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Akihiko Konagaya

Research Profile

Activities & Behaviors

Living Beings

Arabidopsis

Concepts & Ideas

Chemicals & Drugs

Devices

Oligonucleotide Array Sequence Analysis

Procedures

Gene Expression Profiling

Phenomena

Phosphorylation

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Publications

TOP 3
Atsushi Suenaga; Noriaki Okimoto; Noriyuki Futatsugi; Yoshinori Hirano; Tetsu Narumi; Yousuke Ohno; Ryoko Yanai; Takatsugu Hirokawa; Toshikazu Ebisuzaki; Akihiko Konagaya; Makoto Taiji
Structure and dynamics of RNA polymerase II elongation complex.
Atsushi Suenaga; Jay Z Yeh; Makoto Taiji; Akira Toyama; Hideo Takeuchi; Mingyu Son; Kazuyoshi Takayama; Masatoshi Iwamoto; Ikuro Sato; Toshio Narahashi; Akihiko Konagaya; Kunihiko Goto
Bead-like passage of chloride ions through ClC chloride channels.
Ryuzo Azuma; Tetsuji Kitagawa; Hiroshi Kobayashi; Akihiko Konagaya
Particle simulation approach for subcellular dynamics and interactions of biological molecules.

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All Publications

2006: Atsushi Suenaga; Noriaki Okimoto; Noriyuki Futatsugi; Yoshinori Hirano; Tetsu Narumi; Yousuke Ohno; Ryoko Yanai; Takatsugu Hirokawa; Toshikazu Ebisuzaki; Akihiko Konagaya; Makoto Taiji
Structure and dynamics of RNA polymerase II elongation complex.
Biochemical and biophysical research communications 2006;343(1):90-8.
2006: Atsushi Suenaga; Jay Z Yeh; Makoto Taiji; Akira Toyama; Hideo Takeuchi; Mingyu Son; Kazuyoshi Takayama; Masatoshi Iwamoto; Ikuro Sato; Toshio Narahashi; Akihiko Konagaya; Kunihiko Goto
Bead-like passage of chloride ions through ClC chloride channels.
Biophysical chemistry 2006;120(1):36-43.
2006: Ryuzo Azuma; Tetsuji Kitagawa; Hiroshi Kobayashi; Akihiko Konagaya
Particle simulation approach for subcellular dynamics and interactions of biological molecules.
BMC bioinformatics 2006;7 Suppl 4():S20.
2006: Yoshikazu Hasegawa; Motoaki Seki; Yoshiki Mochizuki; Naohiko Heida; Katsura Hirosawa; Naoki Okamoto; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kei Iida; Kisik Lee; Shigehiko Kanaya; Taku Demura; Kazuo Shinozaki; Akihiko Konagaya; Tetsuro Toyoda
A flexible representation of omic knowledge for thorough analysis of microarray data.
Plant methods 2006;2():5.
2005: Eli Kaminuma; Naohiko Heida; Yuko Tsumoto; Miki Nakazawa; Nobuharu Goto; Akihiko Konagaya; Minami Matsui; Tetsuro Toyoda
Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis.
Journal of bioinformatics and computational biology 2005;3(2):401-14.
2005: Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
Bioinformatics (Oxford, England) 2005;21(7):1154-63.
2005: Atsushi Suenaga; Naoki Takada; Mariko Hatakeyama; Mio Ichikawa; Xiaomei Yu; Kentaro Tomii; Noriaki Okimoto; Noriyuki Futatsugi; Tetsu Narumi; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya; Makoto Taiji
Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.
The Journal of biological chemistry 2005;280(2):1321-6.
2005: Kei Iida; Motoaki Seki; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Tetsuro Toyoda; Akihiko Konagaya; Kazuo Shinozaki
RARTF: database and tools for complete sets of Arabidopsis transcription factors.
DNA research : an international journal for rapid publication of reports on genes and genomes 2005;12(4):247-56.
2005: Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kei Iida; Motoaki Seki; Takashi Kuromori; Takuya Ito; Akihiko Konagaya; Tetsuro Toyoda; Kazuo Shinozaki
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
Nucleic acids research 2005;33(Database issue):D647-50.
2004: Naohiko Heida; Yoshikazu Hasegawa; Yoshiki Mochizuki; Katsura Hirosawa; Akihiko Konagaya; Tetsuro Toyoda
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i152-60.
2004: Shuhei Kimura; Takuji Kawasaki; Mariko Hatakeyama; Takashi Naka; Fumikazu Konishi; Akihiko Konagaya
OBIYagns: a grid-based biochemical simulator with a parameter estimator.
Bioinformatics (Oxford, England) 2004;20(10):1646-8.
2004: Mariko Hatakeyama; N Yumoto; X Yu; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase.
Oncogene 2004;23(29):5023-31.
2004: Eli Kaminuma; Naohiko Heida; Yuko Tsumoto; Naoki Yamamoto; Nobuharu Goto; Naoki Okamoto; Akihiko Konagaya; Minami Matsui; Tetsuro Toyoda
Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis.
The Plant journal : for cell and molecular biology 2004;38(2):358-65.
2004: Atsushi Suenaga; Anatoly Kiyatkin; Mariko Hatakeyama; Noriyuki Futatsugi; Noriaki Okimoto; Yoshinori Hirano; Tetsu Narumi; Atsushi Kawai; Ryutaro Susukita; Takahiro Koishi; Hideaki Furusawa; Kenji Yasuoka; Naoki Takada; Yousuke Ohno; Makoto Taiji; Toshikazu Ebisuzaki; Jan B Hoek; Akihiko Konagaya; Boris N Kholodenko
Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.
The Journal of biological chemistry 2004;279(6):4657-62.
2004: Kei Iida; Motoaki Seki; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Tetsuro Toyoda; Akihiko Konagaya; Kazuo Shinozaki
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences.
Nucleic acids research 2004;32(17):5096-103.
2004: Sumi Yoshikawa; Kenji Satou; Akihiko Konagaya
Drug interaction ontology (DIO) for inferences of possible drug-drug interactions.
Studies in health technology and informatics 2004;107(Pt 1):454-8.
2003: Jun Hoseki; Akihiro Okamoto; Naoki Takada; Atsushi Suenaga; Noriyuki Futatsugi; Akihiko Konagaya; Makoto Taiji; Takato Yano; Seiki Kuramitsu; Hiroyuki Kagamiyama
Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution.
Biochemistry 2003;42(49):14469-75.
2003: Mariko Hatakeyama; Shuhei Kimura; Takashi Naka; Takuji Kawasaki; Noriko Yumoto; Mio Ichikawa; Jae-Hoon Kim; Kazuki Saito; Mihoro Saeki; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling.
The Biochemical journal 2003;373(Pt 2):451-63.
2003: Atsushi Suenaga; Mariko Hatakeyama; Mio Ichikawa; Xiaomei Yu; Noriyuki Futatsugi; Tetsu Narumi; Kazuhiko Fukui; Takaho Terada; Makoto Taiji; Mikako Shirouzu; Shigeyuki Yokoyama; Akihiko Konagaya
Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides.
Biochemistry 2003;42(18):5195-200.
2003: Tetsuro Toyoda; Yoshiki Mochizuki; Akihiko Konagaya
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.
Bioinformatics (Oxford, England) 2003;19(3):437-8.
2003: Tetsuro Toyoda; Akihiko Konagaya
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.
Bioinformatics (Oxford, England) 2003;19(3):433-4.