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成果及论文

代表性论文：

  1. Shi A., Lin C., Wang J., Chen Y., Zhong J.*, Lyu J.*(共同通讯作者): EPRIM: an approach of identifying cancer immune-related epigenetic regulators. Molecular Therapy Nucleic Acids, 2024, 35(1). SCI IF = 8.8  中科院1区Top

  2. Shi A., Lin C., Lyu J.*(通讯作者): Decoding functional impact of epigenetic regulator mutations on ligand-receptor interaction perturbations for evaluation of cancer immunotherapy. Journal of Cellular and Molecular Medicine, 2024, accepted. SCI IF = 4.3  中科院2区Top

  3. Lin C., Lyu J.*(通讯作者), Feng Z.*: Intake of dietary flavonoids in relation to overactive bladder among U.S. adults: a nutritional strategy for improving urinary health. Frontiers in Nutrition, 2024, 11:1437923. SCI IF = 4.0 中科院2区

  4. Lin M., Lei S., Chai Y., Xu J., Wang Y., Wu C., Jiang H., Yuan S., Wang J., Lyu J.*(共同通讯作者), Lu M.*, Deng J.*: Immunosuppressive microvesicles-mimetic derived from tolerant dendritic cells target T-lymphocytes for inflammation diseases therapy. Journal of Nanobiotechnology, 2024, 22:201. SCI IF = 10.2  中科院1区Top

  5. Feng Z. (co-first), Chen Y. (co-first), Guo Y., Lyu J.*(通讯作者): Deciphering the environmental chemical basis of muscle quality decline by interpretable machine learning models. American Journal of Clinical Nutrition, 2024, 120(2):407-418. SCI IF = 7.1  中科院1区Top

  6. Wang J. (co-first), Shi A. (co-first), Lyu J.* (co-first, 通讯作者): A Comprehensive Atlas of Epigenetic Regulators Reveals Tissue-specific Epigenetic Regulation Patterns. Epigenetics, 2023, 18(1):2139067. SCI IF = 4.861.  中科院2区

  7. Lyu J. (co-first), et al.: DORGE: Discovery of Oncogenes and Tumor SuppressoR Genes Using Distinct Genetic and Epigenetic Features. Science Advances, 2020, 6(46):eaba6784. SCI IF = 13.6.  中科院1区Top

  8. Mi W., Zhang Y., Lyu J. (co-first), et al.: The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation. Nature Communications, 2018, 9:3759. SCI IF = 16.6.  中科院1区Top

  9. Mi W., Guan H., Lyu J. (co-first), et al.: YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nature Communications, 2017, 8:1088. SCI IF = 16.6.  中科院1区Top

  10. Lv J. (co-first), et al.: Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Research, 2013, 41(22):10044-10061. SCI IF = 14.9.  中科院2区Top

  11. Lv J. (co-first), et al.: DiseaseMeth: a human disease methylation database. Nucleic Acids Research, 2012, 40:D1030-1035. SCI IF = 14.9.  中科院2区Top   

  12. Zhang Y.*(导师), Lv J. (co-first), et al.: HHMD: the human histone modification database. Nucleic Acids Research, 2010, 38 database issue, D149-D154. SCI IF = 14.9.  中科院2区Top

其它论文：

  1. Lin H., Hu H., Feng Z., Xu F., Lyu J., Li X., Liu L., Yang G.*, Shuai J.*: SCTC: inference of developmental potential from single-cell transcriptional complexity. Nucleic Acids Research, 2024, 52(11):6114-6128. SCI IF = 14.9.  中科院2区Top 

  2. Hu H., Feng Z., Shuai X., Lyu J., et al.: Identifying SARS-CoV-2 infected cells with scVDN. Frontiers in Microbiology, 2023, 14:1236653. SCI IF = 5.2.  中科院2区Top

  3. Wan L., Wen H., Li Y., Lyu J., et al.: ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature, 2017, 543(7644):265-269 SCI IF = 64.8.  中科院1区Top

  4. Hu H., Feng Z., Lin H., Cheng J., Lyu J., Zhang Y., Zhao J., Xu F., Lin T., Zhao Q.*, Shuai J.*: Gene function and cell surface protein association analysis based on single-cell multiomics data. Computers in Biology and Medicine, 2023, 157:106733 SCI IF = 7.7.  中科院大类2区top，小类1区

  5. Klein B.J., Jang S.M., Lachance C., Mi W., Lyu J., et al.: Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nature Communications, 2019, 10(1):4724. SCI IF = 16.6.  中科院1区Top   

  6. Wang W., Angulo-Ibanez M., Lyu J., et al.: A Click Chemistry Approach Reveals the Chromatin-Dependent Histone H3K36 Deacylase Nature of SIRT7. Journal of the American Chemical Society, 2019, 141(6):2462-2473 SCI IF = 15.  中科院1区Top

  7. Su J., Huang Y., Cui X., Wang X., Zhang X., Lei Y., Xu J., Lin X., Chen K., Lv J., et al.: Homeobox oncogene activation by pan-cancer DNA hypermethylation. Genome Biology, 2018, 19(1):108. SCI IF = 12.3.  中科院1区Top

  8. Hsu C.C., Shi J., Yuan C., Zhao D., Jiang S., Lyu J., et al.: Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes & Development, 2018, 32(1):58-69 SCI IF = 10.5.  中科院1区Top

  9. Tencer A., Cox K., Di L., Bridgers J., Lyu J., et al.: Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell Reports, 2017, 21(2):455-466. SCI IF = 8.8.  中科院1区Top

  10. Xiong Y., Wei Y., Gu Y., Zhang S., Lyu J., et al.: DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Research, 2017, 45(Database issue): D888–D895 SCI IF = 14.9.  中科院2区Top

  11. Liu H.*, Liu X., Zhang S., Lv J., et al.: Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Nucleic Acids Research, 2016, 44(1):75-94 SCI IF = 14.9.  中科院2区Top

  12. Liu H., Lyu J. (co-first), et al.: Computational identification of putative lincRNAs in mouse embryonic stem cell. Scientific Reports, 2016, 6:34892 SCI IF = 4.6.   中科院2区

  13. Lv J., et al.: Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Molecular Genetics and Genomics, 2015, 290(2):685-97 SCI IF = 3.1.  中科院3区

  14. Cui W., Huang Z., He H., Gu N., Qin G., Lv J., et al.: MiR-1188 at the imprinted Dlk1-Dio3 domain acts as a tumor suppressor in hepatoma cells. Molecular Biology of the Cell, 2015, 26(8):1416-27 SCI IF= 3.3.   中科院3区

  15. Yan H., Zhang D., Liu H.B., Wei Y., Lv J., et al.: Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types. Scientific Reports, 2015, 5:8410 SCI IF = 4.6.   中科院2区

  16. Guo J., He H., Liu Q., Zhang F., Lv J., et al.: Identification and epigenetic analysis of a maternally imprinted gene Qpct. Molecules and cells, 2015, 38(10), 859-865 SCI IF = 3.8.  中科院3区

  17. Lv J., et al.: Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Molecular Genetics and Genomics, 2014, 289 (6), 1225-1235 SCI IF = 3.1.  中科院3区

  18. Wei Y., Su J., Liu H., Lv J., et al.: MetaImprint: an information repository of mammalian imprinted genes. Development, 2014, 141 (12), 2516-2523 SCI IF = 4.6.  中科院2区

  19. Liu H., Zhu R., Lv J. (co-first), et al.: DevMouse, the mouse developmental methylome database. Database, 2014, bat084 SCI IF = 5.8.  中科院4区

  20. Su J., Yan H., Wei Y., Liu H.B., Liu H., Wang F., Lv J., et al.: CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Research, 2013, 41(1):e4 SCI IF = 14.9.  中科院2区Top

  21. Wu X., Liu H., Liu H.B., Su J., Lv J., et al.: Z Curve Theory-Based Analysis of the Dynamic Nature of Nucleosome Positioning in Saccharomyces cerevisiae. Gene, 2013, 530(1):8-18 SCI IF = 3.5.  中科院3区

  22. Liu H., Chen Y., Lv J. (co-first), et al.: Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. Scientific Reports, 2013, 3:2576 SCI IF = 4.6.   中科院2区

  23. Lv J., et al.: Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data. PLoS ONE, 2013, 8(8):e71152 SCI IF=3.7.  中科院3区

  24. Su J., Qi Y., Liu S., Wu X., Lv J., et al.: Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network. Molecular Biology Reports, 2012, 39(2):1701-12 SCI IF=2.8  中科院4区

  25. Yang L., Chen J., Lv J., et al.: Rice protein improves adiposity, body weight and reduces lipids level in rats through modification of triglyceride metabolism. Lipids in health and disease, 2012, 11:24 SCI IF=4.5  中科院2区

  26. Zhang Y.*, Liu H., Lv J. (co-first), et al.: QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Research, 2011, 39:e58 SCI IF = 14.9.  中科院2区Top

  27. Liu H., Su J., Li J., Liu H., Lv J., et al.: Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC systems biology, 2011, 5:158 SCI IF = 2.0.  无中科院分区

  28. Lv J., et al.: Detecting novel hypermethylated genes in Breast cancer benefiting from feature selection. Computers in Biology and Medicine, 2010, 40 (2), 159-167 SCI IF = 7.7.  中科院大类2区top，小类1区

  29. Su J., Zhang Y.*, Lv J. (co-first), et al.: CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Research, 2010,38(1):e6 SCI IF = 14.9.  中科院2区Top

  30. Lv J., et al.: Discovering Cooperative Relationships of Chromatin Modifications in Human T Cells Based on a Proposed Closeness Measure. PLoS ONE, 2010, 5(12),e14219 SCI IF= 3.1.  中科院3区

注：影响因子均为最近，分区为发表时或最近的分区（无特别说明，均为大类分区）。粗体名字表示本课题组人员。


主持课题：

基于多组学数据的机器学习方法识别驱动癌症的表观遗传调控基因，国家自然科学基金面上项目，编号 32170665, 2022.1 ~ 2025.12 在研

癌症诊断分子靶标识别，中国科学院大学温州研究院(温州生物材料与工程研究所)重大项目，编号 WIUCASQD2021006, 2021.1 ~ 2023.12 在研

基于RNA-seq数据识别胚胎发育相关的lncRNA及新候选lncRNA的鉴定及功能研究 (31371478)，国家自然科学基金面上项目，参与，排名第三 （2014-2017）结题

融合高通量信息的癌症表观遗传异常的特征提取技术 (61075023)，国家自然科学基金面上项目，参与，排名第六 （2011-2013）结题

印记基因的机器学习方法预测及候选印记基因的实验鉴定及功能分析 (31171383)，国家自然科学基金面上项目，参与，排名第二 （2012-2015）结题