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Author Carninci [48 articles]

Recent papers posted to CiteULike by the author Carninci.
  • The complexity of the mammalian transcriptome
    The Journal of Physiology, Vol. 575, No. 2. (September 2006), pp. 321-332.
    posted to transcription review by inesdesantiago on 2008-07-24 14:28:32 as *****
  • Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 424-436.
    by Albin Sandelin, Piero Carninci, Boris Lenhard, Jasmina Ponjavic, Yoshihide Hayashizaki, David A Hume
  • Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.
    BioTechniques, Vol. 45, No. 1. (July 2008), pp. 95-97.
    posted to sequencing cage by jyuh on 2008-07-14 04:20:32 as **
  • A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.
    Genomics, Vol. 91, No. 3. (March 2008), pp. 281-288.
    posted to sequencing cage by jyuh on 2008-07-14 04:20:15 as ** along with 1 person gjuggler
  • Genome-wide analysis of mammalian promoter architecture and evolution
    Nature Genetics, Vol. 38, No. 6. (28 April 2006), pp. 626-635.
    by Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin AM Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair RR Forrest, Wynand B Alkema, Sin L Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki
  • Hunting hidden transcripts
    Nat Meth, Vol. 5, No. 7. (July 2008), pp. 587-589.
    by Piero Carninci
    posted to no-tag by megraw on 2008-06-27 17:44:18 as ***
  • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
    Proc Natl Acad Sci U S A, Vol. 100, No. 26. (23 December 2003), pp. 15776-15781.
  • Large-scale clustering of CAGE tag expression data
    BMC Bioinformatics, Vol. 8 (21 May 2007), 161.
    by Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
    posted to promoter cagecluster by antonkratz on 2008-06-16 04:12:08 as ** along with 1 person gjuggler
  • Hidden layers of human small RNAs
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Hideya Kawaji, Mari Nakamura, Yukari Takahashi, Albin Sandelin, Shintaro Katayama, Shiro Fukuda, Carsten Daub, Chikatoshi Kai, Jun Kawai, Jun Yasuda, Piero Carninci, Yoshihide Hayashizaki
    posted to rna human by bertelsen on 2008-06-12 21:54:01 as **** along with 3 people maralena mtagaya heliopais
  • Initial sequencing and comparative analysis of the mouse genome.
    Nature, Vol. 420, No. 6915. (5 December 2002), pp. 520-562.
    by RH Waterston, K Lindblad-Toh, E Birney, J Rogers, JF Abril, P Agarwal, R Agarwala, R Ainscough, M Alexandersson, P An, SE Antonarakis, J Attwood, R Baertsch, J Bailey, K Barlow, S Beck, E Berry, B Birren, T Bloom, P Bork, M Botcherby, N Bray, MR Brent, DG Brown, SD Brown, C Bult, J Burton, J Butler, RD Campbell, P Carninci, S Cawley, F Chiaromonte, AT Chinwalla, DM Church, M Clamp, C Clee, FS Collins, LL Cook, RR Copley, A Coulson, O Couronne, J Cuff, V Curwen, T Cutts, M Daly, R David, J Davies, KD Delehaunty, J Deri, ET Dermitzakis, C Dewey, NJ Dickens, M Diekhans, S Dodge, I Dubchak, DM Dunn, SR Eddy, L Elnitski, RD Emes, P Eswara, E Eyras, A Felsenfeld, GA Fewell, P Flicek, K Foley, WN Frankel, LA Fulton, RS Fulton, TS Furey, D Gage, RA Gibbs, G Glusman, S Gnerre, N Goldman, L Goodstadt, D Grafham, TA Graves, ED Green, S Gregory, R Guigó, M Guyer, RC Hardison, D Haussler, Y Hayashizaki, LW Hillier, A Hinrichs, W Hlavina, T Holzer, F Hsu, A Hua, T Hubbard, A Hunt, I Jackson, DB Jaffe, LS Johnson, M