蔡軍

蔡 軍 ( Jun CAI )

職 稱: 研究員

職 務: 碩士生導師

學科類別: 基因組學/生物信息學

2009年受聘為中國科學院北京基因組研究所研究員，從事基於下一代測序技術的計算生物學和癌症基因組學研究。

研究方向為計算生物學。旨在整合多種來源的生物數據，利用統計學和機器學習方法設計模型，研究相關生物科學問題。曾針對胚胎幹細胞分化/增殖過程，開展了一系列系統生物學研究工作。（1）揭示Klf（Kruppel-like factor）家族在老鼠胚胎幹細胞基因轉錄過程中調節功能；（2）利用統計學模型預測幹細胞基因組中的sox2-nanog-oct4 共轉錄調控模塊；（3）設計新的聚類演演算法，對跨物種的表達數據進行分析，比較物種間保守的調控網路結構，揭示了Klf家族基因調控模塊的物種特異性。目前正從事基於下一代測序技術的基因組/轉錄組的結構變異研究，即利用測序數據：（1）分析癌症基因組中特有的結構變異形式，如大片段刪除以及特異性病毒片斷插入；（2）分析癌症轉錄組的特異性結構類型。

1. 國家自然科學基金委員會面上項目，“HeLa細胞中非整倍體基因組結構與腫瘤細胞適應性關係的研究”，在研，課題負責人;

2.國家重點基礎研究發展計劃項目，基於新一代測序的生物信息學理論與方法,，在研，主要學術骨幹.

1. Caihong Zheng, Xuexia Miao, Yanen Li, Ying Huang, Jue Ruan, Xi Ma, Li Wang, Chung-I Wu, Jun Cai, Determination of genomic copy number alteration emphasizing a restriction-site based strategy of genome re-sequencing, Bioinformatics

2. Lan Jiang, Jing Zhang, Jing-Jing Wang, Lu Wang, Li Zhang, Guoqiang Li, Xiaodan Yang, Xin Ma, Xin Sun, Jun Cai, Jun Zhang, Xingxu Huang, Miao Yu, Xuegeng Wang, Feng Liu, Chung-I Wu, Chuan He, Bo Zhang, Weimin Ci, Jiang Liu. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos

3. Qiang Gong, Yong tao, Jian-rong Yang, Jun Cai, Yunfei Yuan, et al., Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags, BMC Genomics

4. Yong Tao*, Jue Ruan*, Shiou-Hwei Yeh*, Xuemei Lu*, Yu Wang*, Weiwei Zhai*, Jun Cai*, et al., Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data, PNAS

5. 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. Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng and Sheng Zhong. Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Research,

7. Jianming Jiang, Yun-Shen Chan*, Yuin-Han Loh*, Jun Cai*, Guo-Qing Tong, Ching-Aeng Lim, Paul Robson, Sheng Zhong and Huck-Hui Ng. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nature Cell Biology. 10: 353-360, 2008. (* contribute equally) 8. Jun Cai, Ying Huang, Fei Li and Yanda Li. Alteration of protein subcellular location and domain formation by alternative translational initiation. Proteins,

9. Jun Cai, Jing Zhang, Ying Huang and Yanda Li. ATID: a web-oriented database for collection of publicly available alternative translational initiation events. Bioinformatics