Members

Piero Carninci Piero Carninci
Leader of the Functional Genomics Technology Team, Leader of the Omics Resource Development Unit and Deputy Project Director of the LSA Technology Development Group - LSA Technology Development Group
Phone: +81 45 503 9331
Email:

Link to OSC Main Activities: Mouse Genome Encyclopedia FANTOM Genome Network Functional RNA LSA


Research Interest:

Breakthroughs in science depend on the development of novel technologies to solve outstanding biological problems. We have previously developed key technologies including the cap-trapper to comprehensively clone full-length cDNAs and the cap-analysis gene expression (CAGE). The mission of the Functional Genomics Technology Team is to develop novel original approaches to comprehensively study genes, their products and their interactions. The approaches should address biological questions that cannot be addressed with technologies that are the state of the art today. In contrast with classic approaches considering one gene at the time, our mission is to develop approaches that aim at targeting biological problem as systems. This requires to comprehensively analyzing various biological aspects.
The members of the laboratory are engaged in the development of original approaches and to design, propose and realize original genomics technologies and apply these to challenging biological problems. These include the discovery, validation and analysis of novel classes of non-coding RNAs; establishing single-cell CAGE methods and its application to reduced biological samples; and data mining, with particular interest at identifying biological patterns and rules, including genome-wise analysis of novel classes of RNAs and their network. To address these genomics approaches for samples derived from living cells in their biological context, particular emphasis consists in the miniaturization of these technologies, to analyze systematically the biology of few or single isolated cells, such as the characterization of the molecular networks of individual neurons, included in a larger cellular networks. Going beyond simple expression profiling, the ultimate mission is to understand the complex relationships between gene expression regulation, the non-coding RNA world, the epigenome and the biological output.
These developments will be done in collaboration with other teams and units and external collaborator, with particular hope to contribute to the development of the Omics Science Center as an internationally recognized institute and serve the community by ultimately implementing biomedical sciences and increasing our knowledge.



Curriculum Vitae:


Education

-    July 1984, Graduation at the Scientific Lyceum G. Oberdan, Trieste

-    March 1989: Doctor in Biological Science at University of Trieste, mark 106/110, with the experimental thesis "Characterization of a gene specifically expressed during the resting phase (Go) of cell cycle". Thesis prepared at the International Center for Genetic Engineering and Biotechnology (ICGEB, UNIDO), Trieste, Italy, with Prof. C. Schneider.

-    May 1990: National (Italian) Examination for the profession of Biologist, University of Ferrara, Italy.

 

Positions and summary of achievements

-    April 1989- September 1989: researcher, laboratory of Prof. C. Schneider at ICGEB, Trieste, Italy, where he developed a discontinuous buffer system to increase speed and resolution in sequencing electrophoresis and methods for the rapid purification of Genomic DNA from whole blood and yeast.

-    October 1989- September 1990: compulsory Italian army duty as a “health assistant”. Concurrently, part-time consultant of the biotechnology company, TALENT srl, Trieste, Italy.

-    October 1990- March 1995: researcher at TALENT srl (http://www.spin.it/talent/). He has developed DNA extraction and DNA sequencing methods and 7 DNA extraction kits for quick and simplified extraction of high-quality DNA from several substrates. He has developed the chemical reactions for an automated DNA extraction instrument. In collaboration with Prof. C. Schneider at the National Laboratory of Italian Consortium for Biotechnology he has also developed a method for capillary slab gel DNA sequencing.

-    April 1995- September 1995: researcher at the Genome Science Laboratory, RIKEN Tsukuba Institute, Japan

-    October 1995- March 1997: STA Fellow at the Genome Science Laboratory, RIKEN Tsukuba Institute.

-    April 1997- September 2001: tenured Scientist at the Genome Science Laboratory, RIKEN Tsukuba Institute.

-    October 2001- March 2003: tenured Scientist at the Genome Science Laboratory, RIKEN-Wako Main Campus

-    April 2003- March 2008: tenured Senior Scientists” at the Genome Science Laboratory, RIKEN, Wako Main Campus; adjunct appointment as Senior Scientist at RIKEN Genomic Sciences Center, RIKEN Yokohama Institute.

During the activity at RIKEN he has established a comprehensive set of full-length cDNA cloning technologies and widely applied them to construct the mouse full-length cDNA encyclopedia project and other full-length cDNA collections. He has actively lead the Fantom (Functional Annotation of the Mouse) activity, involving functional annotation of cDNA and the discovery of the widespread existence of non-coding RNAs in mammalians. He has also established the CAGE technology and other tagging methods to analyze the transcriptome and transcriptional networks, and produced a comprehensive map of mammalian promoters. Altogether, these technologies have originated more than 4 millions of entries in GenBank and more than 235,000 protein sequences.

-    April 2006-: Adjunct Professor at Department of Molecular Biochemistry, Gunma University Graduate School of Medicine.

-    April 2008-: Leader of the Functional Genomics Technology Team, Leader of the Omics Resource Development Unit and Deputy Project Director of the LSA Technology Development Group and the Omics Science Center, RIKEN Yokohama Institute.

 

Awards

-    First prize Biotec Award 2001, for Italian scientists under 40 year old involved in biotechnology, for the “Construction of the full-length cDNA encyclopedia”. Award ceremony on October 29, 2001 in Milan, Italy.

-    Yamazaki-Teiichi award 2007 (http://www.mst.or.jp/prize/2007/jushou.html) for the development of the cap-trapper technology and its use for the annotation of the transcriptional output of the genome

 

Memberships and Chairs

-    Member of the International Mouse Nomenclature Committee (2003-)

-    Associate Editor of the journal “Genomics” (September 2006-)

-    Scientific Advisory Board of DNAform (January 2009-)

-    Editorial Board of Nature Communications (2010-)

-    Editorial Board of BioEssays (2010-)

-    Member of the IMGC Secretariat (2010-)  

 

Meetings organized

-    Co-organizer (together with Bento Soares) of the “Full-length cDNA Cloning: A Workshop on Problems and Solutions”, The Banbury Center, Cold Spring Harbor Laboratory, NY, USA, March 23-25, 1998.

-    Organizing committee of the International mouse genome conference (IMGC) in 2000 in Narita, Japan.

-    Organizing committee of the “Systems Neurobiology” meeting at the International School for Advanced Studies (SISSA), Trieste, Italy, December 18-19, 2006.

-    Scientific coordinator of the collaborative Fantom 3 “Functional Annotation of the mouse” project and key contribution for other Fantom meetings: annotation organizer (Fantom 1), team organizer (Fantom 2) and chore author (Fantom 4)

 

Summary of presentations and publications

-   Author of more than 180 papers and book chapters (more than 12,000 citations)

-   Inventor in more than 25 patens and applications

-   Author of 250 posters and presentations (more than 30 as invited speaker)



Publications


1.    Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 2010 Apr 29.[Epub ahead of print]

2.    Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO.  Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC Genomics. 11:257.2010

3.    Carninci P. RNA dust: where are the genes? DNA Res. 17:51-9.2010.

4.    Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man.   Cell. 5:744-52.2010.

5.    de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y.  Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res. 20:257-64. 2010.

6.    Davis SW, Castinetti F, Carvalho LR, Ellsworth BS, Potok MA, Lyons RH, Brinkmeier ML, Raetzman LT, Carninci P, Mortensen AH, Hayashizaki Y, Arnhold IJ, Mendonça BB, Brue T, Camper SA. Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes. Mol Cell Endocrinol. 2009 Dec 16. [Epub ahead of print]

7.    Salimullah M, Kato S, Murata N, Kawazu C, Plessy C, Carninci P. Tunable fractionation of nucleic acids. BioTechniques. 47:1041-42.2009

8.    Forrest AR, Abdelhamid RF, Carninci P. Annotating Non-Coding Transcription using Functional Genomics Strategies. Briefings in Functional Genomics and Proteomics. 8:437-43.2009

9.    Carninci P. Is Sequencing Enlightenment ending the Dark Age of the transcriptome? Nature Methods. 6:711-13.2009.

10.    Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle. 8:2895-900.2009.

11.    Biagioli M, Pinto M, Cesselli D, Zaninello M, Lazarevic D, Roncaglia P, Simone R, Viachouli C, Plessy C, Bertin N, Beltrami A, Kobayashi K, Gallo V, Santoro C, Ferre I, Rivella S, Beltrami CA, Carninci P, Raviola E, Gustincich S. Unexpected expression of α- and β-globinin mesencephalic dopaminergic neurons and glial cells. PNAS. 106:15454-9.2009

12.    Taft R, Glazov E, Lassman T, Hayashizaki Y, Carninci P, Mattick J.  Small RNAs derived from snoRNAs. RNA. 15:1233-40.2009

13.    Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol. 10:R79.2009.

14.    Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41:563-71.2009.

15.    Taft R, Glazov EA, Cloonan N, Simons S, Stephen S, Faulkner G, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y and Mattick J. Tiny RNAs associated with transcription start sites in animals, Nat. Genet.41:572-8.2009.

16.    Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 41:553-62. 2009.