Jones, TA Jones, A Joy, M Kamal, EK Karlsson, D Karolchik, A Kasprzyk, J Kawai, E Keibler, C Kells, WJ Kent, A Kirby, DL Kolbe, I Korf, RS Kucherlapati, EJ Kulbokas, D Kulp, T Landers, JP Leger, S Leonard, I Letunic, R Levine, J Li, M Li, C Lloyd, S Lucas, B Ma, DR Maglott, ER Mardis, L Matthews, E Mauceli, JH Mayer, M McCarthy, WR McCombie, S McLaren, K McLay, JD McPherson, J Meldrim, B Meredith, JP Mesirov, W Miller, TL Miner, E Mongin, KT Montgomery, M Morgan, R Mott, JC Mullikin, DM Muzny, WE Nash, JO Nelson, MN Nhan, R Nicol, Z Ning, C Nusbaum, MJ O'Connor, Y Okazaki, K Oliver, E Overton-Larty, L Pachter, G Parra, KH Pepin, J Peterson, P Pevzner, R Plumb, CS Pohl, A Poliakov, TC Ponce, CP Ponting, S Potter, M Quail, A Reymond, BA Roe, KM Roskin, EM Rubin, AG Rust, R Santos, V Sapojnikov, B Schultz, J Schultz, MS Schwartz, S Schwartz, C Scott, S Seaman, S Searle, T Sharpe, A Sheridan, R Shownkeen, S Sims, JB Singer, G Slater, A Smit, DR Smith, B Spencer, A Stabenau, N Stange-Thomann, C Sugnet, M Suyama, G Tesler, J Thompson, D Torrents, E Trevaskis, J Tromp, C Ucla, A Ureta-Vidal, JP Vinson, AC Von Niederhausern, CM Wade, M Wall, RJ Weber, RB Weiss, MC Wendl, AP West, K Wetterstrand, R Wheeler, S Whelan, J Wierzbowski, D Willey, S Williams, RK Wilson, E Winter, KC Worley, D Wyman, S Yang, SP Yang, EM Zdobnov, MC Zody, ES Lander,
  • CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
  • CAGE: cap analysis of gene expression
    Nature Methods, Vol. 3, No. 3., pp. 211-222.
    by Rimantas Kodzius, Miki Kojima, Hiromi Nishiyori, Mari Nakamura, Shiro Fukuda, Michihira Tagami, Daisuke Sasaki, Kengo Imamura, Chikatoshi Kai, Matthias Harbers, Yoshihide Hayashizaki, Piero Carninci
    posted to no-tag by jyuh on 2008-05-09 16:49:58 as ** along with 1 person xiaobeizhao
  • Constructing the landscape of the mammalian transcriptome.
    J Exp Biol, Vol. 210, No. Pt 9. (May 2007), pp. 1497-1506.
    posted to transcriptome review by xingxu on 2008-05-06 20:13:19 as ** along with 1 person jyuh
  • Tag-based approaches for transcriptome research and genome annotation
    Nature Methods, Vol. 2, No. 7., pp. 495-502.
    by Matthias Harbers, Piero Carninci
    posted to sage review by gpappas on 2008-05-05 00:40:57 as ** along with 1 person jyuh
  • Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution
    Proceedings of the National Academy of Sciences, Vol. 100, No. 13. (24 June 2003), pp. 8007-8012.
    by Tomoaki Nishiyama, Tomomichi Fujita, Tadasu Shin-I, Motoaki Seki, Hiroyo Nishide, Ikuo Uchiyama, Asako Kamiya, Piero Carninci, Yoshihide Hayashizaki, Kazuo Shinozaki, Yuji Kohara, Mitsuyasu Hasebe
    posted to no-tag by natstreet on 2008-04-16 09:37:35 as **
  • Transcriptional network dynamics in macrophage activation.
    Genomics, Vol. 88, No. 2. (August 2006), pp. 133-142.
    posted to jfrbib by jfr on 2008-03-30 21:06:50 as read along with 1 person gespim
  • Complex Loci in human and mouse genomes.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    by PG Engström, H Suzuki, N Ninomiya, A Akalin, L Sessa, G Lavorgna, A Brozzi, L Luzi, SL Tan, L Yang, G Kunarso, EL Ng, S Batalov, C Wahlestedt, C Kai, J Kawai, P Carninci, Y Hayashizaki, C Wells, VB Bajic, V Orlando, JF Reid, B Lenhard, L Lipovich
    posted to jfrbib by jfr on 2008-03-30 21:06:21 as read along with 2 people balicea tabu
  • The transcriptional landscape of the mammalian genome.
    Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563.
    by P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, AR Forrest, M Zavolan, MJ Davis, LG Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, SP Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan Babu, M Madera, L Marchionni, H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schönbach, K Sekiguchi, CA Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, V Brusic, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai, Y Hayashizaki, ,
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
    Nature, Vol. 420, No. 6915. (5 December 2002), pp. 563-573.
  • Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    posted to annotation cdna genome-wide mouse transcriptome by raylim on 2008-03-08 23:22:51 as **
  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    PLoS Biol, Vol. 2, No. 6. (June 2004)
    by T Imanishi, T Itoh, Y Suzuki, C O'Donovan, S Fukuchi, KO Koyanagi, RA Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, K Yura, S Miyazaki, K Ikeo, K Homma, A Kasprzyk, T Nishikawa, M Hirakawa, J Thierry-Mieg, D Thierry-Mieg, J Ashurst, L Jia, M Nakao, MA Thomas, N Mulder, Y Karavidopoulou, L Jin, S Kim, T Yasuda, B Lenhard, E Eveno, Y Suzuki, C Yamasaki, J Takeda, C Gough, P Hilton, Y Fujii, H Sakai, S Tanaka, C Amid, M Bellgard, Mde F Bonaldo, H Bono, SK Bromberg, AJ Brookes, E Bruford, P Carninci, C Chelala, C Couillault, SJ de Souza, MA Debily, MD Devignes, I Dubchak, T Endo, A Estreicher, E Eyras, K Fukami-Kobayashi, GR Gopinath, E Graudens, Y Hahn, M Han, ZG Han, K Hanada, H Hanaoka, E Harada, K Hashimoto, U Hinz, M Hirai, T Hishiki, I Hopkinson, S Imbeaud, H Inoko, A Kanapin, Y Kaneko, T Kasukawa, J Kelso, P Kersey, R Kikuno, K Kimura, B Korn, V Kuryshev, I Makalowska, T Makino, S Mano, R Mariage-Samson, J Mashima, H Matsuda, HW Mewes, S Minoshima, K Nagai, H Nagasaki, N Nagata, R Nigam, O Ogasawara, O Ohara, M Ohtsubo, N Okada, T Okido, S Oota, M Ota, T Ota, T Otsuki, D Piatier-Tonneau, A Poustka, SX Ren, N Saitou, K Sakai, S Sakamoto, R Sakate, I Schupp, F Servant, S Sherry, R Shiba, N Shimizu, M Shimoyama, AJ Simpson, B Soares, C Steward, M Suwa, M Suzuki, A Takahashi, G Tamiya, H Tanaka, T Taylor, JD Terwilliger, P Unneberg, V Veeramachaneni, S Watanabe, L Wilming, N Yasuda, HS Yoo, M Stodolsky, W Makalowski, M Go, K Nakai, T Takagi, M Kanehisa, Y Sakaki, J Quackenbush, Y Okazaki, Y Hayashizaki, W Hide, R Chakraborty, K Nishikawa, H Sugawara, Y Tateno, Z Chen, M Oishi, P Tonellato, R Apweiler, K Okubo, L Wagner, S Wiemann, RL Strausberg, T Isogai, C Auffray, N Nomura, T Gojobori, S Sugano
  • Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
    Genome Res., Vol. 12, No. 8. (1 August 2002), pp. 1286-1293.
    by Hiromi Kochiwa, Ryosuke Suzuki, Takanori Washio, Rintaro Saito, The RIKEN Phase, Hidemasa Bono, Piero Carninci, Yasushi Okazaki, Rika Miki, Yoshihide Hayashizaki, Masaru Tomita
    posted to prof_takanori_washio by antonkratz on 2008-03-03 09:56:03 as **
  • Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1758-1763.
