姓       名：张勇

学       位：博士

导师情况：博士生导师

研究领域：生物信息学

E-mail：  yzhang@tongji.edu.cn

实验室主页：https://zhanglab.tongji.edu.cn

联系电话：021-65981196

通讯地址：上海市四平路1239号，同济大学生命科学与技术学院（200092）

个人简介：

张勇，长聘特聘教授，国家杰出青年科学基金获得者。2001年毕业于北京大学地球物理系，获学士学位。2006年毕业于中国科学院生物物理研究所，获得博士学位。2006-2009年，在美国哈佛大学Dana-Farber癌症研究所从事博士后研究。2009年起任同济大学生命科学与技术学院教授，2019年起任生物信息学系系主任。研究方向：通过开发生物信息学算法和人工智能模型，解析细胞命运决定过程中染色质调控信息的建立及作用机制。近年来的主要研究成果包括：开发了一系列表观遗传组及转录调控组数据分析方法，系统研究了表观遗传信息异质性的建立、演进及调控机制，并揭示了早期胚胎发育中表观遗传信息的动态变化规律。已培养博士和博士后二十余名，包括吴瑞奖学金获得者一名、博士后创新人才支持计划获得者两名、上海市超级博士后激励计划获得者五名；培养的博士和博士后已有九位在高校担任教职。

先后主持多项基金委、科技部项目。在国内外学术期刊上发表论文八十余篇，文章总计被引用超过30000次，其中作为通讯作者在Nature、Nature Cell Biology、Cell Stem Cell、Genome Research、Genome Biology、Nature Communications等期刊发表论文四十余篇。先后获得国家基金委优青（2013年）、中组部青年拔尖人才（2015年）、上海市优秀学术带头人（2017年）、教育部青年长江学者（2018年）、教育部自然科学奖一等奖（2019年，排名第4）、国家自然科学奖二等奖（2020年，排名第3）、上海市自然科学奖一等奖（2022年，排名第2）、国家杰出青年科学基金（2023年）等。

代表性论文（按年份降序排列）

^{1. Hua Y, Zhang Y, Guo Z, Bian S, Zhang Y#. ImSpiRE: Image feature-aided spatial resolution enhancement method. Science China Life Sciences 2025; 68:272–83.}

^{2. Zhang M, Zhang Y, Dong K, Lin J, Cui X#, Zhang Y#. Identification of critical phosphorylation sites enhancing kinase activity with a bimodal fusion framework. Molecular & Cellular Proteomics 2025; 24:100889.}

^{3. Yu Z, Wang Q, Zhang Q, Tian Y, Yan G, Zhu J, Zhu G#, Zhang Y#. Decoding the genomic landscape of chromatin-associated biomolecular condensates. Nat Communications 2024; 15:6952.}

^{4. Hou S, Hu J, Yu Z, Li D, Liu C#, Zhang Y#. Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Communications 2024; 15:2147.}

^{5. Xing M, Xiong Y, Zhang Y#. Ku80 is indispensable for repairing DNA double-strand breaks at highly methylated sites in human HCT116 cells. DNA Repair 2024; 134:103627.}

^{6. Yu Z, Zhang Y#. Foundation model for comprehensive transcriptional regulation analysis. National Science Review 2024; 11:nwae355.}

^{7. Wang W, Gao R, Yang D, Ma M, Zang R, Wang X, Chen C, Kou X, Zhao Y, Chen J, Liu X, Lu J, Xu B, Liu J, Huang Y, Chen C, Wang H, Gao S#, Zhang Y#, Gao Y#. ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice. Genes & Development 2024; 38:168-88.}

^{8. Chen Y, Xu R, Zhou S, Zhao C, Hu Z, Hua Y, Xiong Y, Liu X, Lv J, Sun Y#, Li C#, Gao S#, Zhang Y#. Mechanical strain treatment improves nuclear transfer reprogramming efficiency by enhancing chromatin accessibility. Stem Cell Reports 2023; 18(4):807-16.}

^{9. Yang H, Bai D, Li Y, Yu Z, Wang C, Sheng Y, Liu W#, Gao S#, ZhangY#. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nature Cell Biology 2022; 24:783-92.}

