Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

Brief. Bioinformatics     Pascale Gaudet , Michael S Livstone , Suzanna E Lewis , Paul D Thomas

A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

PLoS Biol.     Graciana Diez-Roux , Sandro Banfi , Marc Sultan , Lars Geffers , Santosh Anand , David Rozado , Alon Magen , Elena Canidio , Massimiliano Pagani , Ivana Peluso , Nathalie Lin-Marq , Muriel Koch , Marchesa Bilio , Immacolata Cantiello , Roberta Verde , Cristian De Masi , Salvatore A Bianchi , Juliette Cicchini , Elodie Perroud , Shprese Mehmeti , Emilie Dagand , Sabine Schrinner , Asja Nürnberger , Katja Schmidt , Katja Metz , Christina Zwingmann , Norbert Brieske , Cindy Springer , Ana Martinez Hernandez , Sarah Herzog , Frauke Grabbe , Cornelia Sieverding , Barbara Fischer , Kathrin Schrader , Maren Brockmeyer , Sarah Dettmer , Christin Helbig , Violaine Alunni , Marie-Annick Battaini , Carole Mura , Charlotte N Henrichsen , Raquel Garcia-Lopez , Diego Echevarria , Eduardo Puelles , Elena Garcia-Calero , Stefan Kruse , Markus Uhr , Christine Kauck , Guangjie Feng , Nestor Milyaev , Chuang Kee Ong , Lalit Kumar , MeiSze Lam , Colin A Semple , Attila Gyenesei , Stefan Mundlos , Uwe Radelof , Hans Lehrach , Paolo Sarmientos , Alexandre Reymond , Duncan R Davidson , Pascal Dollé , Stylianos E Antonarakis , Marie-Laure Yaspo , Salvador Martinez , Richard A Baldock , Gregor Eichele , Andrea Ballabio

Antisense transcription in the mammalian transcriptome.

Science     S Katayama , Y Tomaru , T Kasukawa , K Waki , M Nakanishi , M Nakamura , H Nishida , C C Yap , M Suzuki , J Kawai , H Suzuki , P Carninci , Y Hayashizaki , C Wells , M Frith , T Ravasi , K C Pang , J Hallinan , J Mattick , D A Hume , L Lipovich , S Batalov , P G Engström , Y Mizuno , M A Faghihi , A Sandelin , A M Chalk , S Mottagui-Tabar , Z Liang , B Lenhard , C Wahlestedt , RIKEN Genome Exploration Research Group , Genome Science Group (Genome Network Project Core Group) , FANTOM Consortium

The transcriptional landscape of the mammalian genome.

Science     P Carninci , T Kasukawa , S Katayama , J Gough , M C Frith , N Maeda , R Oyama , T Ravasi , B Lenhard , C Wells , R Kodzius , K Shimokawa , V B Bajic , S E Brenner , S Batalov , A R R Forrest , M Zavolan , M J Davis , L G Wilming , V Aidinis , J E Allen , A Ambesi-Impiombato , R Apweiler , R N Aturaliya , T L Bailey , M Bansal , L Baxter , K W Beisel , T Bersano , H Bono , A M Chalk , K P Chiu , V Choudhary , A Christoffels , D R Clutterbuck , M L Crowe , E Dalla , B P Dalrymple , B de Bono , G Della Gatta , D di Bernardo , T Down , P Engstrom , M Fagiolini , G Faulkner , C F Fletcher , T Fukushima , M Furuno , S Futaki , M Gariboldi , P Georgii-Hemming , T R Gingeras , T Gojobori , R E Green , S Gustincich , M Harbers , Y Hayashi , T K Hensch , N Hirokawa , D Hill , L Huminiecki , M Iacono , K Ikeo , A Iwama , T Ishikawa , M Jakt , A Kanapin , M Katoh , Y Kawasawa , J Kelso , H Kitamura , H Kitano , G Kollias , S P T Krishnan , A Kruger , S K Kummerfeld , I V Kurochkin , L F Lareau , D Lazarevic , L Lipovich , J Liu , S Liuni , S McWilliam , M Madan Babu , M Madera , L Marchionni , H Matsuda , S Matsuzawa , H Miki , F Mignone , S Miyake , K Morris , S Mottagui-Tabar , N Mulder , N Nakano , H Nakauchi , P Ng , R Nilsson , S Nishiguchi , S Nishikawa , F Nori , O Ohara , Y Okazaki , V Orlando , K C Pang , W J Pavan , G Pavesi , G Pesole , N Petrovsky , S Piazza , J Reed , J F Reid , B Z Ring , M Ringwald , B Rost , Y Ruan , S L Salzberg , A Sandelin , C Schneider , C Schönbach , K Sekiguchi , C A M Semple , S Seno , L Sessa , Y Sheng , Y Shibata , H Shimada , K Shimada , D Silva , B Sinclair , S Sperling , E Stupka , K Sugiura , R Sultana , Y Takenaka , K Taki , K Tammoja , S L Tan , S Tang , M S Taylor , J Tegner , S A Teichmann , H R Ueda , E van Nimwegen , R Verardo , C L Wei , K Yagi , H Yamanishi , E Zabarovsky , S Zhu , A Zimmer , W Hide , C Bult , S M Grimmond , R D Teasdale , E T Liu , V Brusic , J Quackenbush , C Wahlestedt , J S Mattick , D A Hume , C Kai , D Sasaki , Y Tomaru , S Fukuda , M Kanamori-Katayama , M Suzuki , J Aoki , T Arakawa , J Iida , K Imamura , M Itoh , T Kato , H Kawaji , N Kawagashira , T Kawashima , M Kojima , S Kondo , H Konno , K Nakano , N Ninomiya , T Nishio , M Okada , C Plessy , K Shibata , T Shiraki , S Suzuki , M Tagami , K Waki , A Watahiki , Y Okamura-Oho , H Suzuki , J Kawai , Y Hayashizaki , FANTOM Consortium , RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)

Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.

Nat. Methods     Akira Watahiki , Kazunori Waki , Norihito Hayatsu , Toshiyuki Shiraki , Shinji Kondo , Mari Nakamura , Daisuke Sasaki , Takahiro Arakawa , Jun Kawai , Matthias Harbers , Yoshihide Hayashizaki , Piero Carninci

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Proc. Natl. Acad. Sci. U.S.A.     Robert L Strausberg , Elise A Feingold , Lynette H Grouse , Jeffery G Derge , Richard D Klausner , Francis S Collins , Lukas Wagner , Carolyn M Shenmen , Gregory D Schuler , Stephen F Altschul , Barry Zeeberg , Kenneth H Buetow , Carl F Schaefer , Narayan K Bhat , Ralph F Hopkins , Heather Jordan , Troy Moore , Steve I Max , Jun Wang , Florence Hsieh , Luda Diatchenko , Kate Marusina , Andrew A Farmer , Gerald M Rubin , Ling Hong , Mark Stapleton , M Bento Soares , Maria F Bonaldo , Tom L Casavant , Todd E Scheetz , Michael J Brownstein , Ted B Usdin , Shiraki Toshiyuki , Piero Carninci , Christa Prange , Sam S Raha , Naomi A Loquellano , Garrick J Peters , Rick D Abramson , Sara J Mullahy , Stephanie A Bosak , Paul J McEwan , Kevin J McKernan , Joel A Malek , Preethi H Gunaratne , Stephen Richards , Kim C Worley , Sarah Hale , Angela M Garcia , Laura J Gay , Stephen W Hulyk , Debbie K Villalon , Donna M Muzny , Erica J Sodergren , Xiuhua Lu , Richard A Gibbs , Jessica Fahey , Erin Helton , Mark Ketteman , Anuradha Madan , Stephanie Rodrigues , Amy Sanchez , Michelle Whiting , Anup Madan , Alice C Young , Yuriy Shevchenko , Gerard G Bouffard , Robert W Blakesley , Jeffrey W Touchman , Eric D Green , Mark C Dickson , Alex C Rodriguez , Jane Grimwood , Jeremy Schmutz , Richard M Myers , Yaron S N Butterfield , Martin I Krzywinski , Ursula Skalska , Duane E Smailus , Angelique Schnerch , Jacqueline E Schein , Steven J M Jones , Marco A Marra , Mammalian Gene Collection Program Team

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Nature     Y Okazaki , M Furuno , T Kasukawa , J Adachi , H Bono , S Kondo , I Nikaido , N Osato , R Saito , H Suzuki , I Yamanaka , H Kiyosawa , K Yagi , Y Tomaru , Y Hasegawa , A Nogami , C Schönbach , T Gojobori , R Baldarelli , D P Hill , C Bult , D A Hume , J Quackenbush , L M Schriml , A Kanapin , H Matsuda , S Batalov , K W Beisel , J A Blake , D Bradt , V Brusic , C Chothia , L E Corbani , S Cousins , E Dalla , T A Dragani , C F Fletcher , A Forrest , K S Frazer , T Gaasterland , M Gariboldi , C Gissi , A Godzik , J Gough , S Grimmond , S Gustincich , N Hirokawa , I J Jackson , E D Jarvis , A Kanai , H Kawaji , Y Kawasawa , R M Kedzierski , B L King , A Konagaya , I V Kurochkin , Y Lee , B Lenhard , P A Lyons , D R Maglott , L Maltais , L Marchionni , L McKenzie , H Miki , T Nagashima , K Numata , T Okido , W J Pavan , G Pertea , G Pesole , N Petrovsky , R Pillai , J U Pontius , D Qi , S Ramachandran , T Ravasi , J C Reed , D J Reed , J Reid , B Z Ring , M Ringwald , A Sandelin , C Schneider , C A M Semple , M Setou , K Shimada , R Sultana , Y Takenaka , M S Taylor , R D Teasdale , M Tomita , R Verardo , L Wagner , C Wahlestedt , Y Wang , Y Watanabe , C Wells , L G Wilming , A Wynshaw-Boris , M Yanagisawa , I Yang , L Yang , Z Yuan , M Zavolan , Y Zhu , A Zimmer , P Carninci , N Hayatsu , T Hirozane-Kishikawa , H Konno , M Nakamura , N Sakazume , K Sato , T Shiraki , K Waki , J Kawai , K Aizawa , T Arakawa , S Fukuda , A Hara , W Hashizume , K Imotani , Y Ishii , M Itoh , I Kagawa , A Miyazaki , K Sakai , D Sasaki , K Shibata , A Shinagawa , A Yasunishi , M Yoshino , R Waterston , E S Lander , J Rogers , E Birney , Y Hayashizaki , FANTOM Consortium , RIKEN Genome Exploration Research Group Phase I & II Team

Functional annotation of a full-length mouse cDNA collection.

Nature     J Kawai , A Shinagawa , K Shibata , M Yoshino , M Itoh , Y Ishii , T Arakawa , A Hara , Y Fukunishi , H Konno , J Adachi , S Fukuda , K Aizawa , M Izawa , K Nishi , H Kiyosawa , S Kondo , I Yamanaka , T Saito , Y Okazaki , T Gojobori , H Bono , T Kasukawa , R Saito , K Kadota , H Matsuda , M Ashburner , S Batalov , T Casavant , W Fleischmann , T Gaasterland , C Gissi , B King , H Kochiwa , P Kuehl , S Lewis , Y Matsuo , I Nikaido , G Pesole , J Quackenbush , L M Schriml , F Staubli , R Suzuki , M Tomita , L Wagner , T Washio , K Sakai , T Okido , M Furuno , H Aono , R Baldarelli , G Barsh , J Blake , D Boffelli , N Bojunga , P Carninci , M F de Bonaldo , M J Brownstein , C Bult , C Fletcher , M Fujita , M Gariboldi , S Gustincich , D Hill , M Hofmann , D A Hume , M Kamiya , N H Lee , P Lyons , L Marchionni , J Mashima , J Mazzarelli , P Mombaerts , P Nordone , B Ring , M Ringwald , I Rodriguez , N Sakamoto , H Sasaki , K Sato , C Schönbach , T Seya , Y Shibata , K F Storch , H Suzuki , K Toyo-oka , K H Wang , C Weitz , C Whittaker , L Wilming , A Wynshaw-Boris , K Yoshida , Y Hasegawa , H Kawaji , S Kohtsuki , Y Hayashizaki , RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium

RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

Genome Res.     K Shibata , M Itoh , K Aizawa , S Nagaoka , N Sasaki , P Carninci , H Konno , J Akiyama , K Nishi , T Kitsunai , H Tashiro , M Itoh , N Sumi , Y Ishii , S Nakamura , M Hazama , T Nishine , A Harada , R Yamamoto , H Matsumoto , S Sakaguchi , T Ikegami , K Kashiwagi , S Fujiwake , K Inoue , Y Togawa

Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.

Genome Res.     P Carninci , Y Shibata , N Hayatsu , Y Sugahara , K Shibata , M Itoh , H Konno , Y Okazaki , M Muramatsu , Y Hayashizaki