17.    Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA. Genetics, gene expression and bioinformatics of the pituitary bland. Horm Res. 71:101-15.2009.

18.    Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol.:R40. 2009

19.    Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamis and regulatory interations. Genome Biol. 10:R40.2009

20.    Seki M. Kamiya A. Carninci P. Hayashizaki Y. Shinozaki K. Generation of full-length cDNA libraries: focus on plants. Methods Mol Biol. 533:49-68.2009

21.    Forrest AR. Carninci P. Whole genome transcriptome analysis. RNA Biology. 6:107-12.2009.

22.    Carninci P. Molecular biology: The long and short of RNAs. Nature. 457:974-5. 2009

23.    Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M,    Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Eric Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 19:255-65.2009.

24.    Olivarius S, Plessy C, and Carninci P. High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques. 46:130-2.2009

25.    Brinkmeier ML, Davis SW, Carninci P, Macdonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA.Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches. Genomics. 93:449-60.2009.

26.    Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ, Hide W. Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A. 105:20422-7. 2008.

27.    Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Rapidly evolving human promoter regions. Nat Genet. 40:1262-3.2008.

28.    Shindo Y, Miura H, Carninci P, Kawai J, Hayashizaki Y, Ninomiya Y, Hino A, Kanda T, Kusakabe Y. G alpha14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue. Biochem Biophys Res Commun.376:504-8. 2008.

29.    Carninci P. Non-coding RNA transcription: turning on neighbours. Nat Cell Biol. 10:1023-4.2008.

30.    Plessy C, Fagiolini M, Wagatsuma A, Harasawa N, Kuji T, Asaka-Oba A, Kanzaki Y, Fujishima S, Waki K, Nakahara H, Hensch TK, Carninci P. A resource for transcriptomic analysis in the mouse brain. PLoS ONE. 3:e3012.2008

31.    Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Biotechniques. 45:95-7.2008

32.    Carninci P. Hunting hidden transcripts. Nat Methods. 5:587-9.2008.

33.    Carninci P, Yasuda J, Hayashizaki Y. Multifaceted mammalian transcriptome. Curr Opin Cell Biol. 20:274-80. 2008

34.    Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human small RNAs. BMC Genomics. 10;9:157.2008.

35.    Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91:281-8. 2008

36.    Centlow M, Carninci P, Nemeth K, Mezey E, Brownstein M, Hansson SR. Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes. Fertil Steril. Dec 29 2007.

37.    Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S. Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray. PLoS ONE 2:e1235. 2007

38.    Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome Res 18: 1-12. 2008

39.    Kawai J, Carninci P, Hayashizaki Y. Transcriptomics resources for functional genomics. Brief Funct Genomic Proteomic 6:171-9.2007

40.    Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W. Simplified ontologies allowing comparison of developmental mammalian gene expression. Genome Biol. 8:R229.2007

41.    Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS. Splicing bypasses 3' end formation signals to allow complex gene architectures. Gene. 403:188-93.2007

42.    Sandelin A, Carninci P, Lenhard B, Ponjavic J. Hayashizaki Y, Hume DA.  Mammalian RNA Polymerase II core promoters — insights from genome-wide studies. Nature Rev. Genetics 8:424-36.2007

43.    The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447:799-816.2007

44.    Baxter LL, Hsu BJ, Umayam L, Wolfsberg TG, Larson DM, Frith MC, Kawai J, Hayashizaki Y, Carninci P, Pavan WJ. Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function. Pigment Cell Res. 20:201-9.2007

45.    Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y. Large-scale clustering of CAGE tag expression data. BMC Bioinformatics. 8:161.2007

46.    Carninci P. Constructing the landscape of the mammalian transcriptome. J Exp Biol 210: 1497-1506.2007

47.    Katayama S, Kanamori-Katayama M, Yamaguchi K, Carninci P, Hayashizaki Y. CAGE-TSSchip: promoter-based expression profiling using the 5-leading label of capped transcripts. Genome Biol. 8:R42. 2007

48.    Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S. Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics. 89:580-7. 2007

49.    Todaka N, Moriya S, Saita K, Hondo T, Kiuchi I, Takasu H, Ohkuma M, Carninci P, Hayashizaki Y, Kudo T. Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus. FEMS Microbiol Ecol. 59:592-9. 2007

50.    Carninci P, Hayashizaki Y. Noncoding RNA transcription beyond annotated genes. Curr Opin Genet Dev. 17:139-144. 2007

51.    Brahmachary M, Schonbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan S, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB. Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. BMC Bioinformatics. 7, Suppl 5:S8. 2006

52.    Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y. Dynamic usage of transcription start sites within core promoters. Genome Biol. 7(12):R118. 2006

53.    Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS. Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA. RNA Biol. 3(1). 2006

54.    The Honeybee Genome Sequencing Consortium [Carninci P: Leader of “EST Sequencing”], Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443; 931-949, 2006

55.    Beisel KW, Rocha-Sanchez SM, Ziegenbein SJ, Morris KA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Davis RL. Diversity of Ca(2+)-activated K(+) channel transcripts in inner ear hair cells. Gene. 386:11-23.2007

56.    Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C, Haesler S, Zhao S, Sakaguchi H, Hagiwara M, Shiraki T, Hirozane-Kishikawa T, Skene P, Hayashizaki Y, Carninci P, Jarvis ED. A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A. 103:15212-7.2006

57.    Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A. Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.Genome Biol. 17:R78. 2006

58.    Itoh M, Yasunishi A, Imamura K, Kanamori-Katayama M, Suzuki H, Suzuki M, Carninci P, Kawai J, Hayashizaki Y. Constructing ORFeome resources with removable termination codons. Biotechniques 41: 44, 46, 48.2006.

59.    Carninci P. Tagging mammalian transcription complexity. Trends Genet. 22:501-10. 2006. Review.

60.    Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P. The complexity of the mammalian transcriptome.J. Physiol. 575:321-32.2006. Review.

61.    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. Transcriptional network dynamics in macrophage activation. Genomics. 88:133-42. 2006

62.    Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A. Evolutionary turnover of mammalian transcription start sites. Genome Res. 16:713-22.2006

63.    Maeda N, Kasukawa T, Oyama R, Gough J, Frith M,. Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Colin F. Fletcher, Alistair R. Forest R, 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, Zhu CWY,  Kai C, Kawai J,. Hume DA, Carninci P, Hayashizaki Y. Transcript annotation - Mouse gene catalog based on physical cDNAs, PLoS Genetics 2:e62.2006.

64.    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. Pseudo-Messenger RNA: Phantoms of the Transcriptome, PLoS Genetics 2:e23.2006

65.    Frith MC, Forrest AR, Nourbakhsh E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM. The Abundance of Short Proteins in the Mammalian Proteome, PLoS Genetics 2:e52.2006

66.    Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Jawai J, Hume DA, Carninci P, Hayashizaki Y, Mice and men: Their Promoter properties, PLoS Genetics 2:e54.2006

67.    Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, Bult C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Mattick JS, Suzuki H. Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs, PLoS Genetics 2:e37.2006

68.    Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H. A Method for Similarity Search of Genomic Positional Expression Using CAGE, PLoS Genetics 2:e44.2006

69.    Engström PG, Brozzi A, Luzi L, Sessa L, Lavorgna G, Tan SL, Yang L, Kunarso G, Ng ELC, Kai C, Kawai J, Carninci P, Hayashizak Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L. Complex Loci in Human and Mouse Genomes, PLoS Genetics 2:e47.2006

70.    Martin S. Taylor MS, Chikatoshi Kai C, Jun Kawai J, Carninci P, Hayashizaki Y, Semple CAM, Heterotachy in Mammalian Promoter Evolution, PLoS Genetics 2: e30. 2006

71.    Chern TM, Nimwegen EV, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M. A simple physical model predicts small exon-length variations, PLoS Genetics 2: e45. 2006

72.    Hayashizaki Y and Carninci P. Genome Network and FANTOM 3 special issue of PLoS Genetics: Assessing the complexity of the transcriptome. PLoS Genetics 2: e63. 2006. Review.

73.    Carninci P, Sandelin A, Lenhard B., Katayama S, Shimokawa S, Ponjavic J, Semple C,  Taylor M, Engstrom P, Frith MC, Forrest AR, Alkema W., 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. Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data. Nat. Genetics, 38:626-35. 2006

74.    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. Alternate transcription of the Toll-like receptor signaling cascade. Genome Biol. 7:R10. 2006

75.    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-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol. 7:R5. 2006

76.    Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P. CAGE: cap analysis of gene expression. Nat Methods. 3:211-22. 2006

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

78.    Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD. LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res. 34: D213-7. 2006

79.    Usui K, Katayama S., Kanamori-Katayama M, Ogawa C., Kai C, Okada M.,  Kawai J. Arakawa T., Carninci P., Itoh M. 3, Takio K., Miyano M.,  Kidoaki K., Matsuda T., Hayashizaki Y. and Suzuki H.  Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Genome Biology 6:R98. 2005

80.    Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Moller S, Kazunori W, Gopalakrishnakone P, Ricciardi-Castagnoli P, Thiesen HJ, Hayashizaki Y, Kollias G. Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PLoS Genet. 2005 1:e48. 2005

81.    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 MC, Ravasi T, Pang KC¬, Mattick JS, Hume DA, Lipovich L, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk A, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C. Antisense transcription in the mammalian transcriptome. Science 309:1564-6. 2005.

