基本信息
蔡 军 ( Jun CAI )
职 称: 研究员
职 务: 硕士生导师
学科类别: 基因组学/生物信息学
教育及工作经历
2009年受聘为中国科学院北京基因组研究所研究员，从事基于下一代测序技术的计算生物学和癌症基因组学研究。
专业工作
研究方向为计算生物学。旨在整合多种来源的生物数据，利用统计学和机器学习方法设计模型，研究相关生物科学问题。曾针对胚胎干细胞分化/增殖过程，开展了一系列系统生物学研究工作。（1）揭示Klf（Kruppel-like factor）家族在老鼠胚胎干细胞基因转录过程中调节功能；（2）利用统计学模型预测干细胞基因组中的sox2-nanog-oct4 共转录调控模块；（3）设计新的聚类算法，对跨物种的表达数据进行分析，比较物种间保守的调控网络结构，揭示了Klf家族基因调控模块的物种特异性。目前正从事基于下一代测序技术的基因组/转录组的结构变异研究，即利用测序数据：（1）分析癌症基因组中特有的结构变异形式，如大片段删除以及特异性病毒片断插入；（2）分析癌症转录组的特异性结构类型。
承担科研项目情况
1. 国家自然科学基金委员会面上项目，“HeLa细胞中非整倍体基因组结构与肿瘤细胞适应性关系的研究”，在研，课题负责人;
2.国家重点基础研究发展计划项目，基于新一代测序的生物信息学理论与方法,，在研，主要学术骨干.
代表论著
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
