FANTOM3  papers

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Related papers

• Large-scale correlation of DNA accession numbers to the cDNAs in the FANTOM full-length mouse cDNA clone set.
  Ajioka I, Maeda T, Nakajima K.
  Keio J Med. 2006 Sep;55(3):107-10.
  

• Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized.
  Kiyosawa H, Mise N, Iwase S, Hayashizaki Y, Abe K.
  Genome Res. 2005 Apr;15(4):463-74. Epub 2005 Mar 21.
  

• Development of a spot reliability evaluation score for DNA microarrays.
  Matsumura Y, Shimokawa K, Hayashizaki Y, Ikeo K, Tateno Y, Kawai J.
  Gene. 2005 Mar 18; [Epub ahead of print]

• High-throughput mapping of a dynamic signaling network in mammalian cells.
  Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana JL.
  Science. 2005 Mar 11;307(5715):1621-5.
  

• Differential Expression of Genes within the Cochlea as Defined by a Custom Mouse Inner Ear Microarray.
  Morris KA, Snir E, Pompeia C, Koroleva IV, Kachar B, Hayashizaki Y, Carninci P, Soares MB, Beisel KW.
  J Assoc Res Otolaryngol. 2005 Mar;6(1):75-89. Epub 2005 Apr 22.

• RNAdb--a comprehensive mammalian noncoding RNA database.
  Pang KC, Stephen S, Engstrom PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JS.
  Nucleic Acids Res. 2005 Jan 1;33(Database issue):D125-30.

• Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis.
  Kasukawa T, Katayama S, Kawaji H, Suzuki H, Hume DA, Hayashizaki Y.
  Genomics. 2004 Dec;84(6):913-21.

• Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
  Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P.
  Nat Methods. 2004 Dec;1(3):233-9. Epub 2004 Nov 18.

• Sharing genomes: an integrated approach to funding, managing and distributing genomic clone resources.
  Weaver T, Maurer J, Hayashizaki Y.
  Nat Rev Genet. 2004 Nov;5(11):861-6.

• The responsibility to share: sharing the responsibility.
  Yuille M, Korn B, Moore T, Farmer AA, Carrino J, Prange C, Hayashizaki Y.
  Genome Res. 2004 Oct;14(10B):2015-9. Review. No abstract available.

• A genome-wide and nonredundant mouse transcription factor database.
  Kanamori M, Konno H, Osato N, Kawai J, Hayashizaki Y, Suzuki H.
  Biochem Biophys Res Commun. 2004 Sep 24;322(3):787-93.

• Integrated analysis of the genome and the transcriptome by FANTOM.
  Katayama S, Kanamori M, Hayashizaki Y.
  Brief Bioinform. 2004 Sep;5(3):249-58. Review.

• Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR.
  Suzuki H, Okunishi R, Hashizume W, Katayama S, Ninomiya N, Osato N, Sato K, Nakamura M, Iida J, Kanamori M, Hayashizaki Y.
  FEBS Lett. 2004 Aug 27;573(1-3):214-8.

• Spatial patterns of gene expression in the olfactory bulb.
  Lin DM, Yang YH, Scolnick JA, Brunet LJ, Marsh H, Peng V, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J.
  Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12718-23. Epub 2004 Aug 10.

• Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs.
  Suzuki M, Hayashizaki Y.
  Bioessays. 2004 Aug;26(8):833-43. Review.

• Aptamer-dependent full-length cDNA synthesis by overlap extension PCR.
  Mitani Y, Nakayama T, Harbers M, Hayashizaki Y.
  Biotechniques. 2004 Jul;37(1):124, 126, 128-9.

• Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.
  Beisel KW, Shiraki T, Morris KA, Pompeia C, Kachar B, Arakawa T, Bono H, Kawai J, Hayashizaki Y, Carninci P.
  Genomics. 2004 Jun;83(6):1012-23.

• Gene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray system.
  Nagano Y, Nagahori K, Yoshiro F, Hamaguchi Y, Ishikawa T, Ichikawa Y, Togo S, Okazaki Y, Hayashizaki Y, Shimada H.
  Liver Int. 2004 Jun;24(3):253-8.

