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Taotao Li#, Duo Du#, Dandan Zhang#, Yicheng Lin#, Jiakang Ma, Mengyu Zhou, Weida Meng, Zelin Jin, Ziqiang Chen, Haozhe Yuan, Jue Wang, Shulong Dong, Shaoyang Sun, Wenjing Ye, Bosen Li, Houbao Liu, Zhao Zhang, Yuchen Jiao, Zhi Xie, Wenqing Qiu*, Yun Liu*. CRISPR-based targeted haplotype-resolved assembly of a megabase region. Nature Communications. (2023) 14(1):22. (影响因子: 16.6)
Peng, Q., Liu, Y., Huels, A., Zhang, C., Yu, Yao., Qiu, W., Cai, X., Zhao, Y., Schikowski, T., Merches, K., Liu, Y., Yang, Y., Wang, J., Zhao, Y., Jin, L., Zhang, L., Krutmann, J., Wang, S. Genetic Variants in Telomerase Reverse Transcriptase Contribute to Solar Lentigines. J Invest Dermatol. (2023) 143(6):1062.
Yu Meng#, Mengyu Zhou#, Tuanwei Wang, Guanghui Zhang, Yuting Tu, Shiyang Gong, Yunxia Zhang, David C. Christiani, William Au, Yun Liu, Zhao-Lin Xia. Occupational lead exposure on genome-wide DNA methylation and DNA damage. Environ Pollut. (2022) 304:119252.
Meng, W.#, Sj?holm, LK.#, Kononenko, O.#, Tay, N.#, Zhang, D.#, Sarkisyan, D.#, Geske, JR., Ing, A., Qiu, W., Watanabe, H., Almamoun, R., Frieling, H., Bleich, S., Cui, D., Biernacka, JM., Mayfield, RD., Dang, Y., Karpyak, VM., Schumann, G.; IMAGEN Consortium, Bakalkin, G.#, Ekstr?m, TJ.#,*, Rüegg, J.#, Liu, Y.#,* Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence. Mol Psychiatry. (2021) 26(8):4367. (影响因子: 11.64)
Peiru Liu#, Jing Zhang#, Duo Du, Dandan Zhang, Zelin Jin, Wenqing Qiu, Xiushi Zhou, Shulong Dong, Mengyu Zhou, Heyu Zhao, Wei Zhang, Jiakang Ma, Shaoyang Sun, Weiguo Fu*, Yun Liu*, Lixin Wang*. Altered DNA methylation pattern reveals epigenetic regulation of Hox genes in thoracic aortic dissection and serves as a biomarker in disease diagnosis. Clin Epigenetics. (2021) 13(1):124.
Bin Li, Yongkun Zhan, Qianqian Liang, Chen Xu, Xinyan Zhou, Huanhuan Cai, Yufan Zheng, Yifan Guo, Lei Wang, Wenqing Qiu, Baiping Cui, Chao Lu, Ruizhe Qian, Ping Zhou, Haiyan Chen, Yun Liu, Sifeng Chen, Xiaobo Li, Ning Sun. Isogenic human pluripotent stem cell disease models reveal ABRA deficiency underlies cTnT mutation-induced familial dilated cardiomyopathy. Protein & Cell. (2021) doi: 10.1007/s13238-021-00843-w.
Li, Y., Li, J., Wang, R., Zhang, L., Fu, G., Wang, X., Wang, Y., Fang, C., Zhang, D., Du, D., Ma, X., Pan, M., Guo, Q., Xu, X., Hu, X., Zhou, Y., Mo, S., Wang, H., Gao, J., Huang, S., Liu, Y., Cai, S., Hua, G., Peng, J., Yu, FX. Frequent RNF43 mutation contributes to moderate activation of Wnt signaling in colorectal signet-ring cell carcinoma. Protein & Cell. (2020) 11(4):292-298.
Ma, Y., He, S., Gao, A., Zhang, Y., Zhu, Q., Wang, P., Yang, B., Yin, H., Li, Y., Song, J., Yue, P., Li, M., Zhang, D., Liu, Y., Wang, X., Guo, M., Jiao, Y. Methylation silencing of TGF-β receptor type II is involved in malignant transformation of esophageal squamous cell carcinoma. Clin Epigenetics. (2020) 12(1):25.
