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 邵振 研究员 研究组长 博士生导师

电子邮件  :shaozhenpicb.ac.cn
联系电话  :021-54920367
课题组主页:http://bioinfo.sibs.ac.cn/shaolab/


    研究方向  

•开发针对高通量生物数据分析的统计工具和计算模型
•基因表达调控机制研究


    研究领域  

1.开发用于分析与整合各种高通量生物数据的统计模型和计算工具
我们已经和正在开发一系列的用于生物序列 分析和高通量数据处理的统计模型及相关程序包。例如,我们已开发的MAnorm模型是较早的用于ChIP-Seq数据定量比较的计算模型;它可以定量地刻 画不同ChIP-Seq样本中所研究调控因子结合的定量差异,并通过整合Motif分析找出与差异结合相关的细胞特异性调控因子;现在,我们正在将它拓展 为一个完善的程序包,用于定量比较和整合各种与基因表达调控特别是表观遗传调控相关的高通量组学数据。同时,我们也在进一步向更多数据类型如蛋白组和癌症基因组等拓展。通过开发这些新模型和工具,我们希望能够更深入地
(1)了解不同生物组织或疾病类型里关键的基因表达调控机制,并从中找出潜在的基因或药物治疗靶点;
(2)理解不同人类个体之间的调控和表观基因组差异,为实现个体化的疾病预测和医药设计提供理论基础。
2.与实验生物学家合作,研究组织分化与病变等过程中的动态基因调控及其潜藏机制;
我们与许多实验研究课题组建立了合作关系,通过Genome/ChIP/DNase1/Bisulfite/RNA-sequencing,基因表达芯片、SNP芯片等常用高通量生物数据平台,找出驱动生物组织分化和病变等过程的关键调控因子和基因组元件。
3. 系统生物学研究
通过对已有数据应用统计、机器学习或信息挖掘等手段,我们希望能够发掘基因组中未知的功能片段,如调控元件或非编码RNA等,以及对调控元件的进化和精细结果做深入探索。


    获奖情况  

中国科学院“百人计划”入选者(2015)


    代表论文  

1. Huang J*, Liu X*, Li D*, Shao Z*, Cao H, Zhang YN, Trompouki E, Bowman TV, Zon LI, Yuan GC, Stuart H. Orkin SH#, Xu J#. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Developmental Cell 2016, 36, 9-23.

2. Xu J*, Shao Z*, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH#. Developmental control of Polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Molecular Cell 2015, 57 (2), 304–316.

3. Das PP*, Shao Z*, Beyaz S, Apostolou E, O’Brien K, Atsma JM, Ljuboja D, Guo G, Kerenyi M, Woo A, Yuan GC, Onder T, Hochedlinger K, Kim J, Orkin SH#. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cells identity. Molecular Cell 2014, 53 (1), 32-48.

4. Maroz A, Stachorski L, Emmrich S, Reinhardt K, Xu J, Shao Z, Käbler S, Dertmann T, Hitzler J, Roberts I, Vyas P, Juban G, Hennig C, Hansen G, Li Z, Orkin S, Reinhardt D, Klusmann JH. GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient. Leukemia, 2014, 28, 1259–1270.

5. Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. An erythroid enhancer of BCL11A determines fetal hemoglobin level. Science, 2013, 342 (6155), 253-257.

6. Kerenyi M, Shao Z, Hsu Y, Guo G, Luc S, O’Brien K, Fujiwara Y, Peng C, Nguyen M and Orkin SH. Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation. eLife, 2013, 2:e00633.

7. Baena E, Shao Z, Linn D, Glass K, Hamblen M, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho F, Bronson RT, Mucci L, Loda M, Yuan GC, Orkin SH and Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes & Development, 2013, 27 (6), 683-698.

8. Xu J*, Shao Z*, Bauer DE, Glass K, Pinello L, Handel B, Hou S, Stamatoyannopoulos J, Mikkola H, Yuan GC and Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Developmental Cell, 2012, 23 (4):796-811.

9. Shao Z*, Zhang Y*, Yuan GC, Orkin SH and Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology, 2012, 13 R16 (Method Article).

10. Xu J, Peng C, Sankaran VJ, Shao Z, Esrick E, Chong B, Ippolito G, Fujiwara Y, Ebert B, Tucker P, Orkin SH. Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science, 2011, 334 993-996.