    by Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita
    posted to prof_takanori_washio by antonkratz on 2008-03-03 09:50:58 as **
  • The Abundance of Short Proteins in the Mammalian Proteome
    PLoS Genetics, Vol. 2, No. 4. (1 April 2006), e52.
    by Martin C Frith, Alistair R Forrest, Ehsan Nourbakhsh, Ken C Pang, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey, Sean M Grimmond
    posted to no-tag by mwilkers on 2008-01-30 19:16:33 as ** along with 1 person and 1 group cmm FAB-lab
  • A code for transcription initiation in mammalian genomes
    Genome Res. (21 November 2007), gr.6831208.
    by Martin C Frith, Eivind Valen, Anders Krogh, Yoshihide Hayashizaki, Piero Carninci, Albin Sandelin
  • Genome Network and FANTOM3: assessing the complexity of the transcriptome.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    posted to tss by gjuggler on 2008-01-23 09:51:16 as ** along with 1 person olympos
  • Heterotachy in mammalian promoter evolution.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    by MS Taylor, C Kai, J Kawai, P Carninci, Y Hayashizaki, CA Semple
  • Tagging mammalian transcription complexity
    Trends in Genetics, Vol. 22, No. 9. (September 2006), pp. 501-510.
    by Piero Carninci
  • Evolutionary turnover of mammalian transcription start sites.
    Genome Res (10 May 2006)
    by Martin CC Frith, Jasmina Ponjavic, David Fredman, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayshizaki, Albin Sandelin
  • The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
    Genome Res, Vol. 14, No. 10B. (October 2004), pp. 2121-2127.
    by DS Gerhard, L Wagner, EA Feingold, CM Shenmen, LH Grouse, G Schuler, SL Klein, S Old, R Rasooly, P Good, M Guyer, AM Peck, JG Derge, D Lipman, FS Collins, W Jang, S Sherry, M Feolo, L Misquitta, E Lee, K Rotmistrovsky, SF Greenhut, CF Schaefer, K Buetow, TI Bonner, D Haussler, J Kent, M Kiekhaus, T Furey, M Brent, C Prange, K Schreiber, N Shapiro, NK Bhat, RF Hopkins, F Hsie, T Driscoll, MB Soares, TL Casavant, TE Scheetz, MJ Brown-stein, TB Usdin, S Toshiyuki, P Carninci, Y Piao, DB Dudekula, MS Ko, K Kawakami, Y Suzuki, S Sugano, CE Gruber, MR Smith, B Simmons, T Moore, R Waterman, SL Johnson, Y Ruan, CL Wei, S Mathavan, PH Gunaratne, J Wu, AM Garcia, SW Hulyk, E Fuh, Y Yuan, A Sneed, C Kowis, A Hodgson, DM Muzny, J McPherson, RA Gibbs, J Fahey, E Helton, M Ketteman, A Madan, S Rodrigues, A Sanchez, M Whiting, A Madari, AC Young, KD Wetherby, SJ Granite, PN Kwong, CP Brinkley, RL Pearson, GG Bouffard, RW Blakesly, ED Green, MC Dickson, AC Rodriguez, J Grimwood, J Schmutz, RM Myers, YS Butterfield, M Griffith, OL Griffith, MI Krzywinski, N Liao, R Morin, R Morrin, D Palmquist, AS Petrescu, U Skalska, DE Smailus, JM Stott, A Schnerch, JE Schein, SJ Jones, RA Holt, A Baross, MA Marra, S Clifton, KA Makowski, S Bosak, J Malek,
    posted to no-tag by jyuh on 2008-01-17 04:38:51 as ** along with 1 person Iden-J_GluR
  • Dynamic usage of transcription start sites within core promoters
    Genome Biology, Vol. 7 (12 December 2006), R118.
    by Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
    posted to tss by gjuggler on 2008-01-16 14:14:44 as ** along with 1 person and 1 group icases TNT
  • Transcriptomics resources for functional genomics
    Brief Funct Genomic Proteomic, Vol. 6, No. 3. (1 September 2007), pp. 171-179.
    by Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
    posted to no-tag by jyuh on 2007-12-07 09:50:55 as **