Research Center for Transomics Medicine

Research Output 1994 2020

2012
27 Citations (Scopus)

Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin

Oshikawa, K., Matsumoto, M., Oyamada, K. & Nakayama, K. I., Feb 3 2012, In : Journal of Proteome Research. 11, 2, p. 796-807 12 p.

Research output: Contribution to journalArticle

Ubiquitination
Proteome
Ubiquitin
Lysine
Proteins
19 Citations (Scopus)

Surf4 modulates STIM1-dependent calcium entry

Fujii, Y., Shiota, M., Ohkawa, Y., Baba, A., Wanibuchi, H., Kinashi, T., Kurosaki, T. & Baba, Y., Jun 15 2012, In : Biochemical and Biophysical Research Communications. 422, 4, p. 615-620 6 p.

Research output: Contribution to journalArticle

Endoplasmic Reticulum
Cluster Analysis
Carrier Proteins
B-Lymphocytes
Cell Membrane
2011
112 Citations (Scopus)

A metabolomic approach to lung cancer

Hori, S., Nishiumi, S., Kobayashi, K., Shinohara, M., Hatakeyama, Y., Kotani, Y., Hatano, N., Maniwa, Y., Nishio, W., Bamba, T., Fukusaki, E., Azuma, T., Takenawa, T., Nishimura, Y. & Yoshida, M., Nov 1 2011, In : Lung Cancer. 74, 2, p. 284-292 9 p.

Research output: Contribution to journalArticle

Metabolomics
Lung Neoplasms
Serum
Healthy Volunteers
Biomarkers
7 Citations (Scopus)

CDase is a pan-ceramidase in Drosophila

Yuan, C., Rao, R. P., Jesmin, N., Bamba, T., Nagashima, K., Pascual, A., Preat, T., Fukusaki, E., Acharya, U. & Acharya, J. K., Jan 1 2011, In : Molecular biology of the cell. 22, 1, p. 33-43 11 p.

Research output: Contribution to journalArticle

Ceramidases
Alkaline Ceramidase
Drosophila
Ceramides
Persuasive Communication
22 Citations (Scopus)

Chromatin accessibility and transcription factor binding at the PPARγ2 promoter during adipogenesis is protein kinase A-dependent

Xiao, H., LeBlanc, S. E., Wu, Q., Konda, S., Salma, N., Marfella, C. G. A., Ohkawa, Y. & Imbalzano, A. N., Jan 1 2011, In : Journal of cellular physiology. 226, 1, p. 86-93 8 p.

Research output: Contribution to journalArticle

Adipogenesis
PPAR gamma
Cyclic AMP-Dependent Protein Kinases
Adipocytes
Chromatin
38 Citations (Scopus)

Development of a polar lipid profiling method by supercritical fluid chromatography/mass spectrometry

Lee, J. W., Yamamoto, T., Uchikata, T., Matsubara, A., Fukusaki, E. & Bamba, T., Dec 1 2011, In : Journal of Separation Science. 34, 24, p. 3553-3560 8 p.

Research output: Contribution to journalArticle

Sphingosines
Lipids
Mass spectrometry
Phosphatidylinositols
Acids
22 Citations (Scopus)

Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue

Okada, S., Saiwai, H., Kumamaru, H., Kubota, K., Harada, A., Yamaguchi, M., Iwamoto, Y. & Ohkawa, Y., Feb 1 2011, In : Journal of cellular physiology. 226, 2, p. 552-558 7 p.

Research output: Contribution to journalArticle

Nerve Tissue
Neurology
Sorting
Neuroglia
Nucleoproteins
51 Citations (Scopus)

Functional analyses of the activation loop of phototropin2 in Arabidopsis

Inoue, S. I., Matsushita, T., Tomokiyo, Y., Matsumoto, M., Nakayama, K. I., Kinoshita, T. & Shimazaki, K. I., May 1 2011, In : Plant physiology. 156, 1, p. 117-128 12 p.

Research output: Contribution to journalArticle

Activation Analysis
Arabidopsis
serine
Serine
blue light
4 Citations (Scopus)

Generation of a rat monoclonal antibody specific for Hsp72

Tanaka, M., Shiota, M., Okada, S., Harada, A., Odawara, J., Mun, S., Iwao, H. & Ohkawa, Y., Aug 1 2011, In : Hybridoma. 30, 4, p. 397-400 4 p.

Research output: Contribution to journalArticle

HSP70 Heat-Shock Proteins
Monoclonal Antibodies
Cytoplasm
Heat-Shock Response
Proteins
10 Citations (Scopus)

Partial SPAST and DPY30 deletions in a Japanese spastic paraplegia type 4 family

Miura, S., Shibata, H., Kida, H., Noda, K., Toyama, T., Iwasaki, N., Iwaki, A., Ayabe, M., Aizawa, H., Taniwaki, T. & Fukumaki, Y., Feb 1 2011, In : Neurogenetics. 12, 1, p. 25-31 7 p.

