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| Development of Rice Genome Simulators |
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Publications | ||||
| Last Updated : 2003/10/10 |
| Publications (1998-2003) |
| Subject ID No. | Auther: Title. Journal Volume,Number,Page (Publication_Year) |
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| SY1101 | Sakata,K., Numa,H. et.al.: RiceGAAS. Nucleic Acids Res. Molecular Biology Database Collection, (Jan. 2003) |
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| SY1101 | Katsumi Sakata, Yoshiaki Nagamura, Hisataka Numa, Baltazar A. Antonio,
Hideki Nagasaki, Atsuko Idonuma, Wakako Watanabe, Yuji Shimizu, Ikuo Horiuchi,
Takashi Matsumoto, Takuji Sasaki and Kenichi Higo: RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research 30(1) 98-102 (2002) |
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| SY1101 | Katsumi Sakata, Baltazar A. Antonio, Yoshiyuki Mukai, Hideki Nagasaki,
Yasumichi Sakai, Kazuyoshi Makino and Takuji Sasaki: INE: a rice genome database with an integrated map view. Nucleic Acids Research 28(1) 97-101 (2000) |
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| SY1104 | Hiromi Kochiwa, Ryosuke Suzuki, Takanori Washio, Rintaro Saito, The RIKEN
Genome Exploration Research Group Phase II Team, Hidemasa Bono, Piero Carninci,
Yasushi Okazaki, Rika Miki, Yoshihide Hayashizaki, and Masaru Tomita: Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Research 12(8) 1286-1293 (2002) |
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| SY1105 | Hideo Matsumura, et al.: Overexpression of Bax inhibitor suppresses the fungal elicitor-induced cell death in rice (Oryza sativa L) cells. The Plant Journal 33(3): 425-434 (2003) |
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| SY1106 | Hucka, M., Finny, A., Sauro, H., Doyle, J., Kitano, H., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531 (2003) |
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| SY1106 | T. Yokoyama, N. Izu, K. Watanabe, T. Kudoh, et.al.: Design and Implementation of RHiNET-2/NI0: A Reconfigurable Network Interface for Cluster Computing. IEICE Transaction Vol.E86-D No.5 pp.789-795 (2003) |
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| SY1106 | M. Uno, Y. Shibata, H. Amano: Implementation of Data Driven Applications on a Multi-Context Reconfigurable Device. IEICE Transaction Vol.E86-D No.5 pp.841-849 (2003) |
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| SY1106 | Akashi, H. Kurata, H., Seki, M., Taira, K., Furusaki, S.: Screening for transgenic plant cells that highly express a target gene from genetically mixed cells. Biochem. Eng. J. 10, 175-182 (2002) |
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| SY1106 | Hiroaki Kitano: Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. Current Genetics Vol.41 pp.1-10 (Apr. 2002) |
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| SY1106 | Kitano, H.: A Graphical Notation of Biochemical Networks. ICSB-2002 workshop on SBML/SBW (Stockholm) (2002) |
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| SY1106 | Mineo Morohashi, Amanda E. Winn, Mark T. Borisuk, Hamid Bolouri, John Doyle,
and Hiroaki Kitano: Robustness as a measure of plausibility in models of biochemical networks. J. Theor. Biol. 216(1) 19-30 (2002) |
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| SY1106 | Hiroaki Kitano: Computational systems biology. Nature 420 (6912) 206-210 (2002) |
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| SY1106 | Hiroaki Kitano: Standards for modeling. nature biotechnology Vol.20 p.337 (Apr. 2002) |
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| SY1106 | Naoyuki Izu, Tomonori Yokoyama, Jun-ichiro Tsuchiya, Konosuke Watanabe,
and Hideharu Amano: RHiNET/NI: A reconfigurable network interface for cluster computing. Proceedings of International Conference on Field-Programmable Logic and Applications pp.1118-1121 (Sep. 2002) |
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| SY1106 | Naoto Kaneko and Hideharu Amano: A general hardware design model for multicontext FPGAs. Proceedings of International Conference on Field-Programmable Logic and Applications, pp.1037-1047 (Sep. 2002) |
