张勇教授课题组针对计算表观遗传学核心问题，结合生物信息学方法开发与数据分析，研究脊椎动物早期胚胎发育的表观遗传信息重编程规律及作用，研究成果发表在Nature、Nature Cell Biology、Genome Research、Genome Biology等重要学术期刊，获国家自然科学奖二等奖、教育部自然科学奖一等奖、上海市自然科学一等奖等。课题组目前包括教授1名、副教授2名、助理教授1名、博士后2名、博士研究生8名。课题组已培养博士和博士后二十余位，其中1名博士生获得“吴瑞奖学金”，2名博士后入选“博士后创新人才支持计划”，4名博士后入选上海市“超级博士后”激励计划；课题组培养的博士和博士后已有8位在高校担任教职。

·       国家自然科学基金委员会，杰青项目，32325012，计算表观遗传学，2024.01至2028.12，400万元，主持

·       国家自然科学基金委员会，重点项目，32030022，基于多组学数据整合及模型构建研究合子基因组激活过程中转录调控网络的重建，2021.01至2025.12，293万元，主持

·       国家自然科学基金委员会，面上项目，31970642，整合核小体定位特征解析哺乳动物染色质中非典型DNA结构的组织特异性，2020.01至2023.12，58万元，主持

·       科技部，国家重点研发计划课题，2017YFA0102602，在单细胞层面解析hPSC分化早期异质性建立和演进机制，2017.01至2022.06，810万元，主持

·       上海市科委，优秀学术带头人计划项目，17XD1403600 ，基于单细胞组学技术研究细胞命运决定中的表观遗传调控机制，2017.05至2020.04，40万元，主持

·       国家自然科学基金委员会，面上项目，31571365，基于单细胞组学数据研究早期胚胎发育中表观遗传模式的建立，2016.01至2019.12，60万元，主持

·       国家自然科学基金委员会，优秀青年基金，31322031，生物信息学和表观基因组学，2014.01至2016.12，100万元，主持

·       国家自然科学基金委员会，面上项目，31371288，基于高通量数据挖掘揭示染色质调控因子新的作用机制，2014.01至2017.12，90万元，主持

·       上海市科委，启明星人才计划跟踪项目，13QH1402200，核小体定位与染色质修饰在多能性细胞中的互动机制研究，2013.09至2015.08，15万元，主持

·       国家自然科学基金委员会，面上项目，31071114，基于表观遗传组识别驱动细胞状态变化的核心转录因子，2011.01至2013.12，40万元，主持

·       上海市科委，启明星人才计划，10QA1407300，表观遗传组动态变化的生物信息学模型，2010.04至2012.03，15万元，主持

·       科技部，重大专项课题，2010CB944904，表观遗传组综合分析系统的构建和应用，2010.01至2014.08，638万元，主持

代表性论文

·       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 Rep 2023; 18(4):807-16.

·       Yang H^*, Bai D^*, Li Y^*, Yu Z^*, Wang C, Sheng Y, Liu W^$, Gao S^$, Zhang Y^$. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nat Cell Biol 2022; 24:783-92. (Highlighted by Nat Rev Mol Cell Biol)

·       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 Res 2022; 32(2): 378-88. (Cover story)

·       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. Mol Cell 2022; 82(6):1169-85.

·       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 Res 2022; 32:801-813.

·       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.

·       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.

·       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 Biol 2020; 21: 277.

·       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 Biol 2020; 21: 48.

·       Liu G^*, Wang W^*, Hu S^*, Wang X, Zhang Y^$. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res 2018; 28: 998-1007. (Cover story)

·       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. Nat Cell Biol 2018; 20:620-31. (Recommended by Faculty Opinions)

·       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.

·       Zhu G^*, Yang H^*, Chen X, Wu J, Zhang Y^$, Zhao X^$. CSTEA: a webserver for the cell state transition expression atlas. Nucleic Acids Res 2017; 45: W103-8.

·       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(7621):558-62. (Highlighted by Nature; Recommended by Faculty Opinions)

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

·       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 Res 2016; 26:171-89.

·       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 Discov 2016; 2:16010.

·       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 Res 2015; 25(9):1325-35.

·       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)

·       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.            

·       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. 

·       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.

·       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.

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

·       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.

·       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.

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

·       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.