Jia, T., Chu, C., Liu, Y., et al. Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group. Mol Psychiatry. (2019) doi: 10.1038/s41380-019-0605-z. (影响因子: 11.64)
Huo, X., Ji, L., Zhang, Y., Lv, P., Cao, X., Wang, Q., Yan, Z., Dong, S., Du, D., Zhang, F., Wei, G., Liu, Y., Wen, B. The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation. Mol Cell. (2019) doi: 10.1016/j.molcel.2019.10.001. (影响因子: 14.25)
Ringh, MV., Hagemann-Jensen, M., Needhamsen, M., Kular, L., Breeze, CE., Sj?holm, LK., Slavec, L., Kullberg, S., Wahlstr?m, J., Grunewald, J., Brynedal, B., Liu, Y., Almgren, M., Jagodic, M., ?ckinger, J., Ekstr?m, TJ. Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells. EBioMedicine. (2019) 46:290-304
Qiu, W., Xu, Z., Zhang, M., Zhang, D., Fan, H., Li, T., Wang, Q., Liu, P., Zhu, Z., Du, D., Tan, M., Wen, B., Liu, Y. Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system. Nucleic Acids Res. (2019) 47(9):e52 (影响因子: 11.56)
Cai, M., Zhu, Y., Li, Z., Josephs-Spaulding, J., Zhou, Y., Hu, Y., Chen, H., Liu, Y.*, He, W.*, Zhang, J.* Profiling the Gene Expression and DNA Methylation in the Mouse Brain after Ischemic Preconditioning. Neuroscience. (2019) 406:249-261
Lin, S., Liu, Y., Goldin, LR., Lyu, C., Kong, X., Zhang, Y., Caporaso, NE., Xiang, S., Gao, Y. Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia. Biol Sex Differ. (2019) 10(1):2
Müller, CP., et al. The Cortical Neuroimmune Regulator TANK Affects Emotional Processing and Enhances Alcohol Drinking: A Translational Study. Cerebral Cortex. (2019) 29(4):1736-1751
Tay N#, Macare C#, Liu Y#, Ruggeri B, Jia T, Chu C, Biondo F, Ing A, Luo Q, Sarkysian D, Banaschewski T, Barker GJ, Bokde ALW, Bromberg U, Büchel C, Quinlan EB, Desrivières S, Flor H, Frouin V, Garavan H, Gowland P, Heinz A, Ittermann B, Martinot JL, Artiges E, Nees F, Orfanos DP, Paus T, Poustka L, Hohmann S, Fr?hner JH, Smolka MN, Walter H, Whelan R, Frieling H, Bleich S, Barker ED, Syv?nen AC, Rüegg J#, Ekstr?m TJ#, Bakalkin G#, Schumann G#,*; IMAGEN Consortium. Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse. American Journal of Psychiatry. (2019) 176(2):146-155 (影响因子: 13.40)
Kular L#, Liu Y#, Ruhrmann S, Zheleznyakova G, Marabita F, Gomez-Cabrero D, James T, Ewing E, Lindén M, Górnikiewicz B, Aeinehband S, Stridh P, Link J, Andlauer TFM, Gasperi C, Wiendl H, Zipp F, Gold R, Tackenberg B, Weber F, Hemmer B, Strauch K, Heilmann-Heimbach S, Rawal R, Schminke U, Schmidt CO, Kacprowski T, Franke A, Laudes M, Dilthey AT, Celius EG, S?ndergaard HB, Tegnér J, Harbo HF, Oturai AB, Olafsson S, Eggertsson HP, Halldorsson BV, Hjaltason H, Olafsson E, Jonsdottir I, Stefansson K, Olsson T, Piehl F, Ekstr?m TJ, Kockum I#, Feinberg AP#,*, Jagodic M#,* DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis. Nature Communications. (2018) 9:2397 (影响因子: 12.35)
Hui Fan, Pin Lv, Xiangru Huo, Jicheng Wu, Qianfeng Wang, Lu Cheng, Yun Liu, Qi-Qun Tang, Ling Zhang, Feng Zhang, Xiaoqi Zheng, Hao Wu and Bo Wen*. The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes. Genome Res. (2018). 28(2):192-202
Marabita, F., Almgren, M., Sj?holm, LK., Kular, L., Liu, Y., James, T., Kiss, NB., Feinberg, AP., Olsson, T., Kockum, I., Alfredsson, L., Ekstr?m, TJ., Jagodic, M. Author Correction: Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship. Sci Rep. (2018) 8:4340
Zhu, Z., Meng, W., Liu, P., Zhu, X., Liu, Y.*, Zou, H.* DNA hypomethylation of a transcription factor binding site within the promoter of a gout risk gene NRBP1 upregulates its expression by inhibition of TFAP2A binding. Clin Epigenetics. (2017) 9:99