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| SY1106 | H. El-Samad, M. Khammash, H. Kurata, and J. Doyle: Robustness analysis of the heat shock response in E. coli Proceedings of the 2002 American Control Conference Vol.3 1742 -1747, IEEE (2002) |
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| SY1106 | Hiroaki Kitano: Systems Biology: A Brief Overview. Science Vol.295 pp.1662-1664 (Mar. 2002) |
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| SY1106 | H. Kurata, H. El-Samad, T.-M. Yi, M. Khammash, J. Doyle: Feedback regulation of the heat shock response in E. coli Proceedings of the Control and Decision Conference Vol.1 837-842 (2001) |
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| SY1108 | Shinomura, T., Hanzawa, H., Furuya, M.: Phytochromes A and B: Specificity of photoperception and structure/function analysis of bilin chromophores. Journal of Photoscience 9: 90-93 (2002) |
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| SY1112 | S. Kikuchi et al.: Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301(5631): 376-379 (2003) |
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| SY1112 | Junshi Yazaki, Naoki Kishimoto, Masahiro Ishikawa, and Shoshi Kikuchi: The Rice Expression Database: gateway to rice functional genomics. Trends in Plant Science 7, 563-564 (2002) |
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| SY1114 | N. Doi, H. Takashima, M. Kinjo, K. Sakata, Y. Kawahashi, Y. Oishi, R. Oyama,
E. Miyamoto-Sato, T. Sawasaki, Y. Endo, and H. Yanagawa: Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. Genome Res., 12, 487-492 (2002) |
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| SY2101 | Hasegawa, K., Y. Yukawa, J. Obokata and M. Sugiura: A tRNA(Leu)-like sequence located immediately upstream of an Arabidopsis clock-regulated gene is transcriptionally active: efficient transcription by an RNA polymerase III-dependent in vitro transcription system. Gene 307: 133-139 (2003) |
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| SY2101 | Sasaki, T., Y. Yukawa, T. Miyamoto, J. Obokata, M. Sugiura: Identification of RNA Editing Sites in Chloroplast Transcripts from the Maternal and Paternal Progenitors of Tobacco (Nicotiana tabacum): Comparative Analysis Shows the Involvement of Distinct Trans-Factors for ndhB Editing. Mol Biol Evol. 20(7): 1028-1035 (2003) |
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| SY2101 | M. Sugiura: History of chloroplast genomics. Photosynthesis Res. (2003(in press)) |
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| SY2101 | Hasegawa, K., Y. Yukawa, M. Sugiura: In vitro analysis of transcription initiation and termination from the Lhcb1 gene family in Nicotiana sylvestris: detection of transcription termination sites. Plant J 33(6): 1063-1072 (2003) |
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| SY2101 | Plader, W. and M. Sugiura: The Shine-Dalgarno-like sequence is a negative regulatory element for translation of tobacco chloroplast rps2 mRNA: an additional mechanism for translational control in chloroplasts. Plant J 34(3): 377-382 (2003) |
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| SY2101 | Keiko Hasegawa, Yasushi Yukawa, Mamoru Sugita, and Masahiro Sugiura: Organization and transcription of the gene family encoding chlorophyll a/b-binding proteins in Nicotiana sylvestris. Gene 289 161-168 (2002) |
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| SY2101 | Tetsuya Miyamoto, Junichi Obokata, and Masahiro Sugiura: Recognition of RNA editing sites is directed by unique proteins in chloroplasts: biochemical identification of cis-acting elements and trans-acting factors involved in RNA editing in tobacco and pea chloroplasts. Mol. Cell. Biol. 22(19) 6726-6734 (2002) |
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| SY2101 | Matsuo, M. and Obokata, J.: Dual roles of photosynthetic electron transport in photosystem I biogenesis: light induction of mRNAs and chromatic regulation at post-mRNA level. Plant Cell Physiol. 43: 1189-1197 (2002) |
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| SY2101 | Masayuki Nakamura, Tatsuhiko Tsunoda, and Junichi Obokata: Photosynthesis nuclear genes generally lack TATA-boxes: a tobacco photosystem I gene responds to light through an initiator. Plant J. 29(1) 1-10 (2002) |
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| SY2101 | Olivier Mathieu, Yasushi Yukawa, Masahiro Sugiura, Georges Picard, and
Sylvette Tourmente: 5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis. Plant J. 29(3) 313-323 (2002) |
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| SY2101 | Sherameti, I., Nakamura, M., Yamamoto, Y.Y., Pfannschmidt, T., Obokata,
J. and Oelmueller, R.: Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by photosynthetic electron transport. Plant J. 32: 631-639 (2002) |
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| SY2101 | Yasushi Yukawa, Jaroslav Matousek, Michael Grimm, Lukas Vrba, Gerhard Steger,
Masahiro Sugiura, and Hildburg Beier: Plant 7SL RNA and tRNATyr genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cells. Plant Mol. Biol. 50 713-723 (2002) |
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| SY2101 | Tetsuro Hirose, and Masahiro Sugiura: Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J. 20(5) 1144-1152 (2001) |
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| SY2101 | Yuki Kobayashi, Yuko Dokiya, Masahiro Sugiura, Yasuo Niwa, and Mamoru Sugita: Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris. Gene 279 33-40 (2001) |
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| SY2101 | Takahiro Nakamura, Masaru Ohta, Masahiro Sugiura, and Mamoru Sugita: Chloroplast ribonucleoproteins function as a stabilizing factor of ribosome-free mRNAs in the stroma. J. Biol. Chem. 276(1) 147-152 (2001) |
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| SY2101 | Takahiko Tsudzuki, Tatsuya Wakasugi, and Masahiro Sugiura: Comparative analysis of RNA editing sites in higher plant chloroplasts. J. Mol. Evol. 53 327-332 (2001) |
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| SY2101 | Tatsuya Wakasugi, Takahiko Tsudzuki, and Masahiro Sugiura: The genomics of land plant chloroplasts: Gene content and alteration of genomic information by RNA editing. Photosynthesis Res. 70 107-118 (2001) |
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| SY2101 | Philippe Arnaud, Yasushi Yukawa, Laurence Lavie, Thierry Pélissier,
Masahiro Sugiura, and Jean-Marc Deragon: Analysis of the SINE S1 Pol III promoter from Brassica; impact of methylation and influence of external sequences. Plant J. 26(3) 295-305 (2001) |
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| SY2101 | Yasushi Yukawa, Hao Fan, Kazuhito Akama, Hildburg Beier, Hans J. Gross,
and Masahiro Sugiura: A tobacco nuclear extract supporting transcription, processing, splicing and modification of plant intron-containing tRNA precursors. Plant J. 28(5) 583-594 (2001) |
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| SY2101 | T. Miyamoto, J. Obokata, T. Wakasugi, and Masahiro Sugiura: In vitro analysis of cis-elements and trans-factors for the RNA editing of tobacco chloroplast psbE and petB mRNAs. PS 2001 Proceedings: 12th International Congress on Photosynthesis., CSIRO Publishing, Melbourne, Australia (2001) |
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| SY2101 | J. Tsudzuki, T. Tsudzuki, T. Wakasugi, K. Kinoshita, T. Kondo, and Masahiro
Sugiura: The entire gene organization of rice chloroplast DNA---2001 update. PS 2001 Proceedings: 12th International Congress on Photosynthesis., CSIRO Publishing, Melbourne, Australia (2001) |
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| SY2101 | M. Sugita, T. Tsudzuki, C. Sugita, M. Ishiura, K. Ogata, H. Jikuya, J.
Takano, and Masahiro Sugiura: Genome analysis of Synechococcus sp. strain PCC6301 PS 2001 Proceedings: 12th International Congress on Photosynthesis., CSIRO Publishing, Melbourne, Australia (2001) |
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| SY2101 | M. Nakamura, T. Tsunoda, T. Yoshitsugu, H. Hibino and J. Obokata: Core promoter architecture characteristic of photosynthesis nuclear genes. PS 2001 Proceedings: 12th International Congress on Photosynthesis., CSIRO Publishing, Melbourne, Australia (2001) |
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| SY2101 | M. Matsuo, and J. Obokata: Redox regulation of PSI nuclear genes through photosynthetic electron flow. PS 2001 Proceedings: 12th InternationalCongress on Photosynthesis., CSIRO Publishing, Melbourne, Australia (2001) |
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| SY2102 | Britz-McKibbin, P., Markuszewski, M.J., Iyanahi, T., Matsuda, K., Nishioka,T.
