071022-基因组学
071021-生物信息学
071007-遗传学

体细胞组学分析；单细胞组学
精准基因组医学数据分析

1999-09--2005-12   清华大学   研究生-博士
1995-09--1999-09   清华大学   本科-学士

-- 研究生

-- 博士

   

2009-05~现在, 中国科学院北京基因组研究所, 研究员
2006-03~2008-06,美国伊利诺伊大学香槟分校, 博士后

精准基因组医学新技术前沿研讨课
遗传咨询与未来医疗
基因组学与医学健康研讨课
遗传咨询入门

   

[1] Lifei Wang, Rui Nie, Zhang Zhang, Weiwei Gu, Shuo Wang, Anqi Wang, Jiang Zhang, Jun Cai. A deep generative framework with embedded vector arithmetic and classifier for sample generation, label transfer, and clustering of single-cell data. CELL REPORTS METHODS[J]. 2023, 3(8): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475846/.
[2] Cui, Guanshen, Dong, Kangning, Zhou, JiaYi, Li, Shang, Wu, Ying, Han, Qinghua, Yao, Bofei, Shen, Qunlun, Zhao, YongLiang, Yang, Ying, Cai, Jun, Zhang, Shihua, Yang, YunGui. Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration. NATURE COMMUNICATIONS[J]. 2023, 14(1): http://dx.doi.org/10.1038/s41467-023-39016-0.
[3] Lifei Wang, Rui Nie, Jiang Zhang, Jun Cai. scCapsNet-mask: an updated version of scCapsNet with extended applicability in functional analysis related to scRNA-seq data. BMC Bioinformatics[J]. 2022, [4] Lifei Wang, Xuexia Miao, Rui Nie, Zhang Zhang, Jiang Zhang, Jun Cai. MultiCapsNet: A General Framework for Data Integration and Interpretable Classification. FRONTIERS IN GENETICS[J]. 2021, 12: https://doaj.org/article/5accd7e0eded434394e3092cb1cfcb17.
[5] Miao, Xuexia, Li, Yueying, Zheng, Caihong, Wang, Lifei, Jin, Chen, Chen, Lei, Mi, Shuangli, Zhai, Weiwei, Wang, QianFei, Cai, Jun. A promising iPS-based single-cell cloning strategy revealing signatures of somatic mutations in heterogeneous normal cells. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2020, 18: 2326-2335, http://dx.doi.org/10.1016/j.csbj.2020.08.026.
[6] Wang, Lifei, Nie, Rui, Yu, Zeyang, Xin, Ruyue, Zheng, Caihong, Zhang, Zhang, Zhang, Jiang, Cai, Jun. An interpretable deep-learning architecture of capsule networks for identifying cell-type gene expression programs from single-cell RNA-sequencing data. NATURE MACHINE INTELLIGENCE[J]. 2020, 2(11): 693-+, http://dx.doi.org/10.1038/s42256-020-00244-4.
[7] Zhang, Yuezheng, Li, Yawei, Li, Tao, Shen, Xu, Zhu, Tianqi, Tao, Yong, Li, Xueying, Wang, Di, Ma, Qin, Hu, Zheng, Liu, Jialin, Ruan, Jue, Cai, Jun, Wang, HurngYi, Lu, Xuemei. Genetic Load and Potential Mutational Meltdown in Cancer Cell Populations. MOLECULAR BIOLOGY AND EVOLUTION[J]. 2019, 36(3): 541-552, http://ir.amss.ac.cn/handle/2S8OKBNM/34334, http://www.irgrid.ac.cn/handle/1471x/6869268, http://ir.amss.ac.cn/handle/2S8OKBNM/34335, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000462585100009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[8] Miao, Xuexia, Li, Xi, Wang, Lifei, Zheng, Caihong, Cai, Jun. DSMNC: a database of somatic mutations in normal cells. NUCLEIC ACIDS RESEARCH[J]. 2019, 47(D1): D971-D975, [9] Li, Qiuling, Jiao, Jie, Li, Huijun, Wan, Huajing, Zheng, Caihong, Cai, Jun, Bao, Shilai. Histone arginine methylation by Prmt5 is required for lung branching morphogenesis through repression of BMP signaling. JOURNAL OF CELL SCIENCE[J]. 2018, 131(14): https://www.webofscience.com/wos/woscc/full-record/WOS:000443435600014.
[10] Perry, Elizabeth B, MakohonMoore, Alvin, Zheng, Caihong, Kaufman, Charles K, Cai, Jun, IacobuzioDonahue, Christine A, White, Richard M. Tumor diversity and evolution revealed through RADseq. ONCOTARGET[J]. 2017, 8(26): 41792-41805, [11] 聂瑞, 蔡军. 体细胞谱系追踪研究进展. 发育医学电子杂志[J]. 2017, 5(1): 50-54, http://lib.cqvip.com/Qikan/Article/Detail?id=672989360.
[12] Zou, Xiaoting, Meng, Jiao, Li, Li, Han, Wanhong, Li, Changyin, Zhong, Ran, Miao, Xuexia, Cai, Jun, Zhang, Yong, Zhu, Dahai. Acetoacetate Accelerates Muscle Regeneration and Ameliorates Muscular Dystrophy in Mice. JOURNAL OF BIOLOGICAL CHEMISTRY[J]. 2016, 291(5): 2181-2195, http://dx.doi.org/10.1074/jbc.M115.676510.
[13] Gao, Shuai, Zheng, Caihong, Chang, Gang, Liu, Wenqiang, Kou, Xiaochen, Tan, Kun, Tao, Li, Xu, Kai, Wang, Hong, Cai, Jun, Tian, Jianhui, Gao, Shaorong. Unique features of mutations revealed by sequentially reprogrammed induced pluripotent stem cells. NATURE COMMUNICATIONS[J]. 2015, 6: http://dx.doi.org/10.1038/ncomms7318.
