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Publications

2020

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 (accepted).

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.

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 (advanced online).

2019

Gao H*, Gao R*, Zhang L*, Xiu W, Zang R, Wang H, Zhang Y, Chen J$, Gao Y$, Gao S$. Esrrb plays important roles in maintaining self-renewal of trophoblast stem cells (TSCs) and reprogramming somatic cells to induced TSCs. J Mol Cell Biol 2019; 11:463-73.

2018

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.

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.

Wang Y*$, Zhao C*, Hou Z*, Yang Y*, Bi Y, Wang H, Zhang Y, Gao S$. Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naive state. eLife 2018; 7: e29518.

Zhang Y*, Chang J*, Sun J*, Chen L, Yang X, Tang H, Jing Y, Kang X, He Z, Wu J, Wei H, Wang D, Xu R, Zhu R, Shen Y, Zeng S, Wang C, Liu K, Zhang Y, Mao Z, Jiang C, Sun F$. Histone H3K27 methylation modulates the dynamics of FANCD2 on chromatin to facilitate NHEJ and genome stability. J Cell Sci 2018; 131: jcs215525.

2017

Zhao C, Hu S, Huo X, Zhang Y$. Dr.seq2: a quality control and analysis pipeline for parallel single cell transcriptome and epigenome data. PLoS ONE 2017; 12(7):e0180583.

Hu S*, Chen X*, Liao J, Chen Y, Zhao C, Zhang Y$. CAM: a quality control pipeline for MNase-seq data. PLoS ONE 2017; 12(8):e0182771.

Chen Y*, Zeng S*, Hu R*, Wang X*, Huang W, Liu J, Wang L, Liu G, Cao Y$, Zhang Y$. Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. PLoS ONE 2017; 12(8):e0182528.

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.

Gao R*, Xiu W*, Zhang L, Zang R, Yang L, Wang C, Wang M, Wang M, Yi L, Tang Y, Gao Y, Wang H, Xi J, Liu W, Wang Y, Wen X, Yu Y, Zhang Y, Chen L, Chen J, Gao S. Direct induction of neural progenitor cells transiently passes through a partially reprogrammed state. Biomaterials 2017; 119:53-67.

Xu K, Chen X, Yang H, Xu Y, He Y, Wang C, Huang H, Liu B, Liu W, Li J, Kou X, Zhao Y, Zhao K, Zhang L, Hou Z, Wang H, Wnag H, Li J, Fan H, Wang F, Gao Y, Zhang Y, Chen J, Gao S. Maternal Sall4 is indispensable for epigenetic maturation of mouse oocytes. J Biol Chem 2017; 292:1798-1807.

2016

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.

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.

Fang L, Zhang J, Zhang H, Yang X, Jin X, Zhang L, Skalnik DG, Jin Y, Zhang Y, Huang X, Li J, Wong J. The H3K4 methyltransferase Set1a Is a key Oct4 coactivactor essential for generation of Oct4 positive inner cell mass. Stem Cells 2016; 34:565-80.

Chen Y, Kim J, Zhang R, Yang X, Zhang Y, Fang J, Chen Z, Teng L, Chen X, Ge H, Atadja P, Li E, Chen T, Qi W. Histone demethylase LSD1 promotes adipocyte differentiation through repressing wnt signaling. Cell Chem Biol 2016; 23(10):1228-40.

Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics 2016; 17:404.

2015

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.

Chen J, Gao Y, Huang H, Xu K, Chen X, Jiang Y, Li H, Gao S, Tao Y, Wang H, Zhang Y, Wang H, Cai T, Gao S. The combination of Tet1 with Oct4 generates high-quality mouse induced pluripotent stem cells (iPSCs). Stem Cells 2015; 33(3):686-98.

2014

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 X, Yan Z, Fulciniti M, Li Y, Gkotzamanidou M, Amin SB, Shah PK, Zhang Y, Munshi NC, Li C. Transcription factor-pathway coexpression analysis reveals cooperation between SP1 and ESR1 on dysregulating cell cycle arrest in non-hyperdiploid multiple myeloma. Leukemia 2014; 28:894-903.

