个人简历
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。
研究领域
生物信息学和表观遗传组学
近期论文
Liu G, Wang W, Hu S, Wang X, Zhang Y$. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res 2018; 28: 998-1007. (封面文章)Wang C, Liu X, Gao Y$, 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.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$. Inhibition of aberrant DNA re-methylation improves the development of nuclear transfer embryos. Cell Stem Cell 2018; 23:426–35Liu X, Wang C, Liu W, Li J, Li C, Kou X, Chen J, Zhao Y, Gao H, Wang H, Zhang Y$, Gao Y$, Gao S$. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 2016; 537:558-62. 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$. Comprehensive profiling reveals mechanisms of SOX2-mediated cell fate specification in human ESCs and NPCs. Cell Res 2016; 26:171-89. Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y$, Shou J$. SETDB1 modulates PRC2 activity at developmental genes independent of H3K9 trimethylation in mouse ES cells. Genome Res 2015; 25:1325-35. Zhang Y$, Vastenhouw NL$, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF$, Liu XS$. Canonical nucleosome organization at promoters forms during genome activation. Genome Res 2014; 24:260-6. (封面文章)Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS$, 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. 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. Fu K, Tang Q, Feng J, Liu XS, Zhang Y$. DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 2012; 28:1965-71. Liu L, Zhang Y, Feng J, Zheng N, Yin J, Zhang Y$. GeSICA: genome segmentation from intra-chromosomal associations. BMC Genomics 2012; 13:164. Feng J, Liu T, Qin Bo, Zhang Y$, Liu XS$. Identifying ChIP-seq enrichment using MACS. Nat Protoc 2012; 7:1728-40. 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. 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; 16:847-52. 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.Genome Biology期刊编辑委员会成员、中国细胞生物学学会功能基因组学与系统生物学分会委员、中国遗传学会青年委员会委员、中国生物工程学会计算生物学与生物信息学专业委员会委员、中国细胞生物学学会染色质生物学分会委员、中国生物物理学会生物信息学分会委员等