Research output: Contribution to journalArticle

Genes
Exons
Pedigree
Introns
Mutation
16 Citations (Scopus)

Plasma gelsolin facilitates interaction between β2 glycoprotein I and α5β1 integrin

Bohgaki, M., Matsumoto, M., Atsumi, T., Kondo, T., Yasuda, S., Horita, T., Nakayama, K. I., Okumura, F., Hatakeyama, S. & Koike, T., Jan 1 2011, In : Journal of Cellular and Molecular Medicine. 15, 1, p. 141-151 11 p.

Research output: Contribution to journalArticle

Gelsolin
Integrins
Glycoproteins
Antiphospholipid Antibodies
Antiphospholipid Syndrome
13 Citations (Scopus)

Positive association of Phencyclidine-responsive genes, PDE4A and PLAT, with schizophrenia

Deng, X., Takaki, H., Wang, L., Kuroki, T., Nakahara, T., Hashimoto, K., Ninomiya, H., Arinami, T., Inada, T., Ujike, H., Itokawa, M., Tochigi, M., Watanabe, Y., Someya, T., Kunugi, H., Iwata, N., Ozaki, N., Shibata, H. & Fukumaki, Y., Dec 1 2011, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 156, 7, p. 850-858 9 p.

Research output: Contribution to journalArticle

Phencyclidine
Schizophrenia
Genes
Single Nucleotide Polymorphism
Haplotypes
68 Citations (Scopus)

Practical non-targeted gas chromatography/mass spectrometry-based metabolomics platform for metabolic phenotype analysis

Tsugawa, H., Bamba, T., Shinohara, M., Nishiumi, S., Yoshida, M. & Fukusaki, E., Sep 1 2011, In : Journal of Bioscience and Bioengineering. 112, 3, p. 292-298 7 p.

Research output: Contribution to journalArticle

Metabolomics
Gas chromatography
Gas Chromatography
Gas Chromatography-Mass Spectrometry
Libraries
44 Citations (Scopus)

Predication of Japanese green tea (Sen-cha) ranking by volatile profiling using gas chromatography mass spectrometry and multivariate analysis

Jumtee, K., Komura, H., Bamba, T. & Fukusaki, E., Sep 1 2011, In : Journal of Bioscience and Bioengineering. 112, 3, p. 252-255 4 p.

Research output: Contribution to journalArticle

Tea
Gas chromatography
Gas Chromatography-Mass Spectrometry
Mass spectrometry
Multivariate Analysis
16 Citations (Scopus)

Proteome of ubiquitin/MVB pathway: Possible involvement of iron-induced ubiquitylation of transferrin receptor in lysosomal degradation

Tachiyama, R., Ishikawa, D., Matsumoto, M., Nakayama, K. I., Yoshimori, T., Yokota, S., Himeno, M., Tanaka, Y. & Fujita, H., Apr 1 2011, In : Genes to Cells. 16, 4, p. 448-466 19 p.

Research output: Contribution to journalArticle

Multivesicular Bodies
Transferrin Receptors
Ubiquitination
Proteome
Ubiquitin
49 Citations (Scopus)
Neurites
Proteins
Neurons
Hereditary Spastic Paraplegia
Membranes
18 Citations (Scopus)

Sphingosine kinases and their metabolites modulate endolysosomal trafficking in photoreceptors

Yonamine, I., Bamba, T., Nirala, N. K., Jesmin, N., Kosakowska-Cholody, T., Nagashima, K., Fukusaki, E., Acharya, J. K. & Acharya, U., Feb 21 2011, In : Journal of Cell Biology. 192, 4, p. 557-567 11 p.

Research output: Contribution to journalArticle

Rhodopsin
Membrane Proteins
Transient Receptor Potential Channels
Retinal Degeneration
Intracellular Membranes
20 Citations (Scopus)

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Odawara, J., Harada, A., Yoshimi, T., Maehara, K., Tachibana, T., Okada, S., Akashi, K. & Ohkawa, Y., Oct 20 2011, In : BMC Genomics. 12, 516.

Research output: Contribution to journalArticle

RNA Polymerase II
Phosphorylation
Genome
Messenger RNA
Genes
18 Citations (Scopus)

TRIM8 regulates Nanog via Hsp90β-mediated nuclear translocation of STAT3 in embryonic stem cells

Okumura, F., Okumura, A. J., Matsumoto, M., Nakayama, K. I. & Hatakeyama, S., Oct 1 2011, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1813, 10, p. 1784-1792 9 p.