82.    Carninci P, Kasukawa T, Katayama S, Gough J, Frith M C, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic V B, Brenner S E, Batalov S, Forrest AR, Zavolan M, Davis M J, 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 SPT, Kruger AF, 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, Schönbach C, Sekiguchi K, Semple CAM, Seno 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 Nimwegene 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. The Transcriptional Landscape of the Mammalian Genome. Science. 309:1559-63. 2005

83.    Harbers M and Carninci P. Novel Tag-Based Approaches for Transcriptome Research and Genome Annotation. Nature Methods, 2:495-502. 2005. Review

84.    Nakabachi A, Shigenobu S, Sakazume N, Shiraki T, Hayashizaki Y, Carninci P, Ishikawa H, Kudo T, Fukatsu T. Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci U S A.102:5477-82. 2005

85.    Nakamura M, Carninci P, Tanpakushitsu Kakusan Koso. 49 (17 Suppl):2688-93 [Cap analysis gene expression: CAGE, article in Japanese. 2004. Review.

86.    Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y. Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst. 79:227-32. 2004

87.    Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team.. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 14:2121-7. 2004

88.    Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M. Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics. 21:1758-63. 2005

89.    Caldwell RB, Kierzek AM, Arakawa H, Bezzubov Y, Zaim J, Fiedler P, Kutter S, Blagodatski A, Kostovska D, Koter M, Plachy J, Carninci P, Hayashizaki Y, Buerstedde JM., Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol.;6 :R6. 2005

90.    Morris KA, Snir E, Pompeia C, Koroleva IV, Kachar B, Hayashizaki Y, Carninci P, M. Soares B, and Beisel KW , Differential Expression of Genes within the Cochlea as Defined by a Custom Mouse Inner Ear Microarray, Journal of the Association for Research in Otolaryngology. 6:75-89. 2005

91.    Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P, Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nature Method 1: 233-239 2004

92.    Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Kel E. A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y,Takagi T, Nakai K and Sugano S Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology 4: 0036. 2004

93.    Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, Sakagami N, Terada T, Shirouzu M, Yoshida M, Hirota H, Osanai T, Tanaka A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kinoshita K, Guntert P, Kigawa T, Yokoyama S. Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci. 13: 2089-100 2004

94.    Nagata T, Iizumi S, Satoh K, Ooka H, Kawai J, Carninci P, Hayashizaki Y, Otomo Y, Murakami K, Matsubara K, Kikuchi S. Comparative Analysis of Plant and Animal Calcium Signal Transduction Element Using Plant Full-Length cDNA Data. Mol Biol Evol. 21:1855-70. 2004

95.    Beisel W K, Toshiyuki Shiraki T, Morris A. K, Pompei C, Kachar B, Arakawa T, Bono H, Kawai J, Hayashizaki Y, and Carninci P. Identification of Unique Transcripts from a Mouse Full-Length, Subtracted Inner Ear cDNA Library. Genomics. 83: 1012-23. 2004

96.    Imanishi T, Itoh T, Suzuki Y, O’Donovan C, Fukuchi S, Koyanagi O. K, Barrero A.R, 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 A .M, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eric Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo M, Bono H, Bromberg K. S, Brookes A, Bruford E, Carninci P, Chelala C, Couillault C, De Souza J. S, Debily M, Devignes M, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinathrao G, Graudens E, Hahn Y, Han M, Han Z, 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 H, 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 S, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson J. A, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger D. J, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo H, 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 L. R, Isogai T, Auffray C, Nomura N, Gojobori1 T, Sugano S. Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PloS Biol. 2: 856-75. 2004

97.    Lagonigro S. M, De Cecco L, Carninci P, Di Stasi D, Ranzani T, Rodolf M, and Gariboldi M. CTAB–Urea Method Purifies RNA from Melanin for cDNA MicroarrayAnalysis, Pigment Cell Research, 17:312-5.2004

98.    Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proc Natl Acad Sci USA. 101:5069-74. 2004

99.    Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S. Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. DNA Res. 10:249-61.2003

100.    Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, Kikuchi S. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 10:239-47.2003

101.    Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S. Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics. 17:87-100.2004

102.    Maeda T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, Seki E, Matsuda T, Motoda Y, Kobayashi A, Hiroyasu F, Shirouzu M, Terada T, Hayami N, Ishizuka Y, Shinya N, Tatsuguchi A, Yoshida M, Hirota H, Matsuo Y, Tani K, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kigawa T, Yokoyama S. Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16). J Biol Chem. 279:13174-82.2004

103.    Kasai T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, Seki E, Matsuda T, Matsuda N, Tomo Y, Shirouzu M, Terada T, Obayashi N, Hamana H, Shinya N, Tatsuguchi A, Yasuda S, Yoshida M, Hirota H, Matsuo Y, Tani K, Suzuki H, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kigawa T, Yokoyama S. Solution structure of a BolA-like protein from Mus musculus. Protein Sci. 13: 545-8.2004

104.    Kodzius R. Matsumura Y, Kasukawa K, Shimokawa K, Fukuda S, Shiraki S. Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute Expression Values for Mouse Transcripts: Re-Annotation of the READ Expression Database by the Use of CAGE and EST Sequence Tags. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.FEBS Lett. 559: 22-6.2004

105.    Nagashima T, Matsuda H, Silva DG, Petrovsky N, Konagaya A, Schonbach C, Kasukawa T, Arakawa T, Carninci P, Kawai J, Hayashizaki Y. FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Res. 32: 471-5.2004

106.    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., Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage, Proc.Natl.Acad. Sci. USA, 100:15776-81.2003

107.    Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y., Antisense transcripts with rice full-length cDNAs, Genome Biology, 5:R5, 2003

108.    Fujimori S, Washio T, Higo K, Ohmoto Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M., A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription”, FEBS Lett, 554:17-22, 2003

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

110.    Yamada K, Lim J, Dale J.M, Chen H, Shinn P, Palm C.J, Southwick A.M, Wu H.C,  Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newsmann G, Liu S.X, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach H.L, Tripp M, Chang C.H, Lee J.M, Toriumi M, Chan M.M, Tang C.C, Onodera C.S, Deng J.M, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith A.D, Gurjal M, Hansen N.F, Hayashizaki Y, Johnson-Hopson C, Hsuan V.W, Iida K, Karners M, Khan S, Koesema E, Ishida J, Jiang P.X, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender E.K, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis R.W, Theologis A, Ecker J.R., Empirical analysis of transcriptional activity in the Arabidopsis genome, Science, 302:842-6, 2003

111.    Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A. 100:8007-12, 2003

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

113.    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 W.A, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume D.A, Fagiolini M, Hensch T.K, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y., Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia, Genome Research, 13:1273-89, 2003

114.     Zavolan M, Kondo S, Schonbach C, Adachi J, Hume D.A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Gaasterland T., Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome, Genome Research, 13:1290-300, 2003

115.    Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming L.G, Hume D.A., Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Tomita M., Identification of putative non-coding RNAs amongst the RIKEN mouse full-length cDNA collection, Genome Research, 13:1301-6, 2003

116.    Brusic V, Pillai R.S, Silva D.G, Petrovsky N, Carninci P, Kawai J, Hayashizaki Y, Schonbach C., “Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set, Genome Research, 13:1307-17.2003

117.    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 D.A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Okazaki Y., Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays, Genome Research, 13:1318-23,2003

118.    Kiyosawa H, Yamanaka I, Osato N, Kondo S, Arakawa T, Carninci P, Kawai J,  Hayashizaki Y., Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation, Genome Research, 13:1324-34,2003

119.    Kanapin A, Batalov S, Davis M.J, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale R.D, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Yuan Z., Mouse proteome analysis, Genome Research, 13:1335-44, 2003

120.    Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Okazaki Y., Comprehensive Analysis of the Mouse Metabolome based upon the Transcriptome, Genome Research, 13:1345-59, 2003

121.    Grimmond S.M, Miranda K.C, Yuan Z, Davis M.J, Hume D.A, Arakawa T, Carninci P, Kawai J, Yagi K, Tominaga N, Bono H, Hayashizaki Y, Okazaki Y, Teasdale R.D., The mouse secretome: functional classification of the proteins secreted into the extracellular environment, Genome Research, 13:1350-9, 2003

122.    Wells C, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume D.A, Arakawa T, Kawai J, Hayashizaki Y, Lyons P.A, Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage, Genome Research, 13:1360-5, 2003

123.    Forrest AR, Taylor D, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Grimmond S., Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set, Genome Research, 13:1366-75, 2003

124.    Reed J.C, Doctor K, Rojas A, Zapata J.M, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Arakawa T., Carninci P, Kawai J, Hayashizaki Y, Godzik A., Comparative analysis of apoptosis and inflammation genes of mice and humans, Genome Research, 13:1376-88, 2003

