Education & Training: 

B.A., Peking University, 2001 

Ph.D., Institute of Biophysics, Chinese Academy of Sciences, 2006 

Postdoctoral Research Fellow, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, 2006-2009

Academic appointments: 

Professor of Bioinformatics, School of Life Science and Technology, Tongji University, 2009-

My research interests focus on the design of statistical and computational algorithms on high-throughput data to study epigenetic priming effects on stem cell differentiation.

In the next few decades, the life science studies will no longer be limited by generating data, instead, managing and analyzing high-throughput data will be challenging for the majority of biologists. The aim of my lab is to reveal new features of epigenome phenomena and benefits the epigenome studies of the whole community, through building epigenome analysis platform, designing statistical and computational algorithms, and collaborating with biologists from other fields.

Honors & Recognition:

1. Excellent Young Scholar of NSFC, China (2013)

2. Shanghai Science and Technology Excellent Rising Star, China (2013)

3. New Century Excellent Talents in University, China (2011)

4. Shanghai Science and Technology Rising Star, China (2010)

Representative Publication:

1. Zhang Y$, Vastenhouw NL$, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF$, Liu XS$. Canonical nucleosome organization at promoters forms during genome activation. Genome Res 2014; 24(2):260-6. (Cover story).

2. Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS$, Zhang Y$. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res 2014; 42:D450-8.

3. Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P$, Zhang Y$, Liu XS$. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol 2014; 15:419.

4. Wang S, Sun Hanfei, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y$, Liu XS$. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc 2013; 8:2502-15.

5. Tian R, Feng J, Cai X, Zhang Y$. Local chromatin dynamics of transcription factors imply cell lineage-specific functions during cellular differentiation. Epigenetics 2012; 7(1):55-62.

6. Fu K, Tang Q, Feng J, Liu XS, Zhang Y$. DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 2012; 28(15):1965-71.

7. Liu L, Zhang Y, Feng J, Zheng N, Yin J, Zhang Y$. GeSICA: genome segmentation from intra-chromosomal associations. BMC Genomics 2012; 13:164.

8. Feng J, Meyer CA, Wang Q, Liu JS, Liu XS$, Zhang Y$. GFOLD: a generalized fold change for ranking differentially ex-pressed genes from RNA-seq data. Bioinformatics 2012; 28(21):2782-8.

9. Feng J, Liu T, Qin Bo, Zhang Y$, Liu XS$. Identifying ChIP-seq enrichment using MACS. Nat Protoc 2012; 7:1728-40.

10. Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y$, Liu XS$. CistromeMap: A knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics 2012; 28(10):1411-2 .

11. Zhao Q, Zhang Y$. Epigenome sequencing comes of age in development, differentiation and diseases mechanism research. Epigenomics 2011; 3(2):207-20. 12. Feng J, Liu T, Zhang Y$. Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinform 2011; 34:2.14.

13. Vastenhouw NL*, Zhang Y*, Woods IG, Imam F, Regev A, X. Liu XS, Rinn J, Schier A. Chromatin signature of embryonic pluripotency is established during zygotic genome activation. Nature 2010;464:922-6.

14. Zhang Y, Moqtaderi Z, Rattner B, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 2009;16(8):847-52.

15. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DJ, Myers RM, Bernstein BE, Nussbaum C, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9:R137.

16. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008;9:537. Honors & Recognition: 1. Excellent Young Scholar of NSFC, China (2013) 2. Shanghai Science and Technology Excellent Rising Star, China (2013) 3. New Century Excellent Talents in University, China (2011) 4. Shanghai Science and Technology Rising Star, China (2010)

Positions available for Ph.D. students and postdoctoral research fellows.