Research output: Contribution to journalArticle

Embryonic Stem Cells
Fingers
Down-Regulation
Proteins
2010
23 Citations (Scopus)

A quantitative image cytometry technique for time series or population analyses of signaling networks

Ozaki, Y. I., Uda, S., Saito, T. H., Chung, J., Kubota, H. & Kuroda, S., Sep 10 2010, In : PloS one. 5, 4, e9955.

Research output: Contribution to journalArticle

Image Cytometry
Cell signaling
Time series
time series analysis
Systems Biology
6 Citations (Scopus)

A rat monoclonal antibody against the chromatin remodeling factor CHD5

Yoshimura, S., Yoshimi, T., Ohkawa, Y., Azuma, M. & Tachibana, T., Feb 1 2010, In : Hybridoma. 29, 1, p. 63-66 4 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
DNA-Binding Proteins
Monoclonal Antibodies
Immunoblotting
Antibodies
14 Citations (Scopus)

Comparative analysis of human Src-family kinase substrate specificity in vitro

Takeda, H., Kawamura, Y., Miura, A., Mori, M., Wakamatsu, A., Yamamoto, J. I., Isogai, T., Matsumoto, M., Nakayama, K., Natsume, T., Nomura, N. & Goshima, N., Nov 5 2010, In : Journal of Proteome Research. 9, 11, p. 5982-5993 12 p.

Research output: Contribution to journalArticle

src-Family Kinases
Substrate Specificity
Phosphorylation
Substrates
Signal transduction
17 Citations (Scopus)

Contribution of mevalonate and methylerythritol phosphate pathways to polyisoprenoid biosynthesis in the rubber-producing plant Eucommia ulmoides oliver

Bamba, T., Murayoshi, M., Gyoksen, K., Nakazawa, Y., Okumoto, H., Katto, H., Fukusaki, E. & Kobayashi, A., Jan 1 2010, In : Zeitschrift fur Naturforschung - Section C Journal of Biosciences. 65 C, 5-6, p. 363-372 10 p.

Research output: Contribution to journalArticle

Eucommiaceae
Mevalonic Acid
Biosynthesis
Rubber
Phosphates
46 Citations (Scopus)

Fbxo45, a novel ubiquitin ligase, regulates synaptic activity

Tada, H., Okano, H. J., Takagi, H., Shibata, S., Yao, I., Matsumoto, M., Saiga, T., Nakayama, K. I., Kashima, H., Takahashi, T., Setou, M. & Okano, H., Feb 5 2010, In : Journal of Biological Chemistry. 285, 6, p. 3840-3849 10 p.

Research output: Contribution to journalArticle

Ligases
Ubiquitin
Synapses
Neurons
Degradation
4 Citations (Scopus)

Generation of a rat monoclonal antibody specific for Chd2

Harada, A., Yoshimura, S., Odawara, J., Azuma, M., Okada, S., Nakamura, M., Tachibana, T. & Ohkawa, Y., Apr 1 2010, In : Hybridoma. 29, 2, p. 173-177 5 p.

Research output: Contribution to journalArticle

Monoclonal Antibodies
Gene Expression
Euchromatin
Chromatin Assembly and Disassembly
Antibodies
6 Citations (Scopus)

Generation of a rat monoclonal antibody specific for heat shock cognate protein 70

Shiota, M., Saiwai, H., Mun, S., Harada, A., Okada, S., Odawara, J., Tanaka, M., Iwao, H. & Ohkawa, Y., Oct 1 2010, In : Hybridoma. 29, 5, p. 453-456 4 p.

Research output: Contribution to journalArticle

HSC70 Heat-Shock Proteins
Monoclonal Antibodies
Cytoplasm
Molecular Chaperones
Antibodies
5 Citations (Scopus)

High-throughput and highly sensitive analysis method for polyisoprene in plants by pyrolysis-gas chromatography/mass spectrometry

Takeno, S., Bamba, T., Nakazawa, Y., Fukusaki, E., Okazawa, A. & Kobayashi, A., Feb 5 2010, In : Bioscience, Biotechnology and Biochemistry. 74, 1, p. 13-17 5 p.

Research output: Contribution to journalArticle

Polyisoprenes
Gas chromatography
Gas Chromatography-Mass Spectrometry
Mass spectrometry
coenzyme Q10
19 Citations (Scopus)

Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress

Hayakawa, H., Fujikane, A., Ito, R., Matsumoto, M., Nakayama, K. & Sekiguchi, M., Dec 10 2010, In : Biochemical and Biophysical Research Communications. 403, 2, p. 220-224 5 p.

