Publications

2013

Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldon T, Guigo R, Sumner S.  2013.  Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol. 14:R20. Abstract

2012

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R et al..  2012.  Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.. Genome Res.. 22:1231–1242. Abstract
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al..  2012.  GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res.. 22:1760–1774.
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.
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.
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al..  2012.  Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res.. 22:1698–1710.
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.