主要論文

1. 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.:
   "Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan."
   Nat Methods. 7(7):528-534 (2010)
2. 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.
3. Taft R, Glazov EA, Cloonan N, Simons S, Stephen S, Faulkner G, Lassmann T, Forrest AFF, 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.
4. 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.
5. 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.
6. 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
7. Sandelin, A., Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y., and Hume, DA.:
   "Mammalian RNA Polymerase II core promoters - insights from genome-wide studies."
   Nature Rev. Genetics 8:424-36. (2007).
8. Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, S., Ponjavic, J., Semple, C., Taylor, M., Engstrom, P., Frith, MC., Forrest, ARR., 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., and Hayashizaki, Y.:
   "Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data."
   Nat. Genetics, 38:626-35. (2006).
9. Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., Hayashizaki, Y., and Carninci, P.:
   "CAGE: cap analysis of gene expression."
   Nat Methods. 3:211-22. (2006).
10. 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, ARR., 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., and Hayashizaki, Y.:
    "The Transcriptional Landscape of the Mammalian Genome."
    Science, 309:1559-63. (2005).

メンバー