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
  Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
  PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20.

• Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi.
  Tanaka T, Tomaru Y, Nomura Y, Miura H, Suzuki M, Hayashizaki Y.
  Nucleic Acids Res. 2004 May 17;32(9):2740-50. Print 2004. Erratum in: Nucleic Acids Res. 2004 Jun 29;32(11):3511.

• Gene discovery in genetically labeled single dopaminergic neurons of the retina.
  Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola E.
  Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):5069-74. Epub 2004 Mar 26.

• Dynamic transcriptome of mice.
  Hayashizaki Y, Kanamori M.
  Trends Biotechnol. 2004 Apr;22(4):161-7. Review.

• Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes.
  Kiyosawa H, Kawashima T, Silva D, Petrovsky N, Hasegawa Y, Sakai K, Hayashizaki Y.
  Intern Med J. 2004 Mar;34(3):79-90.

• A new approach to the distribution and storage of genetic resources.
  Hayashizaki Y, Kawai J.
  Nat Rev Genet. 2004 Mar;5(3):223-8. No abstract available.

• Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.
  Kodzius R, Matsumura Y, Kasukawa T, Shimokawa K, Fukuda S, Shiraki T, Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y.
  FEBS Lett. 2004 Feb 13;559(1-3):22-6.

• Large-scale collection and characterization of promoters of human and mouse genes.
  Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Kel AE, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Takagi T, Nakai K, Sugano S.
  In Silico Biol. 2004;4(4):429-44.

• MaXML: mouse annotation XML.
  Kasukawa T, Bono H, Hayashizaki Y, Okazaki Y, Matsuda H.
  In Silico Biol. 2004;4(1):7-15. Epub 2003 Dec 26.

• EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.
  Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y.
  Nucleic Acids Res. 2004 Jan 1;32(Database issue):D548-51.

• FREP: a database of functional repeats in mouse cDNAs.
  Nagashima T, Matsuda H, Silva DG, Petrovsky N, Konagaya A, Schonbach C, Kasukawa T, Arakawa T, Carninci P, Kawai J, Hayashizaki Y; RIKEN GER Group; Genome Science Laoratory Members.
  Nucleic Acids Res. 2004 Jan 1;32(Database issue):D471-5.

• Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
  Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y.
  Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15776-81. Epub 2003 Dec 8.

• A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis.
  Tomaru Y, Kondo S, Suzuki M, Hayashizaki Y.
  Biochem Biophys Res Commun. 2003 Oct 17;310(2):667-74.

• The Riken mouse genome encyclopedia project.
  Hayashizaki Y.
  C R Biol. 2003 Oct-Nov;326(10-11):923-9. Review.

• Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
  Hirozane-Kishikawa T, Shiraki T, Waki K, Nakamura M, Arakawa T, Kawai J, Fagiolini M, Hensch TK, Hayashizaki Y, Carninci P.
  Biotechniques. 2003 Sep;35(3):510-6, 518.

• Genetic control of the innate immune response.
  Wells CA, Ravasi T, Faulkner GJ, Carninci P, Okazaki Y, Hayashizaki Y, Sweet M, Wainwright BJ, Hume DA.
  BMC Immunol. 2003 Jun 26;4(1):5.

• Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
  Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y.
  Genome Res. 2003 Jun;13(6B):1273-89.

• Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.
  Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y, Gaasterland T; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1290-300.

• Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.
  Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1301-6.

• Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set.
  Brusic V, Pillai RS, Silva DG, Petrovsky N, Schonbach C; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1307-17.

• Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.
  Bono H, Yagi K, Kasukawa T, Nikaido I, Tominaga N, Miki R, Mizuno Y, Tomaru Y, Goto H, Nitanda H, Shimizu D, Makino H, Morita T, Fujiyama J, Sakai T, Shimoji T, Hume DA, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1318-23.

• Antisense transcripts with FANTOM2 clone set and their implications for gene regulation.
  Kiyosawa H, Yamanaka I, Osato N, Kondo S, Hayashizaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1324-34.

• Mouse proteome analysis.
  Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale RD, Yuan Z; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1335-44.
  

