​课题组围绕器官再生的表观组学和生物信息学主要进行以下几方面的研究：（1）通过单细胞测序等高通量技术手段检测疾病与器官再生的各种组学图谱，建立相关数据库。（2）开发统计建模、机器学习、网络重构等生物信息学分析方法。（3）揭示疾病与器官再生相关的表观调控机制，确定疾病治疗与器官再生的潜在作用靶点。（4）构建疾病发生与器官再生的多维数学模型，并进行相应的模拟与预测。

   

071010-生物化学与分子生物学
0710J3-生物信息学
0710Z1-基因组学

器官再生的表观组学与生物信息学研究
组学数据分析与算法开发

2009-09--2014-07   中国科学院上海生命科学研究院   生物信息学博士
2005-09--2009-07   重庆大学   学士

   

2020-12~现在, 中国科学院广州生物医药与健康研究院, 研究员
2014-12~2020-11,Johns Hopkins University, 博士后

   

（1） Wilmer杰出博士后奖, 一等奖, 研究所（学校）, 2018

   

[1] Briefings in Bioinformatics. 2024, 第 7 作者  通讯作者  
[2] Nature Communications. 2024, 第 15 作者  通讯作者  
[3] Hepatology. 2024, 第 12 作者  通讯作者  
[4] Dapeng Sun, Xiaojie Gan, Lei Liu, Yuan Yang, Dongyang Ding, Wen Li, Junyao Jiang, Wenbin Ding, Linghao Zhao, Guojun Hou, Jian Yu, Jie Wang, Fu Yang, Shengxian Yuan, Weiping Zhou. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. CELL DEATH AND DISEASE[J]. 2022, 第 12 作者  通讯作者  13(5): 1-12, 
[5] Jiang, Junyao, Lyu, Pin, Li, Jinlian, Huang, Sunan, Tao, Jiawang, Blackshaw, Seth, Qian, Jiang, Wang, Jie. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. ISCIENCE[J]. 2022, 第 8 作者  通讯作者  25(11): http://dx.doi.org/10.1016/j.isci.2022.105359.
[6] Xin, Ying, Lyu, Pin, Jiang, Junyao, Zhou, Fengquan, Wang, Jie, Blackshaw, Seth, Qian, Jiang. LRLoop: a method to predict feedback loops in cell-cell communication. BIOINFORMATICS[J]. 2022, 第 5 作者38(17): 4117-4126, http://dx.doi.org/10.1093/bioinformatics/btac447.
[7] Dapeng Sun, Xiaojie Gan, Lei Liu, Yuan Yang, Dongyang Ding, Wen Li, Junyao Jiang, Wenbin Ding, Linghao Zhao, Guojun Hou, Jian Yu, Jie Wang, Fu Yang, Shengxian Yuan, Weiping Zhou. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. CELL DEATH AND DISEASE[J]. 2022, 第 11 作者13(5): 1-12, 
[8] Jiang, Junyao, Lyu, Pin, Li, Jinlian, Huang, Sunan, Tao, Jiawang, Blackshaw, Seth, Qian, Jiang, Wang, Jie. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. ISCIENCE[J]. 2022, 第 11 作者25(11): http://dx.doi.org/10.1016/j.isci.2022.105359.
[9] Xin, Ying, Lyu, Pin, Jiang, Junyao, Zhou, Fengquan, Wang, Jie, Blackshaw, Seth, Qian, Jiang. LRLoop: a method to predict feedback loops in cell-cell communication. BIOINFORMATICS[J]. 2022, 第 5 作者38(17): 4117-4126, 
[10] Ma, Ding, Zhan, Daqian, Fu, Yi, Wei, Shuang, Lal, Bachchu, Wang, Jie, Li, Yunqing, LopezBertoni, Hernando, Yalcin, Fatih, Dzaye, Omar, Eberhart, Charles G, Laterra, John, Wilson, Mary Ann, Ying, Mingyao, Xia, Shuli. Mutant IDH1 promotes phagocytic function of microglia/macrophages in gliomas by downregulating ICAM1. CANCER LETTERS[J]. 2021, 第 6 作者517: 35-45, http://dx.doi.org/10.1016/j.canlet.2021.05.038.
[11] Ma, Ding, Zhan, Daqian, Fu, Yi, Wei, Shuang, Lal, Bachchu, Wang, Jie, Li, Yunqing, LopezBertoni, Hernando, Yalcin, Fatih, Dzaye, Omar, Eberhart, Charles G, Laterra, John, Wilson, Mary Ann, Ying, Mingyao, Xia, Shuli. Mutant IDH1 promotes phagocytic function of microglia/macrophages in gliomas by downregulating ICAM1. CANCER LETTERS[J]. 2021, 第 6 作者517: 35-45, http://dx.doi.org/10.1016/j.canlet.2021.05.038.