2013

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.

Shin H, Liu T, Duan X,  Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. Quantitative Biology 2013; 1(1):54-70.

Li Y, Wang X, Zheng H, Wang C, Minvielle S, Magrangeas F, Avet-Loiseau H, Shah PK, Zhang Y, Munshi NC, Li C. Classify Hyperdiploidy Status of Multiple Myeloma Patients Using Gene Expression Profiles. PLoS ONE 2013; 8(3):e58809.

Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics 2013; 29(10):1352-4.

Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol 2013; 20(7):908-13.

Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W. BSeQC: Quality Control of Bisulfite Sequencing Experiments. Bioinformatics 2013; 29(24):3227-9.        

2012

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.            

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$, Liu XS$. CistromeMap: A knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics 2012; 28(10):1411-2.

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.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim T, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Meth 2012; 9:609-14.

2011

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

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

Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res 2011; 39(1):D968-74.

Tang Q, Chen Y, Meyer CA, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. A comprehensive view of nuclear receptor cancer cistromes. Cancer Res 2011; 71(22):6940-7.

Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 2011; 12:R83.

2003 - 2010

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.

He HH, Meyer CA, Shin H, Bailey S, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Leib JD, Zhao K, Brown M,Liu XS. Nucleosome dynamics define transcriptional enhancers. Nat Genet 2010;42(4):343-7.

Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Liu XS, Struhl  K. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell 2010; 17(4):348-361.

Zhang Y, Moqtaderi Z, Rattner B, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Evidence against a genomic code for nucleosome positioning Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization". Nat Struct Mol Biol 2010; 17:920-3.

Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A 2010; 107(42):17945-50.

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.

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.

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.

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.

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.

Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell 2008, 132(6):958-970.

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.BMC Bioinformatics 2006; 7:252.

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.

Wu T, Wang J, Liu C, Zhang Y, Shi B, Zhu X, Zhang Z, Skogerbo G, Chen L, Lu H, Zhao Y,  Chen R. NPInter: the Noncoding RNAs and Protein related biomacromolecules Interaction database. Nucleic  Acids Res 2006; 34:D150-152.

Zhang Z, Sun H, Zhang Y, Zhao Y, Shi B, Sun S, Lu H, Bu D, Ling L, Chen R. Genome-wide analysis of mammalian DNA segment fusion/fission. J Theor Biol 2006; 240(2):200-208.

The DNA sequence, annotation and analysis of human  chromosome 3. Nature 2006; 440:1194-8 (list author).

Zhang Z, Liu C, Skogerbo G, Zhu X, Lu H, Chen L,  Shi B, Zhang Y, Wu T, Wang J, Chen  R. Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS  Comput Biol 2006; 2(5):e47.

Lu H, Shi B, Wu G, Zhang Y, Zhu X, Zhang Z, Liu C, Zhao Y, Wu T, Wang J, Chen R. Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochem Biophys Res Commun 2006; 345(1):302-309.

Sun S, Zhao Y, Jiao Y, Yin Y, Cai L, Zhang Y, Lu H, Chen R, Bu D. Faster  and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm. FEBS Lett 2006; 580(7):1891-1896.

Liu C, Bai B, Skogerbo G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 2005; 33(1):112-115.

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.

Zhang Z, Zhang  Y, Shi B, Deng W, Zhao Y, Chen R. Detecting chimeric 5'/3' UTRs with cross-chromosomal  splicing by bioinformatics. Chin Sci Bull 2004; 49(10):1051-1054.

Lu H, Zhu X, Liu H, Skogerbo G, Zhang J, Zhang Y, Cai L, Zhao Y, Sun S, Xu J, Bu  D, Chen R. The interactome as a tree -- an attempt to visualize the protein-protein interaction network in yeast. Nucleic Acids Res 2004; 32(16):4804-4811.

Zhang Y*, Xu  J*, Deng W, Zhang N, Cai L, Zhao Y, Bu D, Chen R. SiRNA designs to the crucial proteins of SARS coronavirus. Prog Biochem Biophys 2003; 30(3):335-338.


 


 


 


 


 

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