基本信息
蔡 軍 ( Jun CAI )
職 稱: 研究員
職 務(wù): 碩士生導(dǎo)師
學(xué)科類別: 基因組學(xué)/生物信息學(xué)
教育及工作經(jīng)歷
2009年受聘為 中國科學(xué)院 北京基因組研究所研究員，從事基于下一代測序技術(shù)的計算生物學(xué)和癌癥基因組學(xué)研究。
專業(yè)工作
研究方向為計算生物學(xué)。旨在整合多種來源的生物數(shù)據(jù)，利用統(tǒng)計學(xué)和機(jī)器學(xué)習(xí)方法設(shè)計模型，研究相關(guān)生物科學(xué)問題。曾針對胚胎干細(xì)胞分化/增殖過程，開展了一系列系統(tǒng)生物學(xué)研究工作。（1）揭示Klf（Kruppel-like factor）家族在老鼠胚胎干細(xì)胞 基因轉(zhuǎn)錄過程中調(diào)節(jié)功能；（2）利用統(tǒng)計學(xué)模型預(yù)測干細(xì)胞基因組中的sox2-nanog-oct4 共轉(zhuǎn)錄調(diào)控模塊；（3）設(shè)計新的聚類算法，對跨物種的表達(dá)數(shù)據(jù)進(jìn)行分析，比較物種間保守的 調(diào)控網(wǎng)絡(luò)結(jié)構(gòu)，揭示了Klf家族基因調(diào)控模塊的物種特異性。目前正從事基于下一代測序技術(shù)的基因組/轉(zhuǎn)錄組的結(jié)構(gòu)變異研究，即利用測序數(shù)據(jù)：（1）分析癌癥基因組中特有的結(jié)構(gòu)變異形式，如大片段刪除以及特異性病毒片斷插入；（2）分析癌癥轉(zhuǎn)錄組的特異性結(jié)構(gòu)類型。
承擔(dān)科研項目情況
1. 國家自然科學(xué)基金委員會面上項目，“HeLa細(xì)胞中非整倍體基因組結(jié)構(gòu)與腫瘤細(xì)胞適應(yīng)性關(guān)系的研究”，在研， 課題負(fù)責(zé)人;
2.國家重點基礎(chǔ)研究發(fā)展計劃項目，基于新一代測序的生物信息學(xué)理論與方法,，在研，主要學(xué)術(shù)骨干.
代表論著
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