FANTOM3 papers

Two milestone papers in the special issue: "Mapping RNA Form & Function", Science.

• The transcriptional landscape of the mammalian genome
  Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
  Science. 2005 Sep 2;309(5740):1559-63.

• Antisense transcription in the mammalian transcriptome
  Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium.
  Science. 2005 Sep 2;309(5740):1564-6.

Another milestone paper in Nature Genetics

• Genome-wide analysis of mammalian promoter architecture and evolution
  Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.
  Nat Genet. 2006 Jun;38(6):626-635.

The Genome Network/FANTOM3 article collection in PLoS Genetics

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.
  Hayashizaki Y, Carninci P.
  PLoS Genet. 2006 Apr;2(4):e63.

• Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
  Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.
  PLoS Genet. 2006 Apr;2(4):e62.

• Mice and men: their promoter properties.
  Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, HofmannO, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.
  PLoS Genet. 2006 Apr;2(4):e54.

• The abundance of short proteins in the mammalian proteome.
  Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P,Hayashizaki Y, Bailey TL, Grimmond SM.
  PLoS Genet. 2006 Apr;2(4):e52.

• Complex Loci in human and mouse genomes.
  Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A,Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L.
  PLoS Genet. 2006 Apr;2(4):e47.

• Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units.
  Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, Kasukawa T, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD.
  PLoS Genet. 2006 Apr;2(4):e46.

• A simple physical model predicts small exon length variations.
  Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, ZavolanM.
  PLoS Genet. 2006 Apr;2(4):e45.
  

• A method for similarity search of genomic positional expression using CAGE.
  Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H.
  PLoS Genet. 2006 Apr;2(4):e44.

• Clusters of internally primed transcripts reveal novel long noncoding RNAs.
  Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, Bult C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Mattick JS, Suzuki H.
  PLoS Genet. 2006 Apr;2(4):e37.

• Heterotachy in mammalian promoter evolution.
  Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA.
  PLoS Genet. 2006 Apr;2(4):e30.

• Pseudo-messenger RNA: phantoms of the transcriptome.
  Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, Wahlestedt C, Bajic VB, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Huminiecki L.
  PLoS Genet. 2006 Apr;2(4):e23.

Other satellite papers

• Transcriptional network dynamics in macrophage activation.
  Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T.
  Genomics. 2006 Aug;88(2):133-42

• Subcellular localization of mammalian type II membrane proteins.
  Aturaliya RN, Fink JL, Davis MJ, Teasdale MS, Hanson KA, Miranda KC, Forrest AR, Grimmond SM, Suzuki H, Kanamori M, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD.
  Traffic. 2006 May;7(5):613-25.

• Alternate transcription of the Toll-like receptor signaling cascade.
  Wells CA, Chalk AM, Forrest A, Taylor D, Waddell N, Schroder K, Himes SR, Faulkner G, Lo S, Kasukawa T, Kawaji H, Kai C, Kawai J, Katayama S, Carninci P, Hayashizaki Y, Hume DA, Grimmond SM.
  Genome Biol. 2006;7(2):R10.

• Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.
  Forrest AR, Taylor DF, Crowe ML, Chalk AM, Waddell NJ, Kolle G, Faulkner GJ, Kodzius R, Katayama S, Wells C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Grimmond SM.
  Genome Biol. 2006;7(1):R5.

• CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
  Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y.
  Nucleic Acids Res. 2006 Jan 1;34(Database issue):D632-6.