125.    Semple C.A.M, Arakawa T, Carninci P, Kawai J, Hayashizaki Y., The comparative proteomics of ubiquitination in mouse, Genome Research, 13:1389-94, 2003

126.    Gustincich S, Batalov S, Beisel K.W, Bono H, Carninci P, Fletcher C.F, Grimmond S, Hirokawa N, Jarvis E.D, Jegla T, Kawasawa Y, LeMieux J, Miki H, Raviola E, Teasdale R.D, Tominaga N, Yagi K, Zimmer A, Hayashizaki Y, Okazaki Y., Analysis of the mouse transcriptome for genes involved in the function of the nervous system, Genome Research, 13:1395-401, 2003

127.    Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris G.A, Lyons PA, Oshimura M, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Okazaki Y., Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling, Genome Research13:1402-9, 2003

128.    Holmes R, Williamson C, Peters J, Denny P, Arakawa T, Carninci P, Kawai J, Wells C.A., Comprehensive transcript map of the mouse Gnas imprinted complex, Genome Research, 13:1410-5, 2003

129.    Ravasi T, Huber T, Zavolan M, Forrest A, Gaasterland T, Grimmond S, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Hume D.A., Systematic characterization of the zinc finger containing proteins in the mouse transcriptome, Genome Research, 13:1430-42, 2003

130.    Forrest A.R, Ravasi T, Taylor D, Huber T, Hume D.A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Grimmond S., Phosphoregulators: protein kinases and protein phosphatases of mouse, Genome Research, 13:1443-54. 2003

131.    Miki H, Setou M, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Hirokawa N., Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome, Genome Research, 13:1455-65. 2003

132.    Kawasawa Y, McKenzie L.M, Hill D.P, Bono H, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Yanagisawa M., G Protein-Coupled Receptor Genes in the FANTOM2 Database, Genome Research, 13:1466-77. 2003

133.    Schriml L.M, Hill D.P, Blake J.A, Kawai J, Wynshaw-Boris A, Pavan W.J, Ring B.Z, Beisel K, Setou M, Arakawa T, Carninci P, Kawai J, Okazaki Y, Hayashizaki Y., Human Disease Genes and their cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Dataset, Genome Research, 13:1496-500. 2003

134.    Tajul-Arifin K, Teasdale R, Ravasi T, Hume D.A., Arakawa T, Carninci P, Kawai J,Hayashizaki Y,  Mattick J.S., Identification and Analysis of Chromodomain-containing proteins encoded in the mouse transcriptome, Genome Research, 13:1416-29.2003

135.    Walsh N.C, Cahill M, Carninci P, Kawai J, Okazaki Y, Hayashizaki Y, Hume D.A, Cassady A.I., Multiple tissue-specific promoters control expression of the tartrate-resistant acid phosphatase gene, GENE, 307:111-23. 2003

136.    Seki M, Nakamura M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enji A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y., Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray, The Plant Journal, 31:279-292. 2002

137.    Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M., Comprehensive sequence analysis of translation termination sites in various eukaryotes, GENE, 300:79-87. 2002

138.    Sakurai A, Fujimori S, Kochiwa H, Kitamura-Abe S, Washio T, Saito R, The RIKEN Genome Exploration Research Group Phase II Team, Carninci P, Hayashizaki Y, Tomita M., On biased distribution of introns in various eukaryotes, GENE, 300:89-95.2002

139.    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 D.P, Bult C, Hume D.A, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel K.W, Blake J.A, Bradt D, Brusic V, Chothia C, Corbani L.E, Cousins S, Dalla E, Dragani T.A, Fletcher C.F, Forrest A, Frazer K.S, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson I.J, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski R.M, King B.L, Konagaya A, Kurochkin I.V, Lee Y, Lenhard B, Lyons PA, Maglott D.R, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan W.J, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius J.U, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed D.J, Reid J, Ring B.Z, Ringwald M, Sandelin A, Schneider C, Semple C.A, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor M.S, Teasdale R.D, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming L.G, 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 E.S, Rogers J, Birney E, Hayashizaki Y, FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team., Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNA, Nature, 420:563-573. 2002. Role: team coordinator.

140.    Waterston R.H, Lindblad-Toh K, Birney E, Rogers J, Abril J.F, 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 M.R, Brown D.G, Brown S.D, Bult C, Burton J, Butler J, Campbell R.D, Carninci P, Cawley S, Chiaromonte F, Chinwalla A.T, Church D.M, Clamp M, Clee C, Collins F.S, Cook L.L, Copley R.R, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty K.D, Deri J, Dermitzakis E.T, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy S.R, Elnitski L, Emes R.D, Eswara P, Eyras E, Felsenfeld A, Fewell G.A, Flicek P, Foley K, Frankel W.N, Fulton L.A, Fulton R.S, Furey T.S, Gage D, Gibbs R.A, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves T.A, Green E.D, Gregory S, Guigo R, Guyer M, Hardison R.C, Haussler D, Hayashizaki Y, Hillier L.W, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe D.B, Johnson L.S, Jones M, Jones T.A, Joy A, Kamal M, Karlsson E.K, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent W.J, Kirby A, Kolbe D.L, Korf I, Kucherlapati R.S, Kulbokas E.J, Kulp D, Landers T, Leger J.P, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott D.R, Mardis E.R, Matthews L, Mauceli E, Mayer J.H, McCarthy M, McCombie W.R, McLaren S, McLay K, McPherson J.D, Meldrim J, Meredith B, Mesirov J.P, Miller W, Miner T.L, Mongin E, Montgomery K.T, Morgan M, Mott R, Mullikin J.C, Muzny D.M, Nash W.E, Nelson J.O, Nhan M.N, Nicol R, Ning Z, Nusbaum C, O'Connor M.J, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin K.H, Peterson J, Pevzner P, Plumb R, Pohl C.S, Poliakov A, Ponce T.C, Ponting C.P, Potter S, Quail M, Reymond A, Roe B.A, Roskin K.M, Rubin E.M, Rust A.G, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz M.S, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith D.R, 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 J.P, Von Niederhausern A.C, Wade C.M, Wall M, Weber R.J, Weiss R.B, Wendl M.C, West A.P, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson R.K, Winter E, Worley K.C, Wyman D, Yang S, Yang S.P, Zdobnov E.M, Zody M.C, Lander E.S; Mouse Genome Sequencing Consortium ., Initial sequencing and comparative analysis of the mouse genome, Nature, 420:520-561. 2002

141.    Jarvis E, Smith V.A, Wada K, Rivas M.V, McElroy M, Smulders T.V, Carninci P, Hayashizaki Y, Dietrich F, Wu X, McConnell P, Yu J, Wang P.P, Hartemink A.J, Lin S., A framework for integrating the songbird brain, J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 188:961-80. 2002

142.    Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K., Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray, Funct Integr Genomics, 2:282-91. 2002

143.    Strausberg R.L, Feingold E.A, Grouse L.H, Derge J.G, Klausner R.D, Collins F.S, Wagner L, Shenmen C.M, Schuler G.D, Altschul S.F, Zeeberg B, Buetow K.H, Schaefer C.F, Bhat N.K, Hopkins R.F, Jordan H, Moore T, Max S.I, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer A.A, Rubin G.M, Hong L, Stapleton M, Soares M.B, Bonaldo M.F, Casavant T.L, Scheetz T.E, Brownstein M.J, Usdin T.B, Toshiyuki S, Carninci P, Prange C, Raha S.S, Loquellano N.A, Peters G.J, Abramson R.D, Mullahy S.J, Bosak S.A, McEwan P.J, McKernan K.J, Malek J.A, Gunaratne P.H, Richards S, Worley K.C, Hale S, Garcia A.M, Gay L.J, Hulyk S.W, Villalon D.K, Muzny D.M, Sodergren E.J, Lu X, Gibbs R.A, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young A.C, Shevchenko Y, Bouffard G.G, Blakesley RW, Touchman J.W, Green E.D, Dickson M.C, Rodriguez A.C, Grimwood J, Schmutz J, Myers R.M, Butterfield Y.S, Krzywinski M.I, Skalska U, Smailus D.E, Schnerch A, Schein J.E, Jones S.J, Marra M.A., Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences, Proc Natl Acad Sci, USA, 99:16899-903. 2002

144.    Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K., Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray, Funct Integr Genomics, 2:301.2002

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

146.    Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y., A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs, Genome Research, 12:1127-34. 2002

147.    Carninci P, Shiraki T, Mizuno Y, Muramatsu M, Hayashizaki Y., Extra-long first-strand cDNA synthesis, Biotechniques, 32:984-5. 2002

148.    Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K., Functional annotation of a full-length Arabidopsis cDNA collection, Science. 296:141-5. 2002

149.    Buerstedde J.M, Arakawa H, Watahiki A, Carninci P, Hayashizaki Y, Korn B, Plachy J, The DT40 web site: sampling and connecting the genes of B cell line, Nucleic Acids Research, 30:230-231. 2002