• Comprehensive analysis of the mouse metabolome based on the transcriptome.
  Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1345-9.

• The mouse secretome: functional classification of the proteins secreted into the extracellular environment.
  Grimmond SM, Miranda KC, Yuan Z, Davis MJ, Hume DA, Yagi K, Tominaga N, Bono H, Hayashizaki Y, Okazaki Y, Teasdale RD; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1350-9.

• Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
  Wells CA, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1360-5.

• Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set.
  Forrest A. R, Taylor D, Grimmond S; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1366-75.

• Comparative analysis of apoptosis and inflammation genes of mice and humans.
  Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1376-88.

• The comparative proteomics of ubiquitination in mouse.
  Semple CA; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1389-94.

• Analysis of the mouse transcriptome for genes involved in the function of the nervous system.
  Gustincich S, Batalov S, Beisel KW, Bono H, Carninci P, Fletcher CF, Grimmond S, Hirokawa N, Jarvis ED, Jegla T, Kawasawa Y, LeMieux J, Miki H, Raviola E, Teasdale RD, Tominaga N, Yagi K, Zimmer A, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1395-401.

• Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.
  Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris GA, Lyons PA, Oshimura M, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1402-9.

• A comprehensive transcript map of the mouse Gnas imprinted complex.
  Holmes R, Williamson C, Peters J, Denny P, Wells C; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1410-5.

• Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome.
  Tajul-Arifin K, Teasdale R, Ravasi T, Hume DA, Mattick JS; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1416-29.

• Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.
  Ravasi T, Huber T, Zavolan M, Forrest A, Gaasterland T, Grimmond S, Hume DA; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1430-42.
  

• Kinesin superfamily proteins (KIFs) in the mouse transcriptome.
  Miki H, Setou M, Hirokawa N; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1455-65.
  

• G protein-coupled receptor genes in the FANTOM2 database.
  Kawasawa Y, McKenzie LM, Hill DP, Bono H, Yanagisawa M; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1466-77.

• CDS annotation in full-length cDNA sequence.
  Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H, Baldarelli R, Hayashizaki Y, Okazaki Y.
  Genome Res. 2003 Jun;13(6B):1478-87.

• DNA book.
  Kawai J, Hayashizaki Y.
  Genome Res. 2003 Jun;13(6B):1488-95.

• Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.
  Schriml LM, Hill DP, Blake JA, Bono H, Wynshaw-Boris A, Pavan WJ, Ring BZ, Beisel K, Setou M, Okazaki Y; RIKEN GER Group; GSL Members.
  Genome Res. 2003 Jun;13(6B):1496-500.
  

• GeneLynx mouse: integrated portal to the mouse genome.
  Lenhard B, Wahlestedt C, Wasserman WW.
  Genome Res. 2003 Jun;13(6B):1501-4.

• Connecting sequence and biology in the laboratory mouse.
  Baldarelli RM, Hill DP, Blake JA, Adachi J, Furuno M, Bradt D, Corbani LE, Cousins S, Frazer KS, Qi D, Yang L, Ramachandran S, Reed D, Zhu Y, Kasukawa T, Ringwald M, King BL, Maltais LJ, McKenzie LM, Schriml LM, Maglott D, Church DM, Pruitt K, Eppig JT, Richardson JE, Kadin JA, Bult CJ.
  Genome Res. 2003 Jun;13(6B):1505-19.

• Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.
  Nagashima T, Silva DG, Petrovsky N, Socha LA, Suzuki H, Saito R, Kasukawa T, Kurochkin IV, Konagaya A, Schonbach C.
  Genome Res. 2003 Jun;13(6B):1520-33.

• The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.
  Suzuki H, Saito R, Kanamori M, Kai C, Schonbach C, Nagashima T, Hosaka J, Hayashizaki Y.
  Genome Res. 2003 Jun;13(6B):1534-41.

• Development and evaluation of an automated annotation pipeline and cDNA annotation system.
  Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.
  Genome Res. 2003 Jun;13(6B):1542-51.

