@Article{Roy:Ernst:Kharchenko:Ident_funct_eleme:2010,
  author =	 {Roy, Sushmita and Ernst, Jason and Kharchenko, Peter V. and 
                  Kheradpour, Pouya and Negre, Nicolas and Eaton, Matthew L. 
                  and Landolin, Jane M. and Bristow, Christopher A. and Ma, 
                  Lijia and Lin, Michael F. and Washietl, Stefan and 
                  Arshinoff, Bradley I. and Ay, Ferhat and Meyer, Patrick E. 
                  and Robine, Nicolas and Washington, Nicole L. and Di 
                  Stefano, Luisa and Berezikov, Eugene and Brown, Christopher 
                  D. and Candeias, Rogerio and Carlson, Joseph W. and Carr, 
                  Adrian and Jungreis, Irwin and Marbach, Daniel and Sealfon, 
                  Rachel and Tolstorukov, Michael Y. and Will, Sebastian and 
                  Alekseyenko, Artyom A. and Artieri, Carlo and Booth, 
                  Benjamin W. and Brooks, Angela N. and Dai, Qi and Davis, 
                  Carrie A. and Duff, Michael O. and Feng, Xin and Gorchakov, 
                  Andrey A. and Gu, Tingting and Henikoff, Jorja G. and 
                  Kapranov, Philipp and Li, Renhua and MacAlpine, Heather K. 
                  and Malone, John and Minoda, Aki and Nordman, Jared and 
                  Okamura, Katsutomo and Perry, Marc and Powell, Sara K. and 
                  Riddle, Nicole C. and Sakai, Akiko and Samsonova, Anastasia 
                  and Sandler, Jeremy E. and Schwartz, Yuri B. and Sher, Noa 
                  and Spokony, Rebecca and Sturgill, David and van Baren, 
                  Marijke and Wan, Kenneth H. and Yang, Li and Yu, Charles and 
                  Feingold, Elise and Good, Peter and Guyer, Mark and Lowdon, 
                  Rebecca and Ahmad, Kami and Andrews, Justen and Berger, 
                  Bonnie and Brenner, Steven E. and Brent, Michael R. and 
                  Cherbas, Lucy and Elgin, Sarah C. R. and Gingeras, Thomas R. 
                  and Grossman, Robert and Hoskins, Roger A. and Kaufman, 
                  Thomas C. and Kent, William and Kuroda, Mitzi I. and 
                  Orr-Weaver, Terry and Perrimon, Norbert and Pirrotta, 
                  Vincenzo and Posakony, James W. and Ren, Bing and Russell, 
                  Steven and Cherbas, Peter and Graveley, Brenton R. and 
                  Lewis, Suzanna and Micklem, Gos and Oliver, Brian and Park, 
                  Peter J. and Celniker, Susan E. and Henikoff, Steven and 
                  Karpen, Gary H. and Lai, Eric C. and MacAlpine, David M. and 
                  Stein, Lincoln D. and White, Kevin P. and Kellis, Manolis},
  title =	 {Identification of functional elements and regulatory 
                  circuits by {Drosophila} {modENCODE}},
  journal =	 {Science},
  year =	 {2010},
  volume =	 {330},
  number =	 {6012},
  pages =	 {1787-97},
  user =	 {will},
  pmid =	 {21177974},
  doi = 	 {10.1126/science.1198374},
  issn = 	 {1095-9203},
  issn = 	 {0036-8075},
  abstract =	 {To gain insight into how genomic information is translated 
                  into cellular and developmental programs, the Drosophila 
                  model organism Encyclopedia of DNA Elements (modENCODE) 
                  project is comprehensively mapping transcripts, histone 
                  modifications, chromosomal proteins, transcription factors, 
                  replication proteins and intermediates, and nucleosome 
                  properties across a developmental time course and in 
                  multiple cell lines. We have generated more than 700 data 
                  sets and discovered protein-coding, noncoding, RNA 
                  regulatory, replication, and chromatin elements, more than 
                  tripling the annotated portion of the Drosophila genome. 
                  Correlated activity patterns of these elements reveal a 
                  functional regulatory network, which predicts putative new 
                  functions for genes, reveals stage- and tissue-specific 
                  regulators, and enables gene-expression prediction. Our 
                  results provide a foundation for directed experimental and 
                  computational studies in Drosophila and related species and 
                  also a model for systematic data integration toward 
                  comprehensive genomic and functional annotation.}
}