邮箱: shaozhen@sinh.ac.cn
电话: +86-21-54920367
研究组网站: http://bioinfo.sibs.ac.cn/shaolab
所属部门: 中国科学院计算生物学重点实验室
2021-至 今：中国科学院上海营养与健康研究所 研究员
2013-2020年：中国科学院-马普学会计算生物学伙伴研究所 研究员
2009-2013年：美国达纳法伯癌症研究所/波士顿儿童医院与哈佛医学院 生物信息博士后
2003-2008年：中国科学院理论物理研究所 理论生物物理博士
1999-2003年：中国科技大学少年班系 物理学士
调控与表观基因组学
1. 结合多组学（表观组、转录组、蛋白质组等）、多尺度（bulk、空间、单细胞等）手段，对肿瘤、糖尿病等疾病的异质性在宏观（病人间差异）和微观（病变组织内部微环境）层面进行计算建模和分析，解析其演化过程和重要靶点。
例如：基于肺腺癌病人表观组异质性统计建模的病人分型和调控网络对比分析（Genome Biology 2021）；基于糖尿病小鼠模型的单细胞基因表达性别差异分析（Genomics, Proteomics & Bioinformatics 2021）等。
2. 开发用于多组学数据定量比较和整合分析的计算模型和平台。
例如：1）用于双样本ChIP-Seq数据定量比较和差异分析的MAnorm模型（Genome Biology 2012），用于多样本ChIP/ATAC-Seq数据分组定量比较和差异分析的MAnorm2模型（Genome Research 2021），以及用于多样本ChIP/ATAC -Seq数据高变分析的HyperChIP模型（Genome Biology 2022）；2）用于转录因子结合motif扫描和富集分析的工具包Motif-Scan，以及进一步寻找细胞类型特异性调控因子的整合分析工具MAmotif（Cell Discovery 2018）；3）用于定量蛋白质组数据双样本比较和差异表达分析的MAP模型（Cell Discovery 2019）和多样本比较的zMAP模型集。
3. 干细胞及早期胚胎发育研究。
基于多组学数据挖掘和整合分析，解析人类胚胎干细胞多能性维持和退出过程的关键调控因子，探究其在早期胚胎发育过程中的作用。
1. Liu G#, Li Y#, Li M#, Li S, He Q, Liu S, Su Q, Chen X, Xu M, Zhang ZN*, Shao Z*, Li W*. Charting a high-resolution roadmap for regeneration of pancreatic β cells by in vivo transdifferentiation from adult acinar cells. Sci Adv 2023 May 24;9(21):eadg2183
2. Chen HJ#, Tu SQ#*, Yuan CZ, Tian FX, Zhang Y, Sun YH, Shao Z*. HyperChIP for identifying hypervariable signals across ChIP/ATAC-seq samples. Genome Biol 2022 Feb 28;23(1):62
3. Liu G#, Li YN#, Zhang TJ#, Li MS#, Li S, He Q, Liu SX, Xu ML, XiaoTH, Shao Z*, Shi WY*, Li WD*. Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells. Genomics Proteomics Bioinformatics 2021 Jun;19(3):408-422
4. Yuan CZ#, Chen HJ#, Tu SQ#, Huang SY#, Pan YJ, Gui XQ, Kuang MY, Shen XX, Zheng Q, Zhang Y, Cheng C, Hong H, Tao XT, Peng YZ, Yao XX, Meng FL*, Ji HB*, Shao Z*, Sun YH*. A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks. Genome Biol 2021 May 17;22(1):156
5. Tu SQ, Li MS, Tan FX, Chen HJ, Xu J, Waxman DJ, Zhang YJ, Shao Z*. MAnorm2 for quantitatively comparing groups of ChIP-seq samples. Genome Res 2021 Jan;31(1):131-145
6. Li MS#, Tu SQ#, Li ZJ, Tan FX, Liu J, Wang Q, Zhang YN, Xu J, Zhang YJ, Zhou F, Shao Z*. MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. Cell Discov 2019 Aug 13:5:40
7. Sun HD#, Wang JW#, Gong ZH#, Yao JY#, Wang YG, Xu J, Yuan GC, Zhang YJ*, Shao Z*. Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters. Cell Discov 2018 Jul 10:4:38
8. Li S, Li MS, Liu XJ, Yang YY, Wei YD, Chen YH, Qiu Y, Zhou TT, Feng ZH, Ma DJ, Fang J, Ying H, Wang H, Musunuru K, Shao Z*, Zhao YX*, Ding QR*. Genetic and Chemical Screenings Identify HDAC3 as a Key Regulator in Hepatic Differentiation of Human Pluripotent Stem Cells. Stem Cell Reports 2018 Jul 10;11(1):22-31
9. Liu X#, Zhang YN#, Chen Y#, Li MS#, Zhou F#, Li KL, Cao H, Ni M, Liu YX, Gu ZM, Dickerson KE, Xie SQ, Hon GC, Xuan ZY, Zhang MQ, Shao Z, Xu J*. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell 2017 Aug 24;170(5):1028-1043
10. Tu SQ, Shao Z*. An introduction to computational tools for differential binding analysis with ChIP-seq data. Quantitative Biology 2017 Aug;5(3):226-235.
11. Liu X#, Zhang YN#, Ni M#, Cao H, Signer RAJ, Li D, Li MS, Gu ZM, Hu ZP, Dickerson KE, Weinberg SE, Chandel NS, DeBerardinis RJ, Zhou F*, Shao Z*, Xu J*. Regulation of Mitochondrial Biogenesis in Erythropoiesis by mTORC1-Mediated Protein Translation. Nat Cell Biol 2017 Jun;19(6):626-638
12. Tu SQ, Yuan GC, Shao Z*. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Sci Rep 2017 Jan 31:7:41669
13. 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. Dev Cell 2016 Jan 11;36(1):9-23
14. 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. Mol Cell 2015 Jan 22;57(2):304-316
15. 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 cells identity. Mol Cell 2014 Jan 9;53(1):32-48
16. 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*, Li Z*. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev 2013 Mar 15;27(6):683-698
17. Xu J#, Shao Z#, Bauer DE, Glass K, Pinello L, Handel B, Hou S, Stamatoyannopoulos J, Mikkola H, Yuan GC*, Orkin SH*. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell 2012 Oct 16;23(4):796-811
18. Shao Z#, Zhang Y#, Yuan GC, Orkin SH*, Waxman DJ*. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol 2012 Mar 16;13(3):R16
19. Liu Y#, Shao Z#, Yuan GC*. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010 Jul;96(1):17-26
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