[12] Thanh Hoang, Wang, Jie, Boyd, Patrick, Wang, Fang, Santiago, Clayton, Jiang, Lizhi, Yoo, Sooyeon, Lahne, Manuela, Todd, Levi J, Jia, Meng, Saez, Cristian, Keuthan, Casey, Palazzo, Isabella, Squires, Natalie, Campbell, Warren A, Rajaii, Fatemeh, Parayil, Trisha, Trinh, Vickie, Kim, Dong Won, Wang, Guohua, Campbell, Leah J, Ash, John, Fischer, Andy J, Hyde, David R, Qian, Jiang, Blackshaw, Seth. Gene regulatory networks controlling vertebrate retinal regeneration. SCIENCE[J]. 2020, 第 2 作者370(6519): 934-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000594441500042.
[13] Wang, Lei, Kaya, Koray D, Kim, Sujung, Brooks, Matthew J, Wang, Jie, Xin, Ying, Qian, Jiang, Swaroop, Anand, Handa, James T. Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. FREE RADICAL BIOLOGY AND MEDICINE[J]. 2020, 第 5 作者156: 176-189, http://dx.doi.org/10.1016/j.freeradbiomed.2020.06.004.
[14] Kallman, Alyssa, Capowski, Elizabeth E, Wang, Jie, Kaushik, Aniruddha M, Jansen, Alex D, Edwards, Kimberly L, Chen, Liben, Berlinicke, Cynthia A, Phillips, M Joseph, Pierce, Eric A, Qian, Jiang, Wang, TzaHuei, Gamm, David M, Zack, Donald J. Investigating cone photoreceptor development using patient-derived NRL null retinal organoids. COMMUNICATIONS BIOLOGY[J]. 2020, 第 3 作者3(1): 1-13, https://doaj.org/article/db517a6b8b0b4b128d88c83365b08645.
[15] Thanh Hoang, Wang, Jie, Boyd, Patrick, Wang, Fang, Santiago, Clayton, Jiang, Lizhi, Yoo, Sooyeon, Lahne, Manuela, Todd, Levi J, Jia, Meng, Saez, Cristian, Keuthan, Casey, Palazzo, Isabella, Squires, Natalie, Campbell, Warren A, Rajaii, Fatemeh, Parayil, Trisha, Trinh, Vickie, Kim, Dong Won, Wang, Guohua, Campbell, Leah J, Ash, John, Fischer, Andy J, Hyde, David R, Qian, Jiang, Blackshaw, Seth. Gene regulatory networks controlling vertebrate retinal regeneration. SCIENCE[J]. 2020, 第 2 作者370(6519): 934-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000594441500042.
[16] Wang, Lei, Kaya, Koray D, Kim, Sujung, Brooks, Matthew J, Wang, Jie, Xin, Ying, Qian, Jiang, Swaroop, Anand, Handa, James T. Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. FREE RADICAL BIOLOGY AND MEDICINE[J]. 2020, 第 5 作者156: 176-189, http://dx.doi.org/10.1016/j.freeradbiomed.2020.06.004.
[17] Kallman, Alyssa, Capowski, Elizabeth E, Wang, Jie, Kaushik, Aniruddha M, Jansen, Alex D, Edwards, Kimberly L, Chen, Liben, Berlinicke, Cynthia A, Phillips, M Joseph, Pierce, Eric A, Qian, Jiang, Wang, TzaHuei, Gamm, David M, Zack, Donald J. Investigating cone photoreceptor development using patient-derived NRL null retinal organoids. COMMUNICATIONS BIOLOGY[J]. 2020, 第 3 作者3(1): 1-13, https://doaj.org/article/db517a6b8b0b4b128d88c83365b08645.
[18] Blackshaw, Seth, Hoang, Thanh, Wang, Jie, Lahne, Manuela, Todd, Levi, Santiago, Clayton, Squires, Nathalie, Boyd, Patrick, Ash, John D, Fischer, Andrew J, Qian, Jiang, Hyde, David R. Comparative transcriptomic and epigenomic analysis identifes regulators of neurogenic competence in retinal Muller glia. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 3 作者59(9): https://www.webofscience.com/wos/woscc/full-record/WOS:000442912502255.
