Research Center for Transomics Medicine

Research Output 1994 2020

2009
8 Citations (Scopus)

Generation of a rat monoclonal antibody specific for Pax7

Harada, A., Okada, S., Saiwai, H., Aoki, M., Nakamura, M. & Ohkawa, Y., Dec 1 2009, In : Hybridoma. 28, 6, p. 451-453 3 p.

Research output: Contribution to journalArticle

Monoclonal Antibodies
Antibodies
Muscle Cells
Euchromatin
Ewing's Sarcoma
43 Citations (Scopus)

Large-scale proteomic analysis of tyrosine-phosphorylation induced by T-cell receptor or B-cell receptor activation reveals new signaling pathways

Matsumoto, M., Oyamada, K., Takahashi, H., Sato, T., Hatakeyama, S. & Nakayama, K., Jul 1 2009, In : Proteomics. 9, 13, p. 3549-3563 15 p.

Research output: Contribution to journalArticle

Phosphorylation
T-Cell Antigen Receptor
Proteomics
Tyrosine
B-Lymphocytes
45 Citations (Scopus)

Nucleolar structure and function are regulated by the deubiquitylating enzyme USP36

Endo, A., Matsumoto, M., Inada, T., Yamamoto, A., Nakayama, K. I., Kitamura, N. & Komada, M., Mar 1 2009, In : Journal of cell science. 122, 5, p. 678-686 9 p.

Research output: Contribution to journalArticle

Ubiquitination
Ribosomes
Enzymes
Basic Amino Acids
Nuclear Proteins
15 Citations (Scopus)

Production of a rat monoclonal antibody against Brg1

Ohkawa, Y., Harada, A., Nakamura, M., Yoshimura, S. & Tachibana, T., Dec 1 2009, In : Hybridoma. 28, 6, p. 463-466 4 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
Monoclonal Antibodies
Genes
Antibodies
Euchromatin

Specific features of transient Ras and sustained Rap1 activation

Ozaki, Y., Uda, S. & Kuroda, S., 2009, Systems Biology: the Challenge of Complexity Springer . p. 121-127

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

11 Citations (Scopus)

The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family

Goto, H., Watanabe, K., Araragi, N., Kageyama, R., Tanaka, K., Kuroki, Y., Toyoda, A., Hattori, M., Sakaki, Y., Fujiyama, A., Fukumaki, Y. & Shibata, H., Oct 12 2009, In : BMC Evolutionary Biology. 9, 1, 224.

Research output: Contribution to journalArticle

amino acid substitution
substitution
amino acid
gene
Pan troglodytes
2008
22 Citations (Scopus)

A High-Throughput and Solvent-free Method for Measurement of Natural Polyisoprene Content in Leaves by Fourier Transform Near Infrared Spectroscopy

Takeno, S., Bamba, T., Nakazawa, Y., Fukusaki, E., Okazawa, A. & Kobayashi, A., Dec 1 2008, In : Journal of Bioscience and Bioengineering. 106, 6, p. 537-540 4 p.

Research output: Contribution to journalArticle

Polyisoprenes
Near infrared spectroscopy
Near-Infrared Spectroscopy
Fourier Transform Infrared Spectroscopy
Least-Squares Analysis
18 Citations (Scopus)

Association study of polymorphisms in the neutral amino acid transporter genes SLC1A4, SLC1A5 and the glycine transporter genes SLC6A5, SLC6A9 with schizophrenia

Deng, X., Sagata, N., Takeuchi, N., Tanaka, M., Ninomiya, H., Iwata, N., Ozaki, N., Shibata, H. & Fukumaki, Y., Jul 18 2008, In : BMC Psychiatry. 8, 58.