[14] Yin, Shanye, Yang, Jing, Lin, Bin, Deng, Wenjun, Zhang, Yuchao, Yi, Xianfu, Shi, Yufang, Tao, Yong, Cai, Jun, Wu, ChungI, Zhao, Guoping, Hurst, Laurence D, Zhang, Jie, Hu, Landian, Kong, Xiangyin. Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients. SCIENTIFIC REPORTS[J]. 2014, 4: http://dx.doi.org/10.1038/srep06036.
[15] Cai, Jun, Miao, Xuexia, Li, Yueying, Smith, Cory, Tsang, Kitman, Cheng, Linzhao, Wang, Qianfei. Whole-Genome Sequencing Identifies Genetic Variances in Culture-Expanded Human Mesenchymal Stem Cells. STEM CELL REPORTS[J]. 2014, 3(2): 227-233, https://doaj.org/article/c40d1277d630445b9132d2280c95f7d3.
[16] Gong, Qiang, Tao, Yong, Yang, JianRong, Cai, Jun, Yuan, Yunfei, Ruan, Jue, Yang, Jin, Liu, Hailiang, Li, Wanghua, Lu, Xuemei, Zhuang, ShiMei, Wang, San Ming, Wu, ChungI. Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags. BMC GENOMICS[J]. 2013, 14(1): 51-51, http://www.corc.org.cn/handle/1471x/2374295.
[17] Zheng, Caihong, Miao, Xuexia, Li, Yanen, Huang, Ying, Ruan, Jue, Ma, Xi, Wang, Li, Wu, ChungI, Cai, Jun. Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing. BIOINFORMATICS[J]. 2013, 29(22): 2813-2821, http://dx.doi.org/10.1093/bioinformatics/btt481.
[18] Jiang, Lan, Zhang, Jing, Wang, JingJing, Wang, Lu, Zhang, Li, Li, Guoqiang, Yang, Xiaodan, Ma, Xin, Sun, Xin, Cai, Jun, Zhang, Jun, Huang, Xingxu, Yu, Miao, Wang, Xuegeng, Liu, Feng, Wu, ChungI, He, Chuan, Zhang, Bo, Ci, Weimin, Liu, Jiang. Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos. CELL[J]. 2013, 153(4): 773-784, http://dx.doi.org/10.1016/j.cell.2013.04.041.
[19] Tao, Yong, Ruan, Jue, Yeh, ShiouHwei, Lu, Xuemei, Wang, Yu, Zhai, Weiwei, Cai, Jun, Ling, Shaoping, Gong, Qiang, Chong, Zecheng, Qu, Zhengzhong, Li, Qianqian, Liu, Jiang, Yang, Jin, Zheng, Caihong, Zeng, Changqing, Wang, HurngYi, Zhang, Jing, Wang, ShengHan, Hao, Lingtong, Dong, Lili, Li, Wenjie, Sun, Min, Zou, Wei, Yu, Caixia, Li, Chaohua, Liu, Guojing, Jiang, Lan, Xu, Jin, Huang, Huanwei, Li, Chunyan, Mi, Shuangli, Zhang, Bing, Chen, Baoxian, Zhao, Wenming, Hu, Songnian, Zhuang, ShiMei, Shen, Yang, Shi, Suhua, Brown, Christopher, White, Kevin P, Chen, DingShinn, Chen, PeiJer, Wu, ChungI. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA[J]. 2011, 108(29): 12042-12047, http://dx.doi.org/10.1073/pnas.1108715108.
[20] Cai, Jun, Xie, Dan, Fan, Zhewen, Chipperfield, Hiram, Marden, John, Wong, Wing H, Zhong, Sheng. Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells. PLOS COMPUTATIONAL BIOLOGY[J]. 2010, 6(3): https://doaj.org/article/5e76a9b9640f42c299e3791a60be2722.
[21] Jiang, Jianming, Chan, YunShen, Loh, YuinHan, Cai, Jun, Tong, GuoQing, Lim, ChingAeng, Robson, Paul, Zhong, Sheng, Ng, HuckHui. A core Klf circuitry regulates self-renewal of embryonic stem cells. NATURE CELL BIOLOGY[J]. 2008, 10(3): 353-U103, https://www.webofscience.com/wos/woscc/full-record/WOS:000253778300018.
[22] Xie, Dan, Cai, Jun, Chia, NaYu, Ng, Huck H, Zhong, Sheng. Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells. GENOME RESEARCH[J]. 2008, 18(8): 1325-1335, https://www.webofscience.com/wos/woscc/full-record/WOS:000258116100013.
[23] Cai Jun. A genome-wide survey of alternative translational initiation events in human.. Science in China Series C: Life Sciences. 2007, [24] Cai, J, Huang, Y, Li, F, Li, YD. Alteration of protein subcellular location and domain formation by alternative translational initiation. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS[J]. 2006, 62(3): 793-799, http://dx.doi.org/10.1002/prot.20785.
[25] Cai, J, Zhang, J, Huang, Y, Li, YD. ATID: a web-oriented database for collection of publicly available alternative translational initiation events. BIOINFORMATICS[J]. 2005, 21(23): 4312-4314, http://dx.doi.org/10.1093/bioinformatics/bti704.
[26] Cai, J, Huang, Y, Ji, L, Li, YD. Inferring protein-protein interactions from messenger RNA expression profiles with SVM. JOURNAL OF BIOLOGICAL SYSTEMS[J]. 2005, 13(3): 287-298, http://dx.doi.org/10.1142/S0218339005001525.
[27] Huang, Y, Cai, J, Ji, L, Li, YD. Classifying G-protein coupled receptors with bagging classification tree. COMPUTATIONAL BIOLOGY AND CHEMISTRY[J]. 2004, 28(4): 275-280, http://dx.doi.org/10.1016/j.compbiolchem.2004.08.001.

   

（ 1 ） 诱导多能干细胞的单细胞起源和特异性基因组变异来源组成的研究, 主持, 国家级, 2016-01--2019-12
（ 2 ） 基因组学与表观遗传信息深度挖掘, 主持, 国家级, 2018-07--2020-12

（1）A survey of somatic genome deletions and HBV DNA insertions in a Hepatocellular Carcinoma (HCC) case   Jun Cai   2010-09-27

已指导学生

张卓凡  硕士研究生  085238-生物工程  

李莹  硕士研究生  071022-基因组学  

庄雯  硕士研究生  0710Z1-基因组学  

李轩  硕士研究生  085238-生物工程  

苗雪霞  博士研究生  0710Z1-基因组学  

赵宁  硕士研究生  0710Z1-基因组学  

现指导学生

王力飞  博士研究生  0710Z1-基因组学  

于泽阳  博士研究生  0710Z1-基因组学  

崔博宇  博士研究生  0710Z1-基因组学  

许雯秋  博士研究生  0710Z1-基因组学  

王晓丹  硕士研究生  0710Z1-基因组学  

肖镜舒  硕士研究生  085238-生物工程  

聂瑞  博士研究生  0710Z1-基因组学  

李溪  硕士研究生  0710Z1-基因组学  

王翠霞  硕士研究生  0710Z1-基因组学  

李盼盼  博士研究生  0710Z1-基因组学