Publications

2012

Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al..  2012.  Modeling gene expression using chromatin features in various cellular contexts.. Genome Biol.. 13:R53. Abstract
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al..  2012.  Landscape of transcription in human cells. Nature. 489:101–108.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al..  2012.  Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res.. 22:1658–1667.
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Dunham I, Kundaje A, Aldred SF, Collins PJ et al..  2012.  An integrated encyclopedia of DNA elements in the human genome. Nature. 489:57–74.
Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R.  2012.  Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res.. 22:1616–1625.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al..  2012.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res.. 22:1775–1789.
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T et al..  2012.  An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol.. 13:418.
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al..  2012.  Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE. 7:e28213. Abstract
Pubmed

2011

Consortium ENCODEP, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E et al..  2011.  A user's guide to the encyclopedia of DNA elements (ENCODE).. PLoS Biol.. 9:e1001046. Abstract
Pubmed

2008

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al..  2008.  Efficient targeted transcript discovery via array-based normalization of RACE libraries.. Nat. Methods. 5:629–635. Abstract
Pubmed