Research output: Contribution to journalArticle

Neutral Amino Acid Transport Systems
Glycine Plasma Membrane Transport Proteins
Schizophrenia
Genes
Sample Size
155 Citations (Scopus)

Blue light-induced autophosphorylation of phototropin is a primary step for signaling

Inoue, S. I., Kinoshita, T., Matsumoto, M., Nakayama, K. I., Doi, M. & Shimazaki, K. I., Apr 8 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 14, p. 5626-5631 6 p.

Research output: Contribution to journalArticle

Phototropins
Phototropism
Chloroplasts
Light
Phosphotransferases
35 Citations (Scopus)

Dynamic regulation of ubiquitylation and deubiquitylation at the central spindle during cytokinesis

Mukai, A., Mizuno, E., Kobayashi, K., Matsumoto, M., Nakayama, K. I., Kitamura, N. & Komada, M., Apr 15 2008, In : Journal of Cell Science. 121, 8, p. 1325-1333 9 p.

Research output: Contribution to journalArticle

Cytokinesis
Ubiquitination
Proteins
Aurora Kinase B
SNARE Proteins
100 Citations (Scopus)

Heterozygous deletion of ITPR1, but not SUMF1, in spinocerebellar ataxia type 16

Iwaki, A., Kawano, Y., Miura, S., Shibata, H., Matsuse, D., Li, W., Furuya, H., Ohyagi, Y., Taniwaki, T., Kira, J. & Fukumaki, Y., Jan 1 2008, In : Journal of medical genetics. 45, 1, p. 32-35 4 p.

Research output: Contribution to journalArticle

Spinocerebellar Ataxias
Haploinsufficiency
Intergenic DNA
Gene Dosage
Real-Time Polymerase Chain Reaction
17 Citations (Scopus)

Integrated metabolite and gene expression profiling revealing phytochrome A regulation of polyamine biosynthesis of Arabidopsis thaliana

Jumtee, K., Bamba, T., Okazawa, A., Fukusaki, E. & Kobayashi, A., Apr 1 2008, In : Journal of Experimental Botany. 59, 6, p. 1187-1200 14 p.

Research output: Contribution to journalArticle

Phytochrome A
Polyamines
Gene Expression Profiling
phytochrome
polyamines
71 Citations (Scopus)
Phanerochaete
Benzoic Acid
Metabolomics
Metabolome
Proteome
2007
33 Citations (Scopus)

Association study of polymorphisms in the glutamate transporter genes SLC1A1, SLC1A3, and SLC1A6 with schizophrenia

Deng, X., Shibata, H., Takeuchi, N., Rachi, S., Sakai, M., Ninomiya, H., Iwata, N., Ozaki, N. & Fukumaki, Y., Apr 5 2007, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 144, 3, p. 271-278 8 p.

Research output: Contribution to journalArticle

Amino Acid Transport System X-AG
Schizophrenia
Genes
Haplotypes
Glutamate Receptors
1 Citation (Scopus)

Erratum: Mutation of the SNF2 family member Chd2 affects mouse development and survival (Journal of Cellular Physiology (2006) 209, (162-171))

Marfella, C. G. A., Ohkawa, Y., Coles, A. H., Garlick, D. S., Jones, S. N. & Imbalzano, A. N., Aug 1 2007, In : Journal of cellular physiology. 212, 2, 1 p.

Research output: Contribution to journalComment/debate

Physiology
8 Citations (Scopus)

Periploca sepium Bunge as a model plant for rubber biosynthesis study

Bamba, T., Sando, T., Miyabashira, A., Gyokusen, K., Nakazawa, Y., Su, Y., Fukusaki, E. & Kobayashi, A., Jan 1 2007, In : Zeitschrift fur Naturforschung - Section C Journal of Biosciences. 62, 7-8, p. 579-582 4 p.

Research output: Contribution to journalArticle

Periploca
Sepia
Biosynthesis
Rubber
Molecular Weight
109 Citations (Scopus)

The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling

Dacwag, C. S., Ohkawa, Y., Pal, S., Sif, S. & Imbalzano, A. N., Jan 1 2007, In : Molecular and cellular biology. 27, 1, p. 384-394 11 p.

