Group leader
Dr. CAI Jun, Principal Investigator. Bachelor degree (Tsinghua University , 1999), PhD (Tsinghua University , 2005), Postdoctoral Research Fellow (University of Illinois at Urbana-Champaign, 2006-2008).
Introduction
Our research group combines Computational biology and Genomics to investigate biological problems related to cancer genomics and stem cell genomics. The group is currently focusing on develop and use the single cell genome sequencing technology, to draw genomic variation map of somatic cells, thus to analyze the accumulation of genetic variation between healthy cell and in the evolutionary process from normal somatic cells into tumor cell.
Selected Publications
1. Lifei Wang, Rui Nie, Zeyang Yu, Ruyue Xin, Caihong Zheng, Zhang Zhang, Jiang Zhang* and Jun Cai*. An interpretable deep-learning architecture of capsule networks for identifying cell-type gene expression programs from single-cell RNA-sequencing data. Nature Machine Intelligence, 2020, 2, 693–703.
2. Xuexia Miao#, Yueying Li#, Caihong Zheng, Lifei Wang, Chen Jin, Lei Chen, Shuangli Mi, Weiwei Zhai, Qian-Fei Wang*, Jun Cai*. A promising iPS-based single-cell cloning strategy revealing signatures of somatic mutations in heterogeneous normal cells, Computational and Structural Biotechnology Journal, 2020, 18: 2326-2335.
3. Xuexia Miao#, Xi Li#, Lifei Wang, Caihong Zheng* and Jun Cai*. DSMNC:a database of somatic mutations in normal cells, Nucleic Acids Research, 2019, 47(D1): D971-D975.
4. Shuai Gao#, Caihong Zheng#, Gang Chang#, Wenqiang Liu, Xiaochen Kou, Kun Tan, Li Tao, Kai Xu, Hong Wang, Jun Cai*, Jianhui Tian* & Shaorong Gao*. Unique features of mutations revealed by sequentially reprogrammed induced pluripotent stem cells, Nature Communications, 2015, 6:6318.
5. Jun Cai, Xuexia Miao, Yueying Li, Cory Smith, Kitman Tsang, Linzhao Cheng* and Qian-fei Wang*. Whole-Genome Sequencing Identifies Genetic Variances in Culture-Expanded Human Mesenchymal Stem Cells, Stem Cell Reports, 2014, 3(2): 227-233.
6. Caihong Zheng, Xuexia Miao, Yanen Li, Ying Huang, Jue Ruan, Xi Ma, Li Wang, Chung-I Wu* and Jun Cai*. Determination of genomic copy number alteration emphasizing a restriction-site based strategy of genome re-sequencing, Bioinformatics, 2013, 29(22): 2813-2821.
7. Yong Tao#, Jue Rua#n, Shiou-Hwei Yeh#, Xuemei Lu#, Yu Wang#, Weiwei Zhai#, Jun Cai#, Shaoping Ling, Qiang Gong, Zecheng Chong, Zhengzhong Qu, Qianqian Li, Jiang Liu, Jin Yang, Caihong Zheng, Changqing Zeng, Hurng-Yi Wang, Jing Zhang, Sheng-Han Wang, Lingtong Hao, Lili Dong, Wenjie Li, Min Sun, Wei Zou, Caixia Yu, Chaohua Li, Guojing Liu, Lan Jiang, Jin Xu, Huanwei Huang, Chunyan Li, Shuangli Mi, Bing Zhang, Baoxian Chen, Wenming Zhao, Songnian Hu, Shi-Mei Zhuang, Yang Shen, Suhua Shi, Christopher Brown, Kevin P. White, Ding-Shinn Chen*, Pei-Jer Chen*, and Chung-I Wu*. 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, 2011, 108(29): 12042-12047.
8. Jun Cai, Dan Xie, Zhewen Fan, John Marden, Wing H. Wong, Sheng Zhong. Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells. PLoS Computational Biology, 6(3), doi:10.1371/journal.pcbi.1000707,2010.
Group Members
Staff
Dr. ZHENG Caihong, Assistant Professor
Dr. MIAO Xuexia, Assistant Professor
Dr. REN Likun, Assistant Professor
Graduate Students
XU Wenqiu, 2014
NIE Rui, 2015
YU Zeyang, 2016
LI Xi, 2018
LI Panpan, 2019
WANG Cuixia, 2019
LU Mengyue, 2020
TENG Yue, 2020
