張勇

姓 名：張勇

學 位：博士

導師情況：博士生導師

研究領域：生物信息學和表觀遺傳組學

研究方向：生物信息學，計算基因組學和表觀基因組學

通訊地址：上海市四平路1239號，同濟大學生命科學與技術學院（200092）

個人簡介：

2001年畢業於北京大學，獲學士學位。2006年畢業於中國科學院生物物理研究所，獲得博士學位。2006-2009年，在美國哈佛大學和Dana-Farber癌症研究所從事博士后研究；在博士後期間，主要針對新一代高通量測序技術，發展生物信息學方法，來解決表觀遺傳組學問題。自2009 年起被聘為同濟大學生命科學與技術學院教授，主要從事生物信息學及表觀遺傳組學的科研及教學工作。近幾年的研究工作主要針對高通量生物學數據分析，發展全新的生物信息學演演算法，進而在基因組尺度上揭示核小體定位、表觀遺傳修飾的建立機制及其與轉錄調控的關聯。

在國內外學術期刊上發表論文三十餘篇，文章總計被引用超過1500次（H-index 為14）其中在Nature, Nature Structural & Molecular Biology, Nature Protocols, Genome Biology, Bioinformatics, BMC Genomics, Epigenetics等期刊發表通訊作者或第一作者論文16篇。先後入選上海市科技啟明星計劃和教育部新世紀優秀人才支持計劃，目前作為負責人承擔973 重大專項課題和國家自然基金委面上項目各一項，

代表性論文（按年份降序排列）

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

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

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

4. Feng J, Meyer CA, Wang Q, Liu JS, Liu XS$, Zhang Y$ (corresponding author). GFOLD: a generalized fold change for ranking differentially ex-pressed genes from RNA-seq data.Bioinformatics(advance online).

5. Feng J, Liu T, Qin Bo, Zhang Y$ (co-corresponding author), Liu XS$. Identifying ChIP-seq enrichment using MACS.Nat Protoc (accepted).

6. 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$ (co-corresponding author), 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 .

7. Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Computational inference of mRNA stability from histone modification and transcriptome profiles.Nucleic Acids Res 2012; 40(14):6414-23.

8. Zhao Q, Zhang Y$徠 (corresponding author). Epigenome sequencing comes of age in development, differentiation and diseases mechanism research.Epigenomics 2011; 3(2):207-20.

9. Feng J, Liu T, Zhang Y$ (corresponding author). Using MACS to identify peaks from ChIP-Seq data.Curr Protoc Bioinform 2011; 34:2.14.

10. Vastenhouw NL*, Zhang Y* (co-first author), 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.

11. 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.

12. Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, Janne OA, Balk SP, Mehra R, Han B, Chinnaiyan AM, Rubin MA, True L, Fiorentino M, Fiore C, Loda M, Kantoff PW, Liu XS, Brown M. Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer.Cell 2009;138:245-56.

13. 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.

14. 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.

15. Lefterova M, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ, Liu XS, Lazar MA. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.Genes Dev 2008, 22: 2941-2952.

16. Zhang Y, Li S, Skogerbo G, Zhang Z, Zhu X, Zhang Z, Sun S, Chen R. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMCBioinformatics2006;7:252.

17. Zhang Y, Sun S, Wu T, Wang J, Liu C, Chen L, Zhu X, Zhao Y, Zhang Z, Shi B, Lu H, Chen R. Identifying Hfq-binding small RNA targets in Escherichia coli.Biochem Biophys Res Commun 2006;343(3):950-955.

18. Zhang Y, Zhang Z, Ling L, Shi B, Chen R. Conservation analysis of small RNA genes in Escherichia coli.Bioinformatics 2004;20(5):599-603.