Research output: Contribution to journalArticle

Protein-Arginine N-Methyltransferases
Chromatin Assembly and Disassembly
Muscle Development
Histones
Adenosine Triphosphate
2006
77 Citations (Scopus)

Alteration of intra-pancreatic target-organ specificity by abrogation of Aire in NOD mice

Niki, S., Oshikawa, K., Mouri, Y., Hirota, F., Matsushima, A., Yano, M., Han, H., Bando, Y., Izumi, K., Matsumoto, M., Nakayama, K. I., Kuroda, N. & Matsumoto, M., May 1 2006, In : Journal of Clinical Investigation. 116, 5, p. 1292-1301 10 p.

Research output: Contribution to journalArticle

Organ Specificity
Inbred NOD Mouse
Acinar Cells
Islets of Langerhans
Thymus Gland
42 Citations (Scopus)

Analysis of CDMA systems that are characterized by eigenvalue spectrum

Takeda, K., Uda, S. & Kabashima, Y., 2006, In : Europhysics Letters. 76, p. 1193-1199

Research output: Contribution to journalArticle

25 Citations (Scopus)

Association study of polymorphisms in the GluR7, KA1 and KA2 kainate receptor genes (GRIK3, GRIK4, GRIK5) with schizophrenia

Shibata, H., Aramaki, T., Sakai, M., Ninomiya, H., Tashiro, N., Iwata, N., Ozaki, N. & Fukumaki, Y., Jan 30 2006, In : Psychiatry research. 141, 1, p. 39-51 13 p.

Research output: Contribution to journalArticle

Kainic Acid Receptors
Single Nucleotide Polymorphism
Schizophrenia
Genes
Haplotypes

Involvement of ubiquitin-proteasome system in polyglutamine disease

Matsumoto, M., Aug 1 2006, In : Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.. 51, 10 Suppl, p. 1428-1432 5 p.

Research output: Contribution to journalReview article

Nerve Tissue Proteins
Ubiquitin-Conjugating Enzymes
Repressor Proteins
Intranuclear Inclusion Bodies
Ubiquitin-Protein Ligases
15 Citations (Scopus)

Metabolic fingerprinting and profiling of Arabidopsis thaliana leaf and its cultured cells T87 by GC/MS

Fukusaki, E., Jumtee, K., Bamba, T., Yamaji, T. & Kobayashi, A., Jan 1 2006, In : Zeitschrift fur Naturforschung - Section C Journal of Biosciences. 61, 3-4, p. 267-272 6 p.

Research output: Contribution to journalArticle

Cell culture
Arabidopsis
Cultured Cells
Suspensions
Cell Culture Techniques
59 Citations (Scopus)

Mutation of the SNF2 family member Chd2 affects mouse development and survival

Marfella, C. G. A., Ohkawa, Y., Coles, A. H., Garlick, D. S., Jones, S. N. & Imbalzano, A. N., Oct 1 2006, In : Journal of cellular physiology. 209, 1, p. 162-171 10 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
DNA-Binding Proteins
Mutation
AT Rich Sequence
DNA Helicases
7 Citations (Scopus)

Technical problems and practical operations in plant metabolomics

Bamba, T. & Fukusaki, E., Aug 31 2006, In : Journal of Pesticide Science. 31, 3, p. 300-304 5 p.

Research output: Contribution to journalReview article

Metabolomics
metabolomics
Informatics
data analysis
Research Design
24 Citations (Scopus)

The contactin 4 gene locus at 3p26 is a candidate gene of SCA16

Miura, S., Shibata, H., Furuya, H., Ohyagi, Y., Osoegawa, M., Miyoshi, Y., Matsunaga, H., Shibata, A., Matsumoto, N., Iwaki, A., Taniwaki, T., Kikuchi, H., Kira, J. & Fukumaki, Y., Oct 1 2006, In : Neurology. 67, 7, p. 1236-1241 6 p.