[19] Santiago, Clayton, Hooper, Marcus, Thanh Hoang, Wang, Jie, Qian, Jiang, Blackshaw, Seth, Ash, John D. Muller cell transcriptional unit to regulate stress induced LIF expression. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 4 作者59(9): 479-484, https://www.webofscience.com/wos/woscc/full-record/WOS:000442912507192.
[20] Hyde, David R, Boyd, Patrick, Lahne, Manuela, Thanh Hoang, Wang, Jie, Santiago, Clayton, Blackshaw, Seth, Qian, Jiang, Ash, John D, Fischer, Andy. Transcriptomics analysis of Muller glia in response to different damage paradigms in the adult zebrafish retina. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 5 作者59(9): https://www.webofscience.com/wos/woscc/full-record/WOS:000442912502256.
[21] Newmann, Elizabeth A, Kim, Dong Won, Wan, Jun, Wang, Jie, Qian, Jiang, Blackshaw, Seth. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. DEVELOPMENTAL BIOLOGY[J]. 2018, 第 4 作者439(2): 102-111, https://www.webofscience.com/wos/woscc/full-record/WOS:000434003600006.
[22] Jie Wang, Cristina Zibetti, Peng Shang, Srinivasa R Sripathi, Pingwu Zhang, Marisol Cano, Thanh Hoang, Shuli Xia, Hongkai Ji, Shannath L Merbs, Donald J Zack, James T Handa, Debasish Sinha, Seth Blackshaw, Jiang Qian. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. NATURE COMMUNICATIONS[J]. 2018, 第 1 作者9(1): https://doaj.org/article/0f18f4981da94ca68e6f36c5fb7554b0.
[23] Shuang Wei, Jie Wang, Olutobi Oyinlade, Ding Ma, Shuyan Wang, Lisa Kratz, Bachchu Lal, Qingfu Xu, Senquan Liu, Sagar R Shah, Hao Zhang, Yunqing Li, Alfredo QuionesHinojosa, Heng Zhu, Zhiyong Huang, Linzhao Cheng, Jiang Qian, Shuli Xia. Heterozygous IDH1 R132H created by "single base editing" inhibits human astroglial cell growth by downregulating YAP. ONCOGENE[J]. 2018, 第 2 作者37(38): 5160-5174, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590918/.
[24] Blackshaw, Seth, Hoang, Thanh, Wang, Jie, Lahne, Manuela, Todd, Levi, Santiago, Clayton, Squires, Nathalie, Boyd, Patrick, Ash, John D, Fischer, Andrew J, Qian, Jiang, Hyde, David R. Comparative transcriptomic and epigenomic analysis identifes regulators of neurogenic competence in retinal Muller glia. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 3 作者59(9): https://www.webofscience.com/wos/woscc/full-record/WOS:000442912502255.
[25] Santiago, Clayton, Hooper, Marcus, Thanh Hoang, Wang, Jie, Qian, Jiang, Blackshaw, Seth, Ash, John D. Muller cell transcriptional unit to regulate stress induced LIF expression. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 4 作者59(9): 479-484, https://www.webofscience.com/wos/woscc/full-record/WOS:000442912507192.
[26] Hyde, David R, Boyd, Patrick, Lahne, Manuela, Thanh Hoang, Wang, Jie, Santiago, Clayton, Blackshaw, Seth, Qian, Jiang, Ash, John D, Fischer, Andy. Transcriptomics analysis of Muller glia in response to different damage paradigms in the adult zebrafish retina. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE[J]. 2018, 第 5 作者59(9): https://www.webofscience.com/wos/woscc/full-record/WOS:000442912502256.
