Graveley BR*, Brooks AN*, Carlson JW*, Duff MO*, Landolin J*, Yang L*, Arieri C, van Baren MJ, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin AD, Li R, Lin W, Mattiuzzo N, Miller D, Sturgill D†, Tuch B, Zaleski C, Zhang D, Blancette M, Clough E, Dudoit S, Eads B, Green RE, Hammonds A, Kapranov P, Langton L, Malone J, Perrimon N, Sandler J, Wan K, Willingham A, Zhang Y, Zou Y , Andrews J, Brenner SE, Brent M, Cherbas P, Gingeras TR, Hoskins RA, Kaufman T, Oliver B, Celniker SE. The Developmental Transcriptome of Drosophila melanogaster. (*equal contribution)  Nature, in press.

The modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Stefano LD, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyneko A, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov A, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine H, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell S, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz Y, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SCR, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda M, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russel S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, in press.

Brooks AN*, Yang L*, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, and Graveley BR. Conservation of an RNA Regulatory Map between Drosophila and Mammals. (*equal contribution)  Genome Research gr.108662.110 Published in advance October 4, 2010, doi:10.1101/gr.108662.110

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. 2009. Unlocking the secrets of the genome. Nature 459:927-930

Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. 2009. Genome-wide analysis of alternative pre-mRNA splicing and RNA binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell 33:438-449.

Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218

Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE. 2007. The coupling of alternative splicing and nonsense mediated mRNA decay. in Blencowe B & Graveley B, eds. Alternative splicing in the postgenomic era. Landes Biosciences. 191-212. review

MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. 2006. Structural Basis for Double-Stranded RNA Processing by Dicer. Science 311(5758):195-198

Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research 33(Web Server issue):W686-689