Research output: Contribution to journalArticle

Contactins
Spinocerebellar Ataxias
Genes
Mutation
3' Untranslated Regions
2005
18 Citations (Scopus)
Flavonoids
Methylation
Liquid chromatography
Liquid Chromatography
Isotopes
38 Citations (Scopus)

Association study of polymorphisms in synaptic vesicle-associated genes, SYN2 and CPLX2, with schizophrenia

Lee, H. J., Song, J. Y., Kim, J. W., Jin, S. Y., Hong, M. S., Park, J. K., Chung, J. H., Shibata, H. & Fukumaki, Y., Aug 31 2005, In : Behavioral and Brain Functions. 1, 15.

Research output: Contribution to journalArticle

Synapsins
Synaptic Vesicles
Schizophrenia
Genes
Haplotypes
9 Citations (Scopus)

Characterization of recombinant amyloidogenic chicken cystatin mutant I66Q expressed in yeast

He, J., Song, Y., Ueyama, N., Harada, A., Azakami, H. & Kato, A., Apr 1 2005, In : Journal of biochemistry. 137, 4, p. 477-485 9 p.

Research output: Contribution to journalArticle

Yeast
Yeasts
Cystatins
Monomers
Dimers
4 Citations (Scopus)

Effect of EPS1 gene deletion in Saccharomyces cerevisiae on the secretion of foreign proteins which have disulfide bridges

He, J., Sakamoto, T., Song, Y., Saito, A., Harada, A., Azakami, H. & Kato, A., Apr 25 2005, In : FEBS Letters. 579, 11, p. 2277-2283 7 p.

Research output: Contribution to journalArticle

Gene Deletion
Cystatins
Muramidase
Disulfides
Yeast
71 Citations (Scopus)

Genomewide high-density SNP linkage analysis of 236 Japanese families supports the existence of schizophrenia susceptibility loci on chromosomes 1p, 14q, and 20p

Arinami, T., Ohtsuki, T., Ishiguro, H., Ujike, H., Tanaka, Y., Morita, Y., Mineta, M., Takeichi, M., Yamada, S., Imamura, A., Ohara, K., Shibuya, H., Ohara, K., Suzuki, Y., Muratake, T., Kaneko, N., Someya, T., Inada, T., Yoshikawa, T., Toyota, T. & 32 others, Yamada, K., Kojima, T., Takahashi, S., Osamu, O., Shinkai, T., Nakamura, M., Fukuzako, H., Hashiguchi, T., Niwa, S. I., Ueno, T., Tachikawa, H., Hori, T., Asada, T., Nanko, S., Kunugi, H., Hashimoto, R., Ozaki, N., Iwata, N., Harano, M., Arai, H., Ohnuma, T., Kusumi, I., Koyama, T., Yoneda, H., Fukumaki, Y., Shibata, H., Kaneko, S., Higuchi, H., Yasui-Furukori, N., Numachi, Y., Itokawa, M. & Okazaki, Y., Dec 2005, In : American journal of human genetics. 77, 6, p. 937-944 8 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Schizophrenia
Chromosomes
Siblings
Chromosome Mapping
21 Citations (Scopus)

Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia

Makino, C., Shibata, H., Ninomiya, H., Tashiro, N. & Fukumaki, Y., Sep 1 2005, In : Psychiatric Genetics. 15, 3, p. 215-221 7 p.

Research output: Contribution to journalArticle

N-Methyl-D-Aspartate Receptors
Single Nucleotide Polymorphism
Schizophrenia
Genes
Gene Frequency
144 Citations (Scopus)

Large-scale analysis of the human ubiquitin-related proteome

Matsumoto, M., Hatakeyama, S., Oyamada, K., Oda, Y., Nishimura, T. & Nakayama, K. I., Nov 1 2005, In : Proteomics. 5, 16, p. 4145-4151 7 p.