Meng, W.#, Zhu, Z.#, Jiang, X., Too, CL., Uebe, S., Jagodic, M., Kockum, I., Murad, S., Ferrucci, L., Alfredsson, L., Zou, H., Klareskog, L., Feinberg, AP., Ekstr?m, TJ., Padyukov, L.*, Liu, Y.* DNA methylation mediates genotype and smoking interaction in the development of anti-citrullinated peptide antibody-positive rheumatoid arthritis. Arthritis Res Ther (2017) 19:71
Liu, Y.#, Duong, W.#, Krawczyk, C., Bretschneider, N., Borbely, G., Varshney, M., Zinser, C., Schar, P., Ruegg, J. Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase. Epigenetics & Chromatin. (2016) 9:7
Zhang, D., Li, Y., Yao, X., Wang, H., Zhao, L., Jiang, H., Yao, X., Zhang, S., Ye, C., Liu, W., Cao, H., Yu, S., Wang, YC., Li, Q., Jiang, J., Liu, Y., Zhang, L., Liu, Y., Iwai, N., Wang, H., Li, J., Li, J., Li, X., Jin, ZB., Ying, H. miR-182 Regulates Metabolic Homeostasis by Modulating Glucose Utilization in Muscle. Cell Rep. (2016) 16:757-768
Li, X., Liu, Y., Salz, T. Hansen, KD., Feinberg, A. Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver. Genome Res. (2016) 26:1730-1741
Schumann, G., et al., KLB is associated with alcohol drinking, and its gene product β-Klotho is necessary for FGF21 regulation of alcohol preference. PNAS. (2016) 113(50):14372-14377
Lu, C., Ward, A., Bettridge, J., Liu, Y., Desiderio, S., An Autoregulatory Mechanism Imposes Allosteric Control on the V(D)J Recombinase by Histone H3 Methylation. Cell Rep. (2015) 10:1-10
Liu, Y.#, Li, X.#, Aryee, MJ., Ekstrom, TJ., Padyukov, L., Klareskog, L., Vandiver, A., Moore, AZ., Tanaka, T., Ferrucci, L., Fallin, MD., Feinberg, AP. GeMes: Clusters of DNA methylation under genetic control can inform genetic and epigenetic analysis of disease. Am J Hum Genet, (2014) 94:485-495 (影响因子: 11.2)
Liu, Y.#, Aryee, MJ.#, Padyukov, L.#, Fallin, MD.#, Hesselberg, E., Runarsson, A., Reinius, L., Acevedo, N., Taub, M., Ronninger, M., Shchetynsky, K., Scheynius, A., Kere, J., Alfredsson, L., Klareskog, L.*, Ekstrom, TJ.*, and Feinberg, AP*. Epigenome-wide association data implicate DNA methylation as an intermediary of generic risk in Rheumatoid Arthritis. Nat. Biotechnol., (2013) 31:142-147 (影响因子: 32.44)
Hansen, KD.#, Timp, W.#, Bravo, HC.#, Sabunciyan, S.#, Langmead, B.#, McDonald, OG., Wen, B., Wu, H., Liu, Y., Diep, D., Briem, E., Zhang, K., Irizarry, RA*, and Feinberg, AP*. Increased Methylation Variation in Epigenetic Domains Across Cancer Types. Nat. Genetics, 2011, 43:768-775 (影响因子: 35.53)
Liu, Y., Subrahmanyam, R., Chakraborty, T., Sen, R. and Desiderio, S. A Plant Homeodomain in RAG-2 that Binds Hypermethylated Lysine 4 of Histone H3 is Necessary For Efficient Antigen-Receptor-Gene Rearrangement. Immunity, (2007) 27:561-571 (封面故事, 影响因子: 21.64)
综述
Qiu, W., Liu, Y. DNA Methylation of the MHC Region in Rheumatoid Arthritis: Perspectives and Challenges. The Journal of Rheumatology, (2020) 47(11):1597-1599
Jin, Z., Liu, Y. DNA methylation in human diseases. Genes & Diseases, (2018) 5:1
Xue, Y., Lameijer, EW., Ye, K., Zhang, K., Chang, S., Wang, X., Wu, J., Gao, G., Zhao, F., Li, J., Han, C., Xu, S., Xiao, J., Yang, X., Ying, X., Zhang, X., Chen, WH., Liu, Y., Zhang, Z., Huang, K., Yu, J. Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics, (2016) 14(5):253-261
Liu, Y., Zhang, L., Desiderio, S. Temporal and Spatial Regulation of V(D)J Recombination Interactions of Extrinsic Factors with the RAG Complex. V(D)J Recombination (2009) Landes Bioscience, ISBN-13: 978-1441902955
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