• Analysis of gene expression in the developing mouse retina.
  Diaz E, Yang YH, Ferreira T, Loh KC, Okazaki Y, Hayashizaki Y, Tessier-Lavigne M, Speed TP, Ngai J.
  Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5491-6. Epub 2003 Apr 17.

• Construction of reliable protein-protein interaction networks with a new interaction generality measure.
  Saito R, Suzuki H, Hayashizaki Y.
  Bioinformatics. 2003 Apr 12;19(6):756-63.

• Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene.
  Walsh NC, Cahill M, Carninci P, Kawai J, Okazaki Y, Hayashizaki Y, Hume DA, Cassady AI.
  Gene. 2003 Mar 27;307:111-23.
  

• Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality.
  Saito R, Suzuki H, Hayashizaki Y.
  Biochem Biophys Res Commun. 2003 Feb 14;301(3):633-40.
  

• Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure.
  Kadota K, Nishimura S, Bono H, Nakamura S, Hayashizaki Y, Okazaki Y, Takahashi K.
  Physiol Genomics. 2003 Feb 6;12(3):251-9.

• Mouse Genome Encyclopedia Project.
  Hayashizaki Y.
  Cold Spring Harb Symp Quant Biol. 2003;68:195-204. Review. No abstract available.
  

• RIKEN mouse genome encyclopedia.
  Hayashizaki Y.
  Mech Ageing Dev. 2003 Jan;124(1):93-102.

• Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
  Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.
  Nature. 2002 Dec 5;420(6915):563-73.

• Initial sequencing and comparative analysis of the mouse genome.
  Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES; Mouse Genome Sequencing Consortium.
  Nature. 2002 Dec 5;420(6915):520-62.

• Molecular analysis of gene expression in the developing pontocerebellar projection system.
  Diaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P.
  Neuron. 2002 Oct 24;36(3):417-34.

• Cytoplasmic RNA extraction from fresh and frozen mammalian tissues.
  Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ.
  Biotechniques. 2002 Aug;33(2):306-9.

• Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
  Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M; RIKEN Genome Exploration Research Group Phase II Team.
  Genome Res. 2002 Aug;12(8):1286-93.

• Extra-long first-strand cDNA synthesis.
  Carninci P, Shiraki T, Mizuno Y, Muramatsu M, Hayashizaki Y.
  Biotechniques. 2002 May;32(5):984-5. No abstract available.

• Exploration of novel motifs derived from mouse cDNA sequences.
  Kawaji H, Schonbach C, Matsuo Y, Kawai J, Okazaki Y, Hayashizaki Y, Matsuda H.
  Genome Res. 2002 Mar;12(3):367-78.
  

• Interaction generality, a measurement to assess the reliability of a protein-protein interaction.
  Saito R, Suzuki H, Hayashizaki Y.
  Nucleic Acids Res. 2002 Mar 1;30(5):1163-8.
  

• Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.
  Mizuno Y, Sotomaru Y, Katsuzawa Y, Kono T, Meguro M, Oshimura M, Kawai J, Tomaru Y, Kiyosawa H, Nikaido I, Amanuma H, Hayashizaki Y, Okazaki Y.
  Biochem Biophys Res Commun. 2002 Feb 8;290(5):1499-505.

• READ: RIKEN Expression Array Database.
  Bono H, Kasukawa T, Hayashizaki Y, Okazaki Y.
  Nucleic Acids Res. 2002 Jan 1;30(1):211-3.

• FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.
  Bono H, Kasukawa T, Furuno M, Hayashizaki Y, Okazaki Y.
  Nucleic Acids Res. 2002 Jan 1;30(1):116-8.

• Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing.
  Shibata Y, Carninci P, Sato K, Hayatsu N, Shiraki T, Ishii Y, Arakawa T, Hara A, Ohsato N, Izawa M, Aizawa K, Itoh M, Shibata K, Shinagawa A, Kawai J, Ota Y, Kikuchi S, Kishimoto N, Muramatsu M, Hayashizaki Y.
  Biotechniques. 2001 Nov;31(5):1042, 1044, 1048-9.
  

• Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
  Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M.
  Gene. 2001 Oct 3;276(1-2):101-5.