[27] Newmann, Elizabeth A, Kim, Dong Won, Wan, Jun, Wang, Jie, Qian, Jiang, Blackshaw, Seth. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. DEVELOPMENTAL BIOLOGY[J]. 2018, 第 4 作者439(2): 102-111, https://www.webofscience.com/wos/woscc/full-record/WOS:000434003600006.
[28] Jie Wang, Cristina Zibetti, Peng Shang, Srinivasa R Sripathi, Pingwu Zhang, Marisol Cano, Thanh Hoang, Shuli Xia, Hongkai Ji, Shannath L Merbs, Donald J Zack, James T Handa, Debasish Sinha, Seth Blackshaw, Jiang Qian. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. NATURE COMMUNICATIONS[J]. 2018, 第 1 作者9(1): https://doaj.org/article/0f18f4981da94ca68e6f36c5fb7554b0.
[29] Shuang Wei, Jie Wang, Olutobi Oyinlade, Ding Ma, Shuyan Wang, Lisa Kratz, Bachchu Lal, Qingfu Xu, Senquan Liu, Sagar R Shah, Hao Zhang, Yunqing Li, Alfredo QuionesHinojosa, Heng Zhu, Zhiyong Huang, Linzhao Cheng, Jiang Qian, Shuli Xia. Heterozygous IDH1 R132H created by "single base editing" inhibits human astroglial cell growth by downregulating YAP. ONCOGENE[J]. 2018, 第 2 作者37(38): 5160-5174, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590918/.
[30] Yuan, Shengxian, Wang, Jie, Yang, Yuan, Zhang, Jin, Liu, Hui, Xiao, Juanjuan, Xu, Qingguo, Huang, Xinhui, Xiang, Bangde, Zhu, Shaoliang, Li, Lequn, Liu, Jingfeng, Liu, Lei, Zhou, Weiping. The Prediction of Clinical Outcome in Hepatocellular Carcinoma Based on a Six-Gene Metastasis Signature. CLINICAL CANCER RESEARCH[J]. 2017, 第 2 作者  通讯作者  23(1): 289-297, http://dx.doi.org/10.1158/1078-0432.CCR-16-0395.
[31] Han, Xiaomei, Wang, Jenny, Wang, Jie, Liu, Sheng, Hu, Jianfei, Zhu, Heng, Qian, Jiang. ScaPD: a database for human scaffold proteins. BMC BIOINFORMATICS[J]. 2017, 第 3 作者18(11): 87-91, http://dx.doi.org/10.1186/s12859-017-1806-6.
[32] Yuan, Shengxian, Wang, Jie, Yang, Yuan, Zhang, Jin, Liu, Hui, Xiao, Juanjuan, Xu, Qingguo, Huang, Xinhui, Xiang, Bangde, Zhu, Shaoliang, Li, Lequn, Liu, Jingfeng, Liu, Lei, Zhou, Weiping. The Prediction of Clinical Outcome in Hepatocellular Carcinoma Based on a Six-Gene Metastasis Signature. CLINICAL CANCER RESEARCH[J]. 2017, 第 11 作者23(1): 289-297, http://dx.doi.org/10.1158/1078-0432.CCR-16-0395.
[33] Han, Xiaomei, Wang, Jenny, Wang, Jie, Liu, Sheng, Hu, Jianfei, Zhu, Heng, Qian, Jiang. ScaPD: a database for human scaffold proteins. BMC BIOINFORMATICS[J]. 2017, 第 3 作者18(11): 87-91, http://dx.doi.org/10.1186/s12859-017-1806-6.
[34] Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian. Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. PLOS COMPUTATIONAL BIOLOGY[J]. 2016, 第 1 作者12(4): https://doaj.org/article/12e4f84d74c94a379817675912e30874.
[35] Yuan, Shengxian, Wang, Jie, Yang, Fu, Tao, Qifei, Zhang, Jin, Wang, Lili, Yang, Yuan, Liu, Hui, Wang, Zhenguang, Xu, Qingguo, Fan, Jia, Liu, Lei, Sun, Shuhan, Zhou, Weiping. Long Noncoding RNA DANCR Increases Stemness Features of Hepatocellular Carcinoma by Derepression of CTNNB1. HEPATOLOGY[J]. 2016, 第 2 作者63(2): 499-511, https://www.webofscience.com/wos/woscc/full-record/WOS:000373296800008.
