List of Selected Publications

1. de Hoon, M.J., Taft, R.J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., Kishima, M., Lassmann, T., Faulkner, G.J., Mattick, J.S., Daub, C.O., 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 Jan 5 (2010)
2. Arner, E., Hayashizaki, Y., Daub, C.O.:
   " NGSView: an extensible open source editor for next-generation sequencing data."
   Bioinformatics Jan 1;26(1):125-6 (2010)
3. Lassmann, T., Hayashizaki, Y., Daub, C.O.:
   " TagDust--a program to eliminate artifacts from next generation sequencing data."
   Bioinformatics Nov 1;25(21):2839-40 (2009)
4. Takahashi, Y., Forrest, A.R., Maeno, E., Hashimoto, T., Daub, CO., Yasuda, J.:
   " MiR-107 and MiR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines."
   PLoS One Aug 18;4(8):e6677 (2009)
5. Balwierz, P.J., Carninci, P., Daub, C.O., 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(7):R79 (2009)
6. Hashimoto, T., de Hoon, M.J., Grimmond, S.M., Daub, C.O., Hayashizaki, Y., Faulkner, G.J.:
   " Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite."
   Bioinformatics 1;25(19):2613-4 (2009)
7. Kawaji, H., Hayashizaki, Y., Daub, C.O.:
   " SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes."
   BMC Bioinformatics 7;10:133 (2009)
8. Taft, R.J., Glazov, E.A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G.J., Lassmann, T., Forrest, A.R., Grimmond, S.M., Schroder, K., Irvine, K., Arakawa, T., Nakamura, M., Kubosaki, A., Hayashida, K., Kawazu, C., Murata, M., Nishiyori, H., Fukuda, S., Kawai, J., Daub, C.O., Hume, D.A., Suzuki, H., Orlando, V., Carninci, P., Hayashizaki, Y., Mattick, J.S.:
   " Tiny RNAs associated with transcription start sites in animals."
   Nat Genet 41(5):572-8 (2009)
9. Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A.R., Suzuki, H., Hayashizaki, Y., Hume, D.A., Orlando, V., Grimmond, S.M., Carninci, P.:
   " The regulated retrotransposon transcriptome of mammalian cells."
   Nat Genet 41(5):563-71 (2009)
10. Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., 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, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Björkegren. J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., 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, M.C., 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, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., 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, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A., 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(5):553-62 (2009)

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