150.    Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin G.M., The Drosophila Gene Collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes, Genome Research, 12:1294-300. 2002

151.    Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein M.J., Cytoplasmic RNA extraction from fresh and frozen mammalian tissues, Biotechniques, 33:306-9. 2002

152.    Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M., Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes, GENE, 276:101-105. 2001

153.    Kawagashira N, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Higo K., Multiple Zinc Finger Motifs with Comparison of Plant and Insect, Genome Informatics Series, 12:368-369. 2001

154.    Seki M, Narusaka M, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K, Arabidopsis encyclopedia using full-length cDNAs and its application, Plant Physiol. Biochem 39:211-220. 2001

155.    Sakaki H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninc P, Konno H, Kawai J, Hayashizak Y, Tomita M., Correlation between sequence conservation of the 50 untranslated region and codon usage bias in Mus musculus genes, Gene, 276:101-105. 2001

156.    Shibata Y, Carninci P, Sato K, Hayatsu N, Shiraki T, Ishi Y, Arakawa T, Hara A, Osato N, Izawa M, Aizawa K, Itoh M, Shibat K, Shinagaw A, Kawai J, Ota Y, Kikuch S, Kishimoto N, Muramatsu M, Hayashizaki Y., Removal of PolyA Tails from Full-Length cDNA Libraries for High-Efficacy Sequencing, BioTechniques, 31:1042-1049. 2001

157.    Yamanaka I, Kiyosawa H, Kondo S, Saito T, Carninci P, Shinagawa A, Aizawa K, Fukuda S, Hara A, Itoh M, Kawai J, Shibata K, Arakawa T, Ishii Y, Hayashizaki Y., “Mapping of 19032 mouse cDNAs on mouse chromosomes”, J. Struct. Genomics, 12:L72-L86. 2001

158.    Carninci P, Shibata Y, Hayatsu N, Itoh M, Shiraki T, Hirozane T, Watahik A, Shibata K, Konno H, Muramatsu M, Hayashizaki Y., Balanced-size and long-size cloning of full-length, Cap-trapped cDNAs into vectors of the novel lambda–FLC family allows enhanced gene discovery rate and functional analysis, Genomics, 77:79-90. 2001

159.    ShibataY, Carninci P, Akira W, Shiraki T, Konno H, Muramatsu M, Hayashizaki Y., Cloning full-length, cap-trapper-selected cDNAs by using SSLLM, Biotechniques, 30:1250-1254. 2001

160.    Hagiwara N, Carninci P, Kozak C.A, Brilliant M.H., 14th International Mouse Genome Conference, Mammalian Genome, 12: 401-401. 2001

161.    Miki R, Kadota, K, Mizuno Y, Yasuhiro T, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Bono H, Tominaga N, Sato K, Tokusimi Y, Kikuchi N Akahira S, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Susumu S, YodaY, Yoshiki Y, Kusakabe M, DeRisi J.L, Iyer, V. R, Eisen M. B, Brown P.O, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y., Gene expression profiling using the 19K set of RIKEN full-length mouse cDNA microarray, Proc Natl Acad Sci USA, 98:2199-2204. 2001

162.    The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. 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 HA, 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 L.M, 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 M.F, Brownstein M.J, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume D.A, Kamiya M, Lee N.H, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang K.H, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y., Functional annotation of a full-length mouse cDNA collection, Nature, 409:685-690. 2001. Role: Senior Manager of annotation.

163.    Sugahara Y, Carninci P, Itoh M, Shibata K, Konno H, Endo T, Muramatsu M,  Hayashizaki Y., Comparative evaluation of 5’-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries, Gene, 263:93-103. 2001

164.    Konno H, Fukunishi Y, Shibata K, Itoh M, Carninci P, Sugahara Y, and Hayashizaki Y., Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library, Genome Res., 11: 281-289. 2001

165.    Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi K, Carninci P, Hayashizaki Y, and Shinozaki K., Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray, Plant Cell, 13:61-72. 2001

166.    Carninci P, Shibata Y, Hayatsu  N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y., Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes, Genome Res, 10:1617-30. 2000

167.    Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, Carninci P, Konno H, Akiyama J, Nishi K, Kitsunai T, Tashiro H,  Itoh M, Sumi N, Ishii Y, Nakamura S, Hazama M, Nishine T, Harada A, Yamamoto R, Matsumoto H, Sakaguchi S, Ikegami T, Kashiwagi K, Fujiwake S, Inoue K, Togawa Y, Izawa M, Ohara E, Watahiki A, Yoneda M,  Ishikawa Y, Ozawa T, Tanaka K, Matsuura T, Kawai J, Okazaki Y, Muramatsu M, Inoue Y, Kira A, Hayashizaki Y., RIKEN Integrated Sequence Analysis (RISA) System-384-Format Sequencing Pipeline with 384 Multicapillary Sequencer, Genome Res., 10:1757-1771.2000

168.    Carninci P, Hayashizaki Y., High-efficiency full-length cDNA cloning, Methods Enzymol, 303:19-44.1999

169.    Itoh M, Kitsunai T, Akiyama J, Shibata K, Izawa M, Kawai J, Tomaru Y, Carninci P, Shibata Y, Ozawa Y, Muramatsu M, Okazaki Y, Hayashizaki Y., Automated filtration-based high-throughput plasmid preparation system, Genome Res, 9:463-70.1999

170.    Mizuno Y, Carninci P, Okazaki Y, Tateno M, Kawai J, Amanuma H, Muramatsu M, Hayashizaki Y, Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display, Nucleic Acids Res, 27:1345-9.1999

171.    Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, and Shinozaki K, High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper, Plant J, 15:707-20.1998

172.    Sasaki N, Nagaoka S, Itoh M, Izawa M, Konno H, Carninci P, Yoshiki A, Kusakabe M, Moriuchi T, Muramatsu M, Okazaki Y, and Hayashizaki Y, Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones, Genomics, 49:167-79.1998

173.    Sasaki N, Izawa M, Watahiki M, Ozawa K, Tanaka T, Yoneda Y, Matsuura S, Carninci P, Muramatsu M, Okazaki Y, and Hayashizaki Y, Transcriptional sequencing: A method for DNA sequencing using RNA polymerase, Proc Natl Acad Sci USA, 95:3455-60.1998

174.    Carninci P, Nishiyama Y, Westover A, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Hayashizaki Y., Thermostabilization and thermoactivation of thermolabile enzymes by trehalose, Proc Natl Acad Sci USA, 95:520-4.1998

175.    Sasaki, N, Izawa M, Shimojo M, Shibata M, Akiyama J, Itoh M, Nagaoka S, Carninci P, Okazaki Y, Moriuchi T, Muramatsu M, Watanabe S and Hayashizaki Y, A novel control system for polymerase chain reaction using a RIKEN GS384 thermal cycler, DNA Res, 4:387-91.1997

176.    Nishiyama Y, Carninci P, Yoneya S and Hayashizaki Y, New approach for an analysis of full-length cDNA library, Article in Japanese, Tanpakushitsu Kakusan Koso, 42:2858-63.1997

177.    Itoh M, Carninci P, Nagaoka S, Sasaki N, Okazaki Y, Ohsumi T, Muramatsu M and Hayashizaki Y. Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates, Nucleic Acids Res 25: 1315-6.1997

178.    Carninci P, Westover A, Nishiyama Y, Ohsumi T, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Schneider C, Hayashizaki Y. High efficiency selection of full-length cDNA by improved biotinylated cap trapper, DNA Research 4:61-6.1997

179.    Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C. High efficiency full length cDNA cloning by biotinylated cap trapper. Genomics 37:327-336.1996

180.    Carninci P, Volpatti F, and Schneider C. A discontinuous buffer system increasing resolution and reproducibility in DNA sequencing on high voltage ultrathin-layer gel electrophoresis. Electrophoresis 16:1836-1845.1995

181.    Gustincich S, Carninci P, Schneider S. A rapid method to extract high quality genomic DNA from Yeast. Techniques 3:76-77.1992

182.    Gustincich S, Carninci P, Manfioletti G, Del Sal G, Schneider C. A fast method for high quality genomic DNA extraction from whole human blood. Biotechniques 11:298-302.1991

183.    Carninci P. Un metodo nuovo per purificare in maniera rapida e semplice DNA genomico umano, utilizzabile in diagnostica molecolare, a partire da sangue umano in toto (Italian). Biochimica Clinica 14: 1467-1471.1990

184.    Carninci P, Gustincich S, Bottega S, Patrosso C, DelSal G, Manfioletti G, Schneider C. A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence. Nucl. Acids Res. 18:204.1990


