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 independently of H3K9 trimethylation in mouse ES cells. Genome Res. 2015. [Abstract] [Full Paper] [Supplementary]

2014

• 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. Nucl Acids Res 2014; 42:D450-8. PMCID:PMC3965064. [Abstract] [Pull Paper]
  

• Wang, J., Lin, X., Wang, S., Wang, C., Wang, Q., Duan, X., ... & Huang, J. (2014). PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression. Scientific reports, 4.[Abstract] [Full paper]    

2013

• Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., ... & Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515.[Abstract] [Pull Paper]

• 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. [Abstract] [Full Paper]

• Du Z#, Li H#, Wei Q#, Zhao X, Wang C, Xu W, Liu XS*, Jin W*, Su Z*. Genome-wide analysis of histone  modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in oryza sativa L. japonica. Mol Plant 2013; Apr 29 epub. [Abstract] [Full Paper]

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

• Qin B#, Zhou M#, Ge Y#, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, 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. PMCID:PMC3448563 [Abstract] [Full Paper]
  

• Feng J#, Liu T#, Qin B, Zhang Y#, Liu XS*. Identifying ChIP-seq enrichment using MACS.  Nat Protoc 2012; 7(9):1728-40. [Abstract] [Full Paper]

• Meyer CA, Tang Q, Liu XS. Applications of next generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol 2012;26(10):1651-9. PMCID:PMC3458226 [Abstract] [Full Paper]

  
  

2011

• 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.
  [Abstract] [Full Paper]

2010

• Cao Q#, Zhou M#, Wang xj#, Meyer CA, Li C, Liu XS. CaSNP: a database for interrogating copy number  alterations of cancer from SNP array data. Nucleic Acids Res 2011; 39(Database issue):D968-74. Epub 2010; Oct 23. PMCID:PMC3013814

  [Abstract] [Full Paper]