Research Areas

1. Combine wet-lab experiments and computational analysis of multi-omics data to investigate the onset and progression of complex diseases such as cancers, the establishment of tissue-specific epigenetic landscape and gene expression program, the characteristic feature and fine structure of regulatory elements, etc.

2. Develop computational models and algorithms for large-scale omics data analysis and integration, which could be generated by a variety of cutting-edge platforms including ChIP-seq, ATAC-seq, RNA-seq, mass spectrum.

Brief Biography (including Education & Academic Background)

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

2013.10 - 2020.12: Principle 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. 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.
2. 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.
3. 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.
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 Biology 2021;22:156.
5. 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.
6. 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.
7. 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.
8. 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.
9. Tu SQ, Shao Z*. An introduction to computational tools for differential binding analysis with ChIP-seq data. Quantitative Biology 2017;5(3):226-235.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. Liu Y^#, Shao Z^#, Yuan GC*. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010;96:17-26.