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Nature 2012-09-06 Djebali S, Davis C, Lagarde J, Dobin A, Merkel A, Zaleski C, Lassmann T, Lin W, Schlesinger F, Xue C, Tanzer A, Mortizavi A, Khatun J, Kokocinsk F, Abdelhamid R, Alioto T, Baer M, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood M, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Johnson R, Kapranov P, Kingswood C, Luo O, Marinov G, Park E, Preall J, Ribeca P, Risk B, Robyr D, Roeder M, Sammeth M, See L, Shahab A, Skancke J, Suzuki A, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Williams B, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Hubbard T, Reymond A, Antonarakis S, Hannon G, Giddings M, Ruan Y, Wold B, Carninci P, Guigo Serra R, Gingeras T
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression.
Genome Res 2012 Sep;22(9):1775-89 Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Genome Res 2012 Sep;22(9):1658-67 Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Genome Res 2012 Aug 30; Batut PJ, Dobin A, Plessy C, Carninci P, Gingeras TR
Site-specific DICER and DROSHA RNA products control the DNA-damage response.
Nature 2012 May 23; Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, di Fagagna FD
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.
Biotechniques 2012 Jun;52(6):381-5 Saxena A, Wagatsuma A, Noro Y, Kuji T, Asaka-Oba A, Watahiki A, Gurnot C, Fagiolini M, Hensch TK, Carninci P
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
PNAS 2012-04-17 Schroder K, Irvine K, Taylor M, Bokil N, Cao K, Masterman K, Labzin L, Semple C, Kapetanovic R, Fairbairn L, Akalin A, Faulkner G, Baillie K, Gongora M, Carsten D, Kawaji H, McLachlan G, Goldman N, Grimmond S, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume D, Sweet M
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Nature Reviews Genetics 2012-04-01 Lenhard B, Sandelin A, Carninci P
5' end-centered expression profiling using Cap-analysis gene expression and next-generation sequencing
Nature Protocols 2012-02-23 Takahashi H, Lassmann T, Murata M, Carninci P
Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
PLoS One 2012;7(1):e30809 Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y
DeepCAGE: Genome-Wide Mapping of Transcription
Tag-based Next Generation Sequencing() 2012-01-23 Harbers M, Dushay M, Carninci P
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks.
Methods Mol Biol 2012;786:181-200 Takahashi H, Kato S, Murata M, Carninci P
Promoter architecture of mouse olfactory receptor genes.
Genome Res 2011 Dec 22; Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Succhelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila.
Nature 2011 Nov 6; Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Sardo FL, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V
Long non-coding RNA modifies chromatin: Epigenetic silencing by long non-coding RNAs.
Bioessays 2011 Sep 14; Saxena A, Carninci P
Somatic retrotransposition alters the genetic landscape of the human brain.
Nature 2011 Oct 30; Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan P, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ
The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi.
PLoS Negl Trop Dis 2011 Aug;5(8):e1283 Franzén O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki Y, Aslund L, Andersson B, Daub CO
Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells.
PLoS One 2011;6(8):e23385 Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P, Hayashizaki Y
Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.
Nature 2011 Jul 3;476(7359):224-7 Caiazzo M, Dell'Anno MT, Dvoretskova E, Lazarevic D, Taverna S, Leo D, Sotnikova TD, Menegon A, Roncaglia P, Colciago G, Russo G, Carninci P, Pezzoli G, Gainetdinov RR, Gustincich S, Dityatev A, Broccoli V
The reality of pervasive transcription.
PLoS Biol 2011 Jul;9(7):e1000625; discussion e1001102 Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS
FXYD6, a Na,K-ATPase regulator, is expressed in type II taste cells.
Biosci Biotechnol Biochem 2011;75(6):1061-6 Shindo Y, Morishita K, Kotake E, Miura H, Carninci P, Kawai J, Hayashizaki Y, Hino A, Kanda T, Kusakabe Y
Unamplified cap analysis of gene expression on a single-molecule sequencer.
Genome Res 2011 May 19; Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y
A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
PLoS Biol 2011 Apr;9(4):e1001046
NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes.
Cold Spring Harb Protoc 2011 Jan 1;2011:pdb.prot5559 Salimullah M, Mizuho S, Plessy C, Carninci P
Whole transcriptome analysis: what are we still missing?
Wiley Interdiscip Rev Syst Biol Med 2010 Dec 31; Saxena A, Carninci P
Genome-wide analysis of promoter architecture in Drosophila melanogaster.
Genome Res 2010 Dec 22; Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.
Nucleic Acids Res 2010 Dec 1;38(22):8141-8 Vitezic M, Lassmann T, Forrest AR, Suzuki M, Tomaru Y, Kawai J, Carninci P, Suzuki H, Hayashizaki Y, Daub CO
Efficient small RNA library preparation protocol
BioTechniques 2010-11-30 Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y
High sensitivity TSS prediction: estimates of locations where TSS cannot occur.
PLoS One 2010 Nov 15;5(11):e13934 Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Nucleic Acids Res 2011 Jan;39(Database issue):D856-60 Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO
Reduction of non-insert sequence reads by “dimer eliminator” LNA oligonucleotide for small RNA deep sequencing
BioTechniques 2010-10-21 Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y
Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes.
Mol Cell Endocrinol 2010 Jul 8;323(1):4-19 Davis SW, Castinetti F, Carvalho LR, Ellsworth BS, Potok MA, Lyons RH, Brinkmeier ML, Raetzman LT, Carninci P, Mortensen AH, Hayashizaki Y, Arnhold IJ, Mendonça BB, Brue T, Camper SA
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Nat Methods 2010 Jul;7(7):528-34 Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome Res 2010 Jun;20(6):791-803 Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.
BMC Genomics 2010 Apr 21;11:257 Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, Suzuki H, Carninci P, Arakawa T, Tomita M, Hayashizaki Y, Daub CO
RNA dust: where are the genes?
DNA Res 2010 Apr;17(2):51-9 Carninci P
An atlas of combinatorial transcriptional regulation in mouse and man.
Cell 2010 Mar 5;140(5):744-52 Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
Genome Res 2010 Feb;20(2):257-64 de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y
Tunable fractionation of nucleic acids.
Biotechniques 2009 Dec;47(6):1041-3 Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P
Altruistic functions for selfish DNA.
Cell Cycle 2009 Sep 15;8(18):2895-900 Faulkner GJ, Carninci P
Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells.
Proc Natl Acad Sci U S A 2009 Sep 8;106(36):15454-9 Biagioli M, Pinto M, Cesselli D, Zaninello M, Lazarevic D, Roncaglia P, Simone R, Vlachouli C, Plessy C, Bertin N, Beltrami A, Kobayashi K, Gallo V, Santoro C, Ferrer I, Rivella S, Beltrami CA, Carninci P, Raviola E, Gustincich S
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
Genome Biol 2009;10(7):R79 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E
Small RNAs derived from snoRNAs.
RNA 2009 Jul;15(7):1233-40 Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS
Genetics, gene expression and bioinformatics of the pituitary gland.
Horm Res 2009 Apr;71 Suppl 2:101-15 Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA
Tiny RNAs associated with transcription start sites in animals.
Nat Genet 2009 May;41(5):572-8 Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS
The regulated retrotransposon transcriptome of mammalian cells.
Nat Genet 2009 May;41(5):563-71 Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nat Genet 2009 May;41(5):553-62 Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Genome Biol 2009;10(4):R40 Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Genome Biol 2009;10(4):R39 Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR
Whole genome transcriptome analysis.
RNA Biol 2009 Apr-Jun;6(2):107-12 Forrest AR, Carninci P
Molecular biology: The long and short of RNAs.
Nature 2009 Feb 19;457(7232):974-5 Carninci P
Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches.
Genomics 2009 May;93(5):449-60 Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA
High-throughput verification of transcriptional starting sites by Deep-RACE.
Biotechniques 2009 Feb;46(2):130-2 Olivarius S, Plessy C, Carninci P
Genome-wide analysis of cancer/testis gene expression.
Proc Natl Acad Sci U S A 2008 Dec 23;105(51):20422-7 Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ, Hide W
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
Genome Res 2009 Feb;19(2):255-65 Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P
Rapidly evolving human promoter regions.
Nat Genet 2008 Nov;40(11):1262-3; author reply 1263-4 Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA
A new recombinant bacille Calmette-Guérin vaccine safely induces significantly enhanced tuberculosis-specific immunity in human volunteers.
J Infect Dis 2008 Nov 15;198(10):1491-501 Hoft DF, Blazevic A, Abate G, Hanekom WA, Kaplan G, Soler JH, Weichold F, Geiter L, Sadoff JC, Horwitz MA
Non-coding RNA transcription: turning on neighbours.
Nat Cell Biol 2008 Sep;10(9):1023-4 Carninci P
A resource for transcriptomic analysis in the mouse brain.
PLoS One 2008 Aug 20;3(8):e3012 Plessy C, Fagiolini M, Wagatsuma A, Harasawa N, Kuji T, Asaka-Oba A, Kanzaki Y, Fujishima S, Waki K, Nakahara H, Hensch TK, Carninci P
Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.