^{10. Wang X, Wang W, Wang Y, Chen J, Liu G#, Zhang Y#. Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN. Genome Research 2022; 32(2): 378-88.}

^{11. Huo D, Yu Z, Li R, Gong M, Sidoli S, Lu X, Hou Y, Dai Z, Kong Y, Liu G, Jensen O, Xie W, Helin K, Xiong C, Li G, Zhang Y#, Wu X#. CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency. Molecular Cell 2022; 82(6):1169-85.}

^{12. Wang C, Chen C, Liu X, Li C, Wu Q, Chen X, Yang L, Kou X, Zhao Y, Wang H, Gao Y#, Zhang Y#, Gao S#. Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Research 2022; 32:801-813.}

^{13. Zhao C#, Xiu W, Hua Y, Zhang N, Zhang Y#. CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data. Bioinformatics 2021; 37(21):3774-80.}

^{14. Ding Y, Wang W, Ma D, Liang G, Kang Z, Xue Y, Zhang Y, Wang L, Heng J, Zhang Y#, Liu F#. Smarca5 mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Blood 2021; 137:190-202.}

^{15. Hu S, Huo D, Yu Z, Chen Y, Liu J, Liu L, Wu X#, Zhang Y#. ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators. Genome Biology 2020; 21: 48.}

^{16. Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W#, Zhang Y#. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biology 2020; 21: 277.}

^{17. Liu G, Wang W, Hu S, Wang X, Zhang Y#. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Research 2018; 28: 998-1007.}

^{18. Wang C, Liu X, Gao Y#, Yang L, Li C, Liu W, Chen C, Kou X, Zhao Y, Chen J, Wang Y, Le R, Wang H, Duan T, Zhang Y#, Gao S#. Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nature Cell Biology 2018; 20:620–31.}

^{19. Gao R, Wang C, Gao Y, Xiu W, Chen J, Kou X, Zhao Y, Liao Y, Bai D, Qiao Z, Yang L, Wang M, Zang R, Jia Y, Li Y, Yin J, Wang H, Wan X, Liu W#, Zhang Y#, Gao S#. Inhibition of aberrant DNA re-methylation improves the development of nuclear transfer embryos. Cell Stem Cell 2018; 23:426–35.}

^{20. Liu X, Wang C, Liu W, Li J, Li C, Kou X, Chen J, Zhao Y, Gao H, Wang H, Zhang Y#, Gao Y#, Gao S#. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 2016; 537:558-62.}

^{21. Huo X, Hu S, Zhao C, Zhang Y#. Dr.seq: a quality control and analysis pipeline for droplet sequencing. Bioinformatics 2016; 32: 2221-3.} 

^{22. Zhou C, Yang X, Sun Y, Yu H, Zhang Y#, Jin Y#. Comprehensive profiling reveals mechanisms of SOX2-mediated cell fate specification in human ESCs and NPCs. Cell Research 2016; 26:171-89.} 

^{23. Liu W, Liu X, Wang C, Gao Y#, Gao R, Kou X, Zhao Y, Li J, Wu Y, Xiu W, Wang S, Yin J, Liu W, Cai T, Wang H, Zhang Y#, Gao S#. Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing. Cell Discovery 2016; 2:16010.}

^{24. Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y#, Shou J#. SETDB1 modulates PRC2 activity at developmental genes independent of H3K9 trimethylation in mouse ES cells. Genome Research 2015; 25:1325-35.}

^{25. 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 Research 2014; 24:260-6.}

^{26. 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 Research 2014; 42:D450-8.}

^{27. 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 Biology 2014; 15:419.}

^{28. 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. Nature Protocols 2013; 8:2502-15.} 

^{29. 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; 28:2782-8.}

^{30. Fu K, Tang Q, Feng J, Liu XS, Zhang Y#. DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 2012; 28:1965-71.}

^{31. Feng J, Liu T, Qin Bo, Zhang Y#, Liu XS#. Identifying ChIP-seq enrichment using MACS. Nature Protocols 2012; 7:1728-40.}

^{32. 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.}

^{33. 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. Nature Structural & Molecular Biology 2009; 16:847-52.} 

^{34. 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 Biology 2008; 9:R137.}