short repeated sequence in eukaryote.
    Sci Rep 12(1):2289. doi: 10.1038/s41598-022-06250-3

  20. Dong Y*, Liu X*, Jiang B, Wei S, Xiang B, Liao R, Wang Q^, He X.^, (2022) A Genome-Wide Investigation of Effects of Aberrant DNA Methylation on the Usage of Alternative Promoters in Hepatocellular Carcinoma.
    Front Oncol. 11:780266. doi: 10.3389/fonc.2021.780266

  21. Huang H, Liu X., Cheng J, Xu L, He X., Xiao C, Huang D.^, Yi S.^, (2022) A novel multiplex assay system based on 10 methylation markers for forensic identification of body fluids.
    J Forensic Sci. 67(1):136-148 doi: 10.1111/1556-4029.14872

    2021

  22. Zhou Q.*, Cao H*, Hang X, Liang H, Zhu M, Fan Y, Shi J, Dong N^, He X.^, (2021) Midkine Prevents Calcification of Aortic Valve Interstitial Cells via Intercellular Crosstalk.
    Front Cell Dev Biol 9:794058 doi: 10.3389/fcell.2021.794058

  23. Peng P, Cheng F, Dong Y, Chen Z, Zhang X, Guo D, Yu X, Lu Y, Ke Y, Zhang B^, He X.^, Wan F^.(2021) High expression of TXNDC11 indicated unfavorable prognosis of glioma.
    Transl Cancer Res 10(12):5040-5051. doi: 10.21037/tcr-21-1326

  24. Sun KY*, Guo SM*, Cheng GP*, Yin Y., He X.^, Zhou LQ.^, (2021) Cleavage-embryo genes and transposable elements are regulated by histone variant H2A.X.
    J Reprod Dev. doi: 10.1262/jrd.2021-065

  25. 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 doi: 10.14336/AD.2020.0926

  26. 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 13(8):11646-11664 doi: 10.18632/aging.202857

  27. Yin Y., Liu X., He X.^, Zhou LQ.^, (2021) Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells.
    Front Cell Infect Microbiol. 11:609160 doi: 10.3389/fcimb.2021.609160

    2020

  28. Jin J., He X.^, Silva E.^, (2020) Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties.
    BMC Genomics 21(1):287 doi: 10.1186/s12864-020-6687-9

  29. Fan Y.,Hang X., He X.^, (2020) The impact factors of 3D genome organization.
    Scientia Sinica Vitae 50(5):465-483 (Invited Review)

    2019

  30. 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 doi: 10.3389/fgene.2019.00814

    2017

  31. 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 doi: 10.1021/acs.biochem.7b00741

  32. 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

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

  34. 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.

  35. 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.

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

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

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

  53. 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

  54. 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

  55. 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

  56. 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

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