Biotechniques 2008 Jul;45(1):95-7 Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H
Hunting hidden transcripts.
Nat Methods 2008 Jul;5(7):587-9 Carninci P
Multifaceted mammalian transcriptome.
Curr Opin Cell Biol 2008 Jun;20(3):274-80 Carninci P, Yasuda J, Hayashizaki Y
Hidden layers of human small RNAs.
BMC Genomics 2008 Apr 10;9:157 Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.
Genomics 2008 Mar;91(3):281-8 Faulkner GJ, Forrest AR, Chalk AM, Schroder K, Hayashizaki Y, Carninci P, Hume DA, Grimmond SM
A rescue strategy for multi-mapping short sequence tags refines surveys of transcriptional activity by CAGE
Genomics 2008-02-14 Faulkner G, Forrest A, Chalk A, Schroder K, Hayashizaki Y, Carninci P, Hume D, Grimmond S
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.
PLoS One 2007 Nov 28;2(11):e1235 Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S
A code for transcription initiation in mammalian genomes.
Genome Res 2008 Jan;18(1):1-12 Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A
Transcriptomics resources for functional genomics.
Brief Funct Genomic Proteomic 2007 Sep;6(3):171-9 Kawai J, Carninci P, Hayashizaki Y
Splicing bypasses 3' end formation signals to allow complex gene architectures.
Gene 2007 Nov 15;403(1-2):188-93 Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS
Simplified ontologies allowing comparison of developmental mammalian gene expression.
Genome Biol 2007;8(10):R229 Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W
Genome-wide analysis of mammalian promoter architecture and evolution.
Nat Genet 2006 Jun;38(6):626-35 Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström 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
Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function.
Pigment Cell Res 2007 Jun;20(3):201-9 Baxter LL, Hsu BJ, Umayam L, Wolfsberg TG, Larson DM, Frith MC, Kawai J, Hayashizaki Y, Carninci P, Pavan WJ
Large-scale clustering of CAGE tag expression data.
BMC Bioinformatics 2007 May 21;8:161 Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y
Mammalian RNA polymerase II core promoters: insights from genome-wide studies.
Nat Rev Genet 2007 Jun;8(6):424-36 Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA
Noncoding RNA transcription beyond annotated genes.
Curr Opin Genet Dev 2007 Apr;17(2):139-44 Carninci P, Hayashizaki Y
CAGE-TSSchip: promoter-based expression profiling using the 5-leading label of capped transcripts
Genome Biol 2007-03-26 Katayama S, Kanamori-Katayama M, Yamaguchi K, Carninci P, Hayashizaki Y
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.
Genomics 2007 May;89(5):580-7 Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S
Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus.
FEMS Microbiol Ecol 2007 Mar;59(3):592-9 Todaka N, Moriya S, Saita K, Hondo T, Kiuchi I, Takasu H, Ohkuma M, Piero C, Hayashizaki Y, Kudo T
Dynamic usage of transcription start sites within core promoters.
Genome Biol 2006;7(12):R118 Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.
Proc Natl Acad Sci U S A 2006 Oct 10;103(41):15212-7 Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C, Haesler S, Zhao S, Sakaguchi H, Hagiwara M, Shiraki T, Hirozane-Kishikawa T, Skene P, Hayashizaki Y, Carninci P, Jarvis ED
Tagging mammalian transcription complexity.
Trends Genet 2006 Sep;22(9):501-10 Carninci P
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.
Genome Biol 2006;7(8):R78 Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A
Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells.
Gene 2007 Jan 15;386(1-2):11-23 Beisel KW, Rocha-Sanchez SM, Ziegenbein SJ, Morris KA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Davis RL
Constructing ORFeome resources with removable termination codons.
Biotechniques 2006 Jul;41(1):44, 46, 48 passim Itoh M, Yasunishi A, Imamura K, Kanamori-Katayama M, Suzuki H, Suzuki M, Carninci P, Kawai J, Hayashizaki Y
The complexity of the mammalian transcriptome.
J Physiol 2006 Sep 1;575(Pt 2):321-32 Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P
Transcriptional network dynamics in macrophage activation.
Genomics 2006 Aug;88(2):133-42 Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Björkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T
Evolutionary turnover of mammalian transcription start sites.
Genome Res 2006 Jun;16(6):713-22 Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A
Subcellular localization of mammalian type II membrane proteins.
Traffic 2006 May;7(5):613-25 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
Genome Network and FANTOM3: assessing the complexity of the transcriptome.
PLoS Genet 2006 Apr;2(4):e63 Hayashizaki Y, Carninci P
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
PLoS Genet 2006 Apr;2(4):e62 Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström 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
Mice and men: their promoter properties.
PLoS Genet 2006 Apr;2(4):e54 Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y
The abundance of short proteins in the mammalian proteome.
PLoS Genet 2006 Apr;2(4):e52 Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM
Complex Loci in human and mouse genomes.
PLoS Genet 2006 Apr;2(4):e47 Engström 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
Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units.
PLoS Genet 2006 Apr;2(4):e46 Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, Kasukawa T, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD
A simple physical model predicts small exon length variations.
PLoS Genet 2006 Apr;2(4):e45 Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M
A method for similarity search of genomic positional expression using CAGE.
PLoS Genet 2006 Apr;2(4):e44 Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H
Clusters of internally primed transcripts reveal novel long noncoding RNAs.
PLoS Genet 2006 Apr;2(4):e37 Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, Bult C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Mattick JS, Suzuki H
Heterotachy in mammalian promoter evolution.
PLoS Genet 2006 Apr;2(4):e30 Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA
Pseudo-messenger RNA: phantoms of the transcriptome.
PLoS Genet 2006 Apr;2(4):e23 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
Genome-wide analysis of mammalian promoter architecture and evolution.
Nat Genet 2006 Jun;38(6):626-35 Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström 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
CAGE: cap analysis of gene expression.
Nat Methods 2006 Mar;3(3):211-22 Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P
Alternate transcription of the Toll-like receptor signaling cascade.
Genome Biol 2006;7(2):R10 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-wide review of transcriptional complexity in mouse protein kinases and phosphatases.
Genome Biol 2006;7(1):R5 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
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA Biol 2006 Jan-Mar;3(1):40-8 Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
Nucleic Acids Res 2006 Jan 1;34(Database issue):D632-6 Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y
LOCATE: a mouse protein subcellular localization database.
Nucleic Acids Res 2006 Jan 1;34(Database issue):D213-7 Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Genome Biol 2005;6(12):R98 Usui K, Katayama S, Kanamori-Katayama M, Ogawa C, Kai C, Okada M, Kawai J, Arakawa T, Carninci P, Itoh M, Takio K, Miyano M, Kidoaki S, Matsuda T, Hayashizaki Y, Suzuki H
Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.
PLoS Genet 2005 Oct;1(4):e48 Aidinis V, Carninci P, Armaka M, Witke W, Harokopos V, Pavelka N, Koczan D, Argyropoulos C, Thwin MM, Möller S, Waki K, Gopalakrishnakone P, Ricciardi-Castagnoli P, Thiesen HJ, Hayashizaki Y, Kollias G
Tag-based approaches for transcriptome research and genome annotation.
Nat Methods 2005 Jul;2(7):495-502 Harbers M, Carninci P
Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera.
Proc Natl Acad Sci U S A 2005 Apr 12;102(15):5477-82 Nakabachi A, Shigenobu S, Sakazume N, Shiraki T, Hayashizaki Y, Carninci P, Ishikawa H, Kudo T, Fukatsu T
Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray.
J Assoc Res Otolaryngol 2005 Mar;6(1):75-89 Morris KA, Snir E, Pompeia C, Koroleva IV, Kachar B, Hayashizaki Y, Carninci P, Soares MB, Beisel KW
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
Bioinformatics 2005 May 1;21(9):1758-63 Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.
Genome Biol 2005;6(1):R6 Caldwell RB, Kierzek AM, Arakawa H, Bezzubov Y, Zaim J, Fiedler P, Kutter S, Blagodatski A, Kostovska D, Koter M, Plachy J, Carninci P, Hayashizaki Y, Buerstedde JM
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
Genome Res 2004 Oct;14(10B):2121-7 Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J, MGC Project Team
Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data.
Mol Biol Evol 2004 Oct;21(10):1855-70 Nagata T, Iizumi S, Satoh K, Ooka H, Kawai J, Carninci P, Hayashizaki Y, Otomo Y, Murakami K, Matsubara K, Kikuchi S
Solution structure of the RWD domain of the mouse GCN2 protein.
Protein Sci 2004 Aug;13(8):2089-100 Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, Sakagami N, Terada T, Shirouzu M, Yoshida M, Hirota H, Osanai T, Tanaka A, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kinoshita K, Güntert P, Kigawa T, Yokoyama S
Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags.
Genes Genet Syst 2004 Aug;79(4):227-32 Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Physiol Genomics 2004 Apr 13;17(2):87-100 Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S
Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).
J Biol Chem 2004 Mar 26;279(13):13174-82 Maeda T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, Seki E, Matsuda T, Motoda Y, Kobayashi A, Hiroyasu F, Shirouzu M, Terada T, Hayami N, Ishizuka Y, Shinya N, Tatsuguchi A, Yoshida M, Hirota H, Matsuo Y, Tani K, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kigawa T, Yokoyama S
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
Nat Methods 2004 Dec;1(3):233-9 Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P
Large-scale collection and characterization of promoters of human and mouse genes.
In Silico Biol 2004;4(4):429-44 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
Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.
Genomics 2004 Jun;83(6):1012-23 Beisel KW, Shiraki T, Morris KA, Pompeia C, Kachar B, Arakawa T, Bono H, Kawai J, Hayashizaki Y, Carninci P
CTAB-urea method purifies RNA from melanin for cDNA microarray analysis.
Pigment Cell Res 2004 Jun;17(3):312-5 Lagonigro MS, De Cecco L, Carninci P, Di Stasi D, Ranzani T, Rodolfo M, Gariboldi M
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS Biol 2004 Jun;2(6):e162 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
Gene discovery in genetically labeled single dopaminergic neurons of the retina.
Proc Natl Acad Sci U S A 2004 Apr 6;101(14):5069-74 Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola E
Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.
FEBS Lett 2004 Feb 13;559(1-3):22-6 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
Solution structure of a BolA-like protein from Mus musculus.
Protein Sci 2004 Feb;13(2):545-8 Kasai T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, Seki E, Matsuda T, Matsuda N, Tomo Y, Shirouzu M, Terada T, Obayashi N, Hamana H, Shinya N, Tatsuguchi A, Yasuda S, Yoshida M, Hirota H, Matsuo Y, Tani K, Suzuki H, Arakawa T, Carninci P, Kawai J, Hayashizaki Y, Kigawa T, Yokoyama S
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Proc Natl Acad Sci U S A 2003 Dec 23;100(26):15776-81 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
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription.
FEBS Lett 2003 Nov 6;554(1-2):17-22 Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M
Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
DNA Res 2003 Dec 31;10(6):249-61 Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.
DNA Res 2003 Dec 31;10(6):239-47 Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, Kikuchi S
Antisense transcripts with rice full-length cDNAs.
Genome Biol 2003;5(1):R5 Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y
Empirical analysis of transcriptional activity in the Arabidopsis genome.
Science 2003 Oct 31;302(5646):842-6 Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR
Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
Biotechniques 2003 Sep;35(3):510-6, 518 Hirozane-Kishikawa T, Shiraki T, Waki K, Nakamura M, Arakawa T, Kawai J, Fagiolini M, Hensch TK, Hayashizaki Y, Carninci P
Genetic control of the innate immune response.
BMC Immunol 2003 Jun 26;4:5 Wells CA, Ravasi T, Faulkner GJ, Carninci P, Okazaki Y, Hayashizaki Y, Sweet M, Wainwright BJ, Hume DA
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
Genome Res 2003 Jun;13(6B):1273-89 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
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution.
Proc Natl Acad Sci U S A 2003 Jun 24;100(13):8007-12 Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M
Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene.
Gene 2003 Mar 27;307:111-23 Walsh NC, Cahill M, Carninci P, Kawai J, Okazaki Y, Hayashizaki Y, Hume DA, Cassady AI
Mapping of 19032 mouse cDNAs on mouse chromosomes.
J Struct Funct Genomics 2002;2(1):23-8 Yamanaka I, Kiyosawa H, Kondo S, Saito T, Carninci P, Shinagawa A, Aizawa K, Fukuda S, Hara A, Itoh M, Kawai J, Shibata K, Arakawa T, Ishii Y, Hayashizaki Y
A framework for integrating the songbird brain.
J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2002 Dec;188(11-12):961-80 Jarvis ED, Smith VA, Wada K, Rivas MV, McElroy M, Smulders TV, Carninci P, Hayashizaki Y, Dietrich F, Wu X, McConnell P, Yu J, Wang PP, Hartemink AJ, Lin S
Comprehensive sequence analysis of translation termination sites in various eukaryotes.
Gene 2002 Oct 30;300(1-2):79-87 Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray.
Funct Integr Genomics 2002 Nov;2(6):282-91 Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K
Cytoplasmic RNA extraction from fresh and frozen mammalian tissues.
Biotechniques 2002 Aug;33(2):306-9 Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.
Genome Res 2002 Aug;12(8):1294-300 Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin GM
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.
Plant J 2002 Aug;31(3):279-92 Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K
A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.
Genome Res 2002 Jul;12(7):1127-34 Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y
Extra-long first-strand cDNA synthesis.
Biotechniques 2002 May;32(5):984-5 Carninci P, Shiraki T, Mizuno Y, Muramatsu M, Hayashizaki Y
Functional annotation of a full-length Arabidopsis cDNA collection.
Science 2002 Apr 5;296(5565):141-5 Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K
The DT40 web site: sampling and connecting the genes of a B cell line.
Nucleic Acids Res 2002 Jan 1;30(1):230-1 Buerstedde JM, Arakawa H, Watahiki A, Carninci PP, Hayashizaki YY, Korn B, Plachy J
Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis.
Genomics 2001 Sep;77(1-2):79-90 Carninci P, Shibata Y, Hayatsu N, Itoh M, Shiraki T, Hirozane T, Watahiki A, Shibata K, Konno H, Muramatsu M, Hayashizaki Y
Meeting Report: 14th International mouse genome conference
Mamm Genome 2001-01-01 Hagiwara N, Carninci P, Kozak C, Brilliant M
Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing.
Biotechniques 2001 Nov;31(5):1042, 1044, 1048-9 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
Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
Gene 2001 Oct 3;276(1-2):101-5 Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M
Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method.
Biotechniques 2001 Jun;30(6):1250-4 Shibata Y, Carninci P, Watahiki A, Shiraki T, Konno H, Muramatsu M, Hayashizaki Y
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
Proc Natl Acad Sci U S A 2001 Feb 27;98(5):2199-204 Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y
Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries.
Gene 2001 Jan 24;263(1-2):93-102 Sugahara Y, Carninci P, Itoh M, Shibata K, Konno H, Endo T, Muramatsu M, Hayashizaki Y
Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray.
Plant Cell 2001 Jan;13(1):61-72 Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K
Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.
Genome Res 2001 Feb;11(2):281-9 Konno H, Fukunishi Y, Shibata K, Itoh M, Carninci P, Sugahara Y, Hayashizaki Y
RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.
Genome Res 2000 Nov;10(11):1757-71 Shibata K, Itoh M, Aizawa K, Nagaoka S, Sasaki N, Carninci P, Konno H, Akiyama J, Nishi K, Kitsunai T, Tashiro H, Itoh M, Sumi N, Ishii Y, Nakamura S, Hazama M, Nishine T, Harada A, Yamamoto R, Matsumoto H, Sakaguchi S, Ikegami T, Kashiwagi K, Fujiwake S, Inoue K, Togawa Y
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.
Genome Res 2000 Oct;10(10):1617-30 Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y
Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display.
Nucleic Acids Res 1999 Mar 1;27(5):1345-9 Mizuno Y, Carninci P, Okazaki Y, Tateno M, Kawai J, Amanuma H, Muramatsu M, Hayashizaki Y
High-efficiency full-length cDNA cloning.
Methods Enzymol 1999;303:19-44 Carninci P, Hayashizaki Y
Automated filtration-based high-throughput plasmid preparation system.
Genome Res 1999 May;9(5):463-70 Itoh M, Kitsunai T, Akiyama J, Shibata K, Izawa M, Kawai J, Tomaru Y, Carninci P, Shibata Y, Ozawa Y, Muramatsu M, Okazaki Y, Hayashizaki Y
High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper.
Plant J 1998 Sep;15(5):707-20 Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, Shinozaki K
Transcriptional sequencing: A method for DNA sequencing using RNA polymerase.
Proc Natl Acad Sci U S A 1998 Mar 31;95(7):3455-60 Sasaki N, Izawa M, Watahiki M, Ozawa K, Tanaka T, Yoneda Y, Matsuura S, Carninci P, Muramatsu M, Okazaki Y, Hayashizaki Y
Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA.
Proc Natl Acad Sci U S A 1998 Jan 20;95(2):520-4 Carninci P, Nishiyama Y, Westover A, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Hayashizaki Y
A novel control system for polymerase chain reaction using a RIKEN GS384 thermalcycler.
DNA Res 1997 Dec 31;4(6):387-91 Sasaki N, Izawa M, Shimojo M, Shibata K, Akiyama J, Itoh M, Nagaoka S, Carninci P, Okazaki Y, Moriuchi T, Muramatsu M, Watanabe S, Hayashizaki Y
High efficiency selection of full-length cDNA by improved biotinylated cap trapper.
DNA Res 1997 Feb 28;4(1):61-6 Carninci P, Westover A, Nishiyama Y, Ohsumi T, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Schneider C, Hayashizaki Y
Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates.
Nucleic Acids Res 1997 Mar 15;25(6):1315-6 Itoh M, Carninci P, Nagaoka S, Sasaki N, Okazaki Y, Ohsumi T, Muramatsu M, Hayashizaki Y
High-efficiency full-length cDNA cloning by biotinylated CAP trapper.
Genomics 1996 Nov 1;37(3):327-36 Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C
Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M.
Nat Genet 1996 Sep;14(1):106-9 Plass C, Shibata H, Kalcheva I, Mullins L, Kotelevtseva N, Mullins J, Kato R, Sasaki H, Hirotsune S, Okazaki Y, Held WA, Hayashizaki Y, Chapman VM