Now showing items 1-6 of 6

    • ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline 

      Qin, Qian; Mei, Shenglin; Wu, Qiu; Sun, Hanfei; Li, Lewyn; Taing, Len; Chen, Sujun; Li, Fugen; Liu, Tao; Zang, Chongzhi; Xu, Han; Chen, Yiwen; Meyer, Clifford A.; Zhang, Yong; Brown, Myles; Long, Henry W.; Liu, X. Shirley (BioMed Central, 2016)
      Background: Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard ...
    • Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia 

      Wu, Jennifer N.; Pinello, Luca; Yissachar, Elinor; Wischhusen, Jonathan W.; Yuan, Guo-Cheng; Roberts, Charles W. M. (BioMed Central, 2015)
      Background: Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription ...
    • Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo 

      Wei, Gong-Hong; Badis, Gwenael; Berger, Michael F; Kivioja, Teemu; Palin, Kimmo; Enge, Martin; Bonke, Martin; Jolma, Arttu; Varjosalo, Markku; Gehrke, Andrew R; Yan, Jian; Talukder, Shaheynoor; Turunen, Mikko; Taipale, Mikko; Stunnenberg, Hendrik G; Ukkonen, Esko; Hughes, Timothy R; Taipale, Jussi; Bulyk, Martha Leonia (Nature Publishing Group, 2010)
      Members of the large ETS family of transcription factors (TFs) have highly similar DNA-binding domains (DBDs)—yet they have diverse functions and activities in physiology and oncogenesis. Some differences in DNA-binding ...
    • An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer 

      Sulahian, R; Casey, F; Shen, J; Qian, Zhirong; Shin, H; Ogino, Shuji; Weir, Barbara Ann; Vazquez, F; Liu, Xiaole (Shirley) Shirley; Hahn, William Chun; Bass, Adam Joel; Chan, Vivian; Shivdasani, Ramesh Arjun (Springer Nature, 2013)
      Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors, but the molecular bases of their oncogenic properties are largely unknown. Because ...
    • Large-Scale Quality Analysis of Published ChIP-seq Data 

      Marinov, Georgi K.; Kundaje, Anshul; Park, Peter J.; Wold, Barbara J. (Genetics Society of America, 2014)
      ChIP-seq has become the primary method for identifying in vivo protein–DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and ...
    • Multiplexed Illumina sequencing libraries from picogram quantities of DNA 

      Bowman, Sarah K; Simon, Matthew D; Deaton, Aimee M; Tolstorukov, Michael; Borowsky, Mark L; Kingston, Robert E (BioMed Central, 2013)
      Background: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin ...