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Combined evidence annotation of transposable elements in genome sequences.
Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. Quesneville H, et al. Among authors: ashburner m. PLoS Comput Biol. 2005 Jul;1(2):166-75. doi: 10.1371/journal.pcbi.0010022. Epub 2005 Jul 29. PLoS Comput Biol. 2005. PMID: 16110336 Free PMC article.
EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG. Guigó R, et al. Among authors: ashburner m. Genome Biol. 2006;7 Suppl 1(Suppl 1):S2.1-31. doi: 10.1186/gb-2006-7-s1-s2. Epub 2006 Aug 7. Genome Biol. 2006. PMID: 16925836 Free PMC article. Review.
The ribosomal protein genes and Minute loci of Drosophila melanogaster.
Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR. Marygold SJ, et al. Among authors: ashburner m. Genome Biol. 2007;8(10):R216. doi: 10.1186/gb-2007-8-10-r216. Genome Biol. 2007. PMID: 17927810 Free PMC article.
Functional annotation of a full-length mouse cDNA collection.
Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Kawai J, et al. Among authors: ashburner m. Nature. 2001 Feb 8;409(6821):685-90. doi: 10.1038/35055500. Nature. 2001. PMID: 11217851
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