Research output: Contribution to journalArticle

Oxidative stress
Heterogeneous-Nuclear Ribonucleoproteins
Oxidative Stress
RNA
Hydrogen Peroxide

Monoclonal antibodies 2F12H4 and 3C3F1 against mouse Pax7

Ohkawa, Y., Feb 1 2010, In : Hybridoma. 29, 1, 1 p.

Research output: Contribution to journalShort survey

Monoclonal Antibodies

Monoclonal antibodies 6D2 and 8H3 against mouse Chd2

Ohkawa, Y., Jun 1 2010, In : Hybridoma. 29, 3, 1 p.

Research output: Contribution to journalShort survey

Monoclonal Antibodies

Monoclonal antibody 1E2G4 against mouse Myf5

Ohkawa, Y., Feb 1 2010, In : Hybridoma. 29, 1, 1 p.

Research output: Contribution to journalShort survey

Monoclonal Antibodies

Monoclonal antibody 1H7A10 against mouse Brm

Ohkawa, Y., Feb 1 2010, In : Hybridoma. 29, 1, 1 p.

Research output: Contribution to journalShort survey

Monoclonal Antibodies

Monoclonal antibody 8E3 against mouse Dhx9/NDHII/RHA

Ohkawa, Y., Jun 1 2010, In : Hybridoma. 29, 3, 1 p.

Research output: Contribution to journalShort survey

Monoclonal Antibodies
3 Citations (Scopus)

Monoclonal antibody specific for Dhx9/NDHII/RHA

Kotani, M., Harada, A., Odawara, J., Azuma, M., Okada, S., Nishiyama, Y., Nakamura, M., Tachibana, T. & Ohkawa, Y., Jun 1 2010, In : Hybridoma. 29, 3, p. 259-261 3 p.

Research output: Contribution to journalArticle

Monoclonal Antibodies
RNA Helicases
Antibodies
Proteins
Adenosine Triphosphate
20 Citations (Scopus)

Myogenic microRNA expression requires ATP-dependent chromatin remodeling enzyme function

Mallappa, C., Nasipak, B. T., Etheridge, L., Androphy, E. J., Jones, S. N., Sagerström, C. G., Ohkawa, Y. & Imbalzano, A. N., Jul 1 2010, In : Molecular and cellular biology. 30, 13, p. 3176-3186 11 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
MicroRNAs
Adenosine Triphosphate
Enzymes
Chromatin
11 Citations (Scopus)
Connexin 43
Lysosomes
Half-Life
Ubiquitination
Gap Junctions
6 Citations (Scopus)

Ossification of the posterior longitudinal ligament of the lumbar spine: A case series

Okada, S., Maeda, T., Saiwai, H., Ohkawa, Y., Shiba, K. & Iwamoto, Y., Nov 1 2010, In : Neurosurgery. 67, 5, p. 1311-1318 8 p.

Research output: Contribution to journalArticle

Ossification of Posterior Longitudinal Ligament
Pathologic Constriction
Ossification of the posterior longitudinal ligament of the spine
Osteogenesis
Spine
26 Citations (Scopus)

Phosphorylation of the chromodomain changes the binding specificity of Cbx2 for methylated histone H3

Hatano, A., Matsumoto, M., Higashinakagawa, T. & Nakayama, K. I., Jun 18 2010, In : Biochemical and Biophysical Research Communications. 397, 1, p. 93-99 7 p.

Research output: Contribution to journalArticle

Phosphorylation
Histones
Chromatin
Histone Code
Lysine
5 Citations (Scopus)

Production of a rat monoclonal antibody specific for Myf5

Harada, A., Okada, S., Odawara, J., Kumamaru, H., Saiwai, H., Aoki, M., Nakamura, M., Nishiyama, Y. & Ohkawa, Y., Feb 1 2010, In : Hybridoma. 29, 1, p. 59-62 4 p.

Research output: Contribution to journalArticle

Myogenic Regulatory Factors
Myoblasts
Monoclonal Antibodies
Helix-Loop-Helix Motifs
Myogenin
24 Citations (Scopus)

Pyrolysis GC-MS-based metabolite fingerprinting for quality evaluation of commercial Angelica acutiloba roots

Tianniam, S., Bamba, T. & Fukusaki, E., Jan 1 2010, In : Journal of Bioscience and Bioengineering. 109, 1, p. 89-93 5 p.

Research output: Contribution to journalArticle

Angelica
Discriminant Analysis
Discriminant analysis
Metabolites
Least-Squares Analysis
5 Citations (Scopus)

Rat monoclonal antibody specific for MyoD

Harada, A., Ohkawa, Y., Ao, S., Odawara, J., Okada, S., Azuma, M., Nishiyama, