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SHAO Zhen

Ph.D.

Professor, Principal Investigator

Laboratory of Regulatory and Systems Genomics

Email: shaozhen@sinh.ac.cn

Tel: 86-21-54920367

Lab Page Link: http://bioinfo.cemps.ac.cn/shaolab

Research Areas

1. Develop computational models and algorithms for quantitative analysis and integration of multi-omics data.

2. Combine wet-lab experiments and computational analysis to dissect the regulatory mechanisms of various life processes, such as cancer progression, self-renewal and differentiation of stem cells, etc.

 

Brief Biography (including Education & Academic Background)

2021.01 - Present: Professor, Principal Investigator, Shanghai Institute of Nutrition and Health (SINH), CAS

2013.10 - 2020.12: Principal Investigator of Regulatory and Systems Genomics group, CAS-MPG Partner Institute for Computational Biology (PICB), Chinese Academy of Sciences

2010.06 - 2013.09: Research Fellow, Department of Pediatric Oncology, Dana Farber Cancer Institute; Division of Hematology/Oncology, Children’s Hospital Boston; Harvard Medical School

2009.04 - 2010.05: Research Fellow, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health

2003.09 - 2008.12: Ph. D. in Theoretical Biophysics, Institute of Theoretical Physics, Chinese Academy of Sciences, China

1999.09 - 2003.07: B.S. in Physics, Department of Special Class for Gifted Young, University of Science and Technology of China

 

Selected Publications (*Corresponding Author, #Contributed Equally)

1. Gui X#, Huang J#, Ruan L#, Wu Y#, Guo X#, Cao R, Zhou S, Tan F, Zhu H, Li M, Zhang G, Zhou H, Zhan L*, Liu X*, Tu S* and Shao Z*. zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation. Genome Biology 2024, 25:267.

2. 

Yu J#, Gui XQ#, Zou YH#, Liu Q#, Yang ZC, An JS，Guo X, Wang KH, Guo JM, Huang MN, Zhou SH, Zuo J, Chen YM, Deng L, Yuan GW, Li N, Song Y, Jia J, Zeng J, Zhao YX, Liu XM, Du XX, Liu YS, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Zhou H*, Shao Z*, Wu LY* and Gao DM*. A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights. Nature Communications 2024, 15, 10114.

3. Ge T#, Gui X#, Xu JX#, Xia W#, Wang CH, Yang W, Huang K, Walsh C, Umen JG, Walter J, Du YR, Chen H*, Shao Z*, and Xu GL*. DNA cytosine methylation suppresses meiotic recombination at the sex-determining region. Science Advances 2024, 10, eadr2345.

4. 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. Science Advances 2023 May 24;9(21):eadg2183.

5. 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 Biology 2022;23:62.

6. Liu G#, Li YN#, Zhang TJ#, Li MS#, Li S, He Q, Liu SX, Xu ML, XiaoTH, Shao Z*, Shi WY*, Li WD*. Mouse Single Islet Beta Cell Transcriptomic Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes. Genomics, Proteomics & Bioinformatics 2021;19:408-422.

7. 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 Research 2021;31:131-145.

8. 

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 Biology 2021;22:156.
9. 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 Discovery 2019;5:40.
10. 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 Discovery 2018;4(1):38.
11. 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;11(1):22-31.
12. 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;170(5):1028–1043.
13. Tu SQ, Shao Z*. An introduction to computational tools for differential binding analysis with ChIP-seq data. Quantitative Biology 2017;5(3):226-235.
14. 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. Nature Cell Biology 2017;19:626–638.
15. Tu SQ, Yuan GC, Shao Z*. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Scientific Reports 2017;7:41669.
16. 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.
17. 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.
18. 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. Molecular Cell 2014;53(1):32-48.
19. 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. Gene & Development 2013;27(6):683-698.
20. 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. Developmental Cell 2012;23(4):796-811.
21. Shao Z#, Zhang Y#, Yuan GC, Orkin SH*, Waxman DJ*. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology 2012;13:R16.
22. Liu Y#, Shao Z#, Yuan GC*. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010;96:17-26.

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