[36] Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian. Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. PLOS COMPUTATIONAL BIOLOGY[J]. 2016, 第 1 作者12(4): https://doaj.org/article/12e4f84d74c94a379817675912e30874.
[37] Yuan, Shengxian, Wang, Jie, Yang, Fu, Tao, Qifei, Zhang, Jin, Wang, Lili, Yang, Yuan, Liu, Hui, Wang, Zhenguang, Xu, Qingguo, Fan, Jia, Liu, Lei, Sun, Shuhan, Zhou, Weiping. Long Noncoding RNA DANCR Increases Stemness Features of Hepatocellular Carcinoma by Derepression of CTNNB1. HEPATOLOGY[J]. 2016, 第 2 作者63(2): 499-511, https://www.webofscience.com/wos/woscc/full-record/WOS:000373296800008.
[38] Xinlu Yuan, Jie Wang, Xiaoyan Tang, Yixue Li, Pu Xia, Xin Gao. Berberine ameliiorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and IncRNA expression profiles.. Journal of Translational Medicine[J]. 2015, 第 2 作者13(1): 1-11, https://pubmed.ncbi.nlm.nih.gov/25623289.
[39] Xinlu Yuan, Jie Wang, Xiaoyan Tang, Yixue Li, Pu Xia, Xin Gao. Berberine ameliiorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and IncRNA expression profiles.. Journal of Translational Medicine[J]. 2015, 第 2 作者13(1): 1-11, https://pubmed.ncbi.nlm.nih.gov/25623289.
[40] Yuan, ShengXian, Tao, QiFei, Wang, Jie, Yang, Fu, Liu, Lei, Wang, LiLi, Zhang, Jin, Yang, Yuan, Liu, Hui, Wang, Fang, Sun, ShuHan, Zhou, WeiPing. Antisense long non-coding RNA PCNA-AS1 promotes tumor growth by regulating proliferating cell nuclear antigen in hepatocellular carcinoma. CANCER LETTERS[J]. 2014, 第 3 作者349(1): 87-94, http://dx.doi.org/10.1016/j.canlet.2014.03.029.
[41] Yuan, ShengXian, Tao, QiFei, Wang, Jie, Yang, Fu, Liu, Lei, Wang, LiLi, Zhang, Jin, Yang, Yuan, Liu, Hui, Wang, Fang, Sun, ShuHan, Zhou, WeiPing. Antisense long non-coding RNA PCNA-AS1 promotes tumor growth by regulating proliferating cell nuclear antigen in hepatocellular carcinoma. CANCER LETTERS[J]. 2014, 第 3 作者349(1): 87-94, http://dx.doi.org/10.1016/j.canlet.2014.03.029.
[42] Jie Wang, Yu Wang, Zhuo Wang, Lei Liu, Xin-Guang Zhu, Xiaotu Ma. Synchronization of cytoplasm and transferred mitochondrial ribosomal protein gene espression in land plants is linked to telo-box motif enrichment. BMC Evolutionary Biology[J]. 2011, 第 1 作者11(1): 1-15, https://pubmed.ncbi.nlm.nih.gov/21668973/.
[43] Jie Wang, Yu Wang, Zhuo Wang, Lei Liu, Xin-Guang Zhu, Xiaotu Ma. Synchronization of cytoplasm and transferred mitochondrial ribosomal protein gene espression in land plants is linked to telo-box motif enrichment. BMC Evolutionary Biology[J]. 2011, 第 1 作者11(1): 1-15, https://pubmed.ncbi.nlm.nih.gov/21668973/.

   

（ 1 ） 肝再生与肝纤维化的表观组学研究, 负责人, 研究所自选, 2020-12--2024-12
（ 2 ） 单细胞测序确定药物引起肝损伤后再生的核心调控因子, 负责人, 国家任务, 2022-01--2025-12
（ 3 ） 组织再生与疾病发生的多组学研究, 负责人, 国家任务, 2023-01--2025-12

现指导学生

周广琦  硕士研究生  071009-细胞生物学  

汤杪庥  硕士研究生  071010-生物化学与分子生物学  

李金连  博士研究生  071010-生物化学与分子生物学  

梁嫣然  硕士研究生  086000-生物与医药  

蒋熙平  硕士研究生  071009-细胞生物学