Research output: Contribution to journalArticle

Proteome
Ubiquitin
Proteins
Ubiquitination
Ribosome Subunits
43 Citations (Scopus)

Mammalian E4 is required for cardiac development and maintenance of the nervous system

Kaneko-Oshikawa, C., Nakagawa, T., Yamada, M., Yoshikawa, H., Matsumoto, M., Yada, M., Hatakeyama, S., Nakayama, K. & Nakayama, K. I., Dec 1 2005, In : Molecular and cellular biology. 25, 24, p. 10953-10964 12 p.

Research output: Contribution to journalArticle

Nervous System
Maintenance
Endoplasmic Reticulum Stress
Myocardium
Enzymes
8 Citations (Scopus)

Mapping of ubiquitination sites on target proteins

Hatakeyama, S., Matsumoto, M. & Nakayama, K., Jan 1 2005, In : Methods in enzymology. 399, p. 277-286 10 p., 19.

Research output: Contribution to journalReview article

Ubiquitinated Proteins
Ubiquitination
Lysine
Mass Spectrometry
Polyubiquitin
50 Citations (Scopus)
Phanerochaete
Hydroxylation
Benzoic Acid
Benzoates
Fungi
191 Citations (Scopus)

MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex

De La Serna, I. L., Ohkawa, Y., Berkes, C. A., Bergstrom, D. A., Dacwag, C. S., Tapscott, S. J. & Imbalzano, A. N., May 1 2005, In : Molecular and cellular biology. 25, 10, p. 3997-4009 13 p.

Research output: Contribution to journalArticle

Myogenin
Chromatin Assembly and Disassembly
DNA
Muscle Proteins
Enzymes
7 Citations (Scopus)

Purification, primary structures and evolution of coagulant proteases from Deinagkistrodon actus venom

Nikandrov, N. N., Deshimaru, M., Tani, A., Chijiwa, T., Shibata, H., Chang, C. C., Fukumaki, Y., Ito, T. & Ohno, M., Dec 15 2005, In : Toxicon. 46, 8, p. 907-917 11 p.

Research output: Contribution to journalArticle

Coagulants
Venoms
Purification
Peptide Hydrolases
Complementary DNA
36 Citations (Scopus)

Stable isotope dilution-based accurate comparative quantification of nitrogen-containing metabolites in Arabidopsis thaliana T87 cells using in vivo 15N-isotope enrichment

Kim, J. K., Harada, K., Bamba, T., Fukusaki, E. I. & Kobayashi, A., Sep 1 2005, In : Bioscience, Biotechnology and Biochemistry. 69, 7, p. 1331-1340 10 p.

Research output: Contribution to journalArticle

S-Adenosylhomocysteine
Metabolites
Arabidopsis
Isotopes
S-Adenosylmethionine
11 Citations (Scopus)

Statistical mechanical development of a sparse Bayesian classifier

Uda, S. & Kabashima, Y., 2005, In : Journal of the Physical Society of Japan. 74, p. 2233-2242

Research output: Contribution to journalArticle

68 Citations (Scopus)

Structural characterization of α-terminal group of natural rubber. 1. Decomposition of branch-points by lipase and phosphatase treatments

Tarachiwin, L., Sakdapipanich, J., Ute, K., Kitayama, T., Bamba, T., Fukusaki, E. I., Kobayashi, A. & Tanaka, Y., Jul 1 2005, In : Biomacromolecules. 6, 4, p. 1851-1857 7 p.

Research output: Contribution to journalArticle

Phosphatases
Rubber
Lipases
Lipase
Phosphoric Monoester Hydrolases
17 Citations (Scopus)

The yeast eIF4E-associated protein Eap1p attenuates GCN4 translation upon TOR-inactivation

Matsuo, R., Kubota, H., Obata, T., Kito, K., Ota, K., Kitazono, T., Ibayashi, S., Sasaki, T., Iida, M. & Ito, T., Apr 25 2005, In : FEBS Letters. 579, 11, p. 2433-2438 6 p.

