Areas of Focus
- Bioinformatics
Work Experience
- 2006-2009 - Dana-Farber Cancer Institute, Harvard University: Postdoctoral Researcher
- 2009-present - Tongji University, School of Life Sciences and Technology: Professor
- 2019-present - Department of Bioinformatics: Department Head
Academic Background & Achievements
- 2001 - Bachelor's Degree: Peking University
- 2006 - PhD: Institute of Biophysics, Chinese Academy of Sciences
- Recipient of the National Science Fund for Distinguished Young Scholars
Publications
- Mechanical strain treatment improves nuclear transfer reprogramming efficiency by enhancing chromatin accessibility, 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, 2023
- Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo, Yang H, Bai D, Li Y, Yu Z, Wang C, Sheng Y, Liu W, Gao S, Zhang Y, 2022
- Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN, Wang X, Wang W, Wang Y, Chen J, Liu G, Zhang Y, 2022
- CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency, 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, 2022
- Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation, 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, 2022
- CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data, Zhao C, Xiu W, Hua Y, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, 2021
- Smarca5 mediated epigenetic programming facilitates fetal HSPC development in vertebrates, Ding Y, Wang W, Ma D, Liang G, Kang Z, Xue Y, Zhang Y, Wang L, Heng J, Zhang Y, Liu F, 2021
- ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators, Hu S, Huo D, Yu Z, Chen Y, Liu J, Liu L, Wu X, Zhang Y, 2020
- A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos, Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, 2020
- Inherited DNA methylation primes the establishment of accessible chromatin during genome activation, Liu G, Wang W, Hu S, Wang X, Zhang Y, 2018
- Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development, 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, 2018
- Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos, 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, 2016
- Dr.seq: a quality control and analysis pipeline for droplet sequencing, Huo X, Hu S, Zhao C, Zhang Y, 2016
- Comprehensive profiling reveals mechanisms of SOX2-mediated cell fate specification in human ESCs and NPCs, Zhou C, Yang X, Sun Y, Yu H, Zhang Y, Jin Y, 2016
- Identification of key factors conqueringdevelopmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing, 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, 2016
- SETDB1 modulates PRC2 activity at developmental genes independent of H3K9 trimethylation in mouse ES cells, 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, 2015
- Canonical nucleosome organization at promoters forms during genome activation, Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS, 2014
- CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse, Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS, Zhang Y, 2014
- MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes, 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, 2014
- Target analysis by integration of transcriptome and ChIP-seq data with BETA, Wang S, Sun Hanfei, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS, 2013
- GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data, Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y, 2012
- DiNuP: a systematic approach to identify regions of differential nucleosome positioning, Fu K, Tang Q, Feng J, Liu XS, Zhang Y, 2012
- Identifying ChIP-seq enrichment using MACS, Feng J, Liu T, Qin Bo, Zhang Y, Liu XS, 2012
- Chromatin signature of embryonic pluripotency is established during zygotic genome activation, Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, X. Liu XS, Rinn J, Schier A, 2010
- Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo, Zhang Y, Moqtaderi Z, Rattner B, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K, 2009
- Model-based analysis of ChIP-Seq (MACS), Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DJ, Myers RM, Bernstein BE, Nussbaum C, Brown M, Li W, Liu XS, 2008
Awards
- 2013: National Science Fund for Distinguished Young Scholars
- 2015: Youth Top-notch Talent Support Program
- 2017: Shanghai Outstanding Academic Leader
- 2018: Ministry of Education Yangtze River Scholar Award
- 2019: First Prize in Natural Science Award by the Ministry of Education
- 2020: Second Prize in National Natural Science Award
- 2022: First Prize in Shanghai Natural Science Award
- 2023: National Science Fund for Distinguished Young Scholars