& Terabe, S.: Picomolar analysis of flavins in biological samples by dynamic pH junction-sweeping capillary electrophoresis with laser-induced fluorescence detection. Anal. Biochem. 313(1): 89-96 (2003) |
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| SY2102 | Tomoyoshi Soga, Yuki Ueno, Hisako Naraoka, Yoshiaki Ohashi, Masaru Tomita,
and Takaaki Nishioka: Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal. Chem. 74(10) 2233-2239 (2002) |
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| SY2102 | T. Soga, Y. Ueno, H. Naraoka, K. Matsuda, M. Tomita and T. Nishioka: Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal. Chem. 74, 6224-6229 (2002) |
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| SY2102 | Philip Britz-McKibbin, Koji Otsuka, and Shigeru Terabe: On-line focusing of flavin derivatives using Dynamic pH junction-sweeping capillary electrophoresis with laser-induced fluorescence detection. Anal. Chem.,74, 3736-3743 (2002) |
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| SY2102 | Shigeru Terabe, Michal J. Markuszewski, Naoko Inoue, Koji Otsuka, and Takaaki
Nishioka: Capillary Electrophoretic Techniques toward the Metabolome Analysis. Pure Appl. Chem. 73, 1563-1572 (2001) |
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| SY2105 | Tomonari Watanabe, P. M. Room, and J. S. Hanan: Virtual rice: simulating the development of plant architecture. International Rice Research Notes 26(2) 60-62 (2001) |
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| SY2106 | Trillana, N., Chaudhary, R., Inamura, T. and Horie, T.: Maintaining predawn leaf water potential in two upland rice cultivars during drought stress and recovery. International Rice Res. Notes, 27(1): 49-50 (2002) |
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| SY2106 | Kobayashi, K., Horie, Y. and Imaki, T.: Relationship between apical dome diameter at panicle initiation and the size of panicle components in rice grown under different nitrogen conditions during the vegetative stage. Plant Prod. Sci., 5: 3-7 (2002) |
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| SY2106 | Suzuki, T., Shiraiwa, T., and Horie, T.: Competitiveness of four rice cultivars against barnyard grass, Echinochlora oryzicola Vasting, with reference to root and shoot competition. Plant Prod. Sci., 5: 77-82 (2002) |
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| SY2106 | Koki Homma, Takeshi Horie, Masao Ohnishi, Tatsuhiko Shiraiwa, Nopporn Supapoj,
Naruo Matsumoto, and Nobuyuki Kabaki: Quantifying the toposequential distribution of environmental resources and its relationship with rice productivity. ACIAR Proc. 101 281-291 (2001) |
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| SY2106 | Hidetaka Nishida, Yutaka Okumoto, Hiroshi Nakagawa, Katsuyuki Ichitani,
Hiromo Inoue, and Takatoshi Tanisaka: Analysis of tester lines for rice (Oryza sativa L.) heading-time genes using reciprocal photoperiodic transfer treatments Ann. Bot. 88 527-536 (2001) |
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| SY2106 | Takeshi Horie: Increasing yield potential in irrigated rice: breaking the yield barrier. In Peng, S. and Hardy, B.(eds.) Rice research for Food Security and Poverty Alleviation.(IRRI, Philippines) P. 3-25 (2001) |
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| SY2106 | Tsutomu Matsui, Kenji Omasa, and Takeshi Horie: Comparison between anthers of two rice (Oryza sativa L.) cultivars with tolerance to high temperatures at flowering or susceptibility Plant Prod. Sci. 4(1) 36-40 (2001) |
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| SY2106 | Tsutomu Matsui, Kenji Omasa, and Takeshi Horie: The difference in sterility due to high temperatures during the flowering period among Japonica-rice varieties. Plant Prod. Sci. 4(2) 90-93 (2001) |
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| SY2107 | Yukihiro Ito, Hirohiko Hirochika, and Nori Kurata: Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice. Gene 288 41-47 (2002) |
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| SY2107 | Yukihiro Ito, Mitsugu Eiguchi, and Nori Kurata: KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice. Genesis 30 231-238 (2001) |
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| SY2107 | Y. Ito, M. Eiguchi, and Nori Kurata: Somatic and germinal transposition of a maize transposable element Ds in rice. Rice Genet. Newsl. 17, 110-111 (2000) |
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