Research output: Contribution to journalArticle

Sirolimus
Yeast
Yeasts
Proteins
Amino Acids
2004
6 Citations (Scopus)

A BP-Based Algorithm for Performing Bayesian Inference in Large Perceptron-Type Networks

Kabashima, Y. & Uda, S., 2004, International Conference on Algorithmic Learning Theory. p. 479-493

Research output: Chapter in Book/Report/Conference proceedingConference contribution

39 Citations (Scopus)

Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia

Deng, X., Shibata, H., Ninomiya, H., Tashiro, N., Iwata, N., Ozaki, N. & Fukumaki, Y., Aug 6 2004, In : BMC Psychiatry. 4, 21.

Research output: Contribution to journalArticle

Excitatory Amino Acid Transporter 2
Schizophrenia
Haplotypes
Genes
Single Nucleotide Polymorphism
318 Citations (Scopus)

Cytoplasmic ubiquitin ligase KPC regulates proteolysis of p27Kip1 at G1 phase

Kamura, T., Hara, T., Matsumoto, M., Ishida, N., Okumura, F., Hatakeyama, S., Yoshida, M., Nakayama, K. & Nakayama, K., Dec 1 2004, In : Nature Cell Biology. 6, 12, p. 1229-1235 7 p.

Research output: Contribution to journalArticle

Ubiquitination
G1 Phase
Ligases
Ubiquitin
Proteolysis
49 Citations (Scopus)
Dodecanol
Phanerochaete
Cytochromes
Fungi
Piperonyl Butoxide
70 Citations (Scopus)

Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones

Hatakeyama, S., Matsumoto, M., Yada, M. & Nakayama, K., Jun 1 2004, In : Genes to Cells. 9, 6, p. 533-548 16 p.

Research output: Contribution to journalArticle

Molecular Chaperones
Ubiquitin-Protein Ligases
Proteins
Two-Hybrid System Techniques
Proteolysis
6 Citations (Scopus)

Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data

Tsuda, K., Uda, S., Kin, T. & Asai, K., 2004, In : Neural Processing Letters. 19, p. 63-72

Research output: Contribution to journalArticle

113 Citations (Scopus)

Molecular clearance of ataxin-3 is regulated by a mammalian E4

Matsumoto, M., Yada, M., Hatakeyama, S., Ishimoto, H., Tanimura, T., Tsuji, S., Kakizuka, A., Kitagawa, M. & Nakayama, K. I., Feb 11 2004, In : EMBO Journal. 23, 3, p. 659-669 11 p.

Research output: Contribution to journalArticle

Machado-Joseph Disease
Degradation
Ubiquitin
Gene therapy
Ubiquitination
42 Citations (Scopus)

Positive associations of polymorphisms in the metabotropic glutamate receptor type 8 gene (GRM8) with schizophrenia

Takaki, H., Kikuta, R., Shibata, H., Ninomiya, H., Tashiro, N. & Fukumaki, Y., Jul 1 2004, In : American Journal of Medical Genetics - Neuropsychiatric Genetics. 128 B, 1, p. 6-14 9 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Schizophrenia
Genes
Linkage Disequilibrium
Haplotypes
88 Citations (Scopus)

U-box protein carboxyl terminus of Hsc70-interacting protein (CHIP) mediates poly-ubiquitylation preferentially on four-repeat Tau and is involved in neurodegeneration of tauopathy

Hatakeyama, S., Matsumoto, M., Kamura, T., Murayama, M., Chui, D. H., Planel, E., Takahashi, R., Nakayama, K. I. & Takashima, A., Oct 1 2004, In : Journal of Neurochemistry. 91, 2, p. 299-307 9 p.

Research output: Contribution to journalArticle

HSC70 Heat-Shock Proteins
Tauopathies
Ubiquitination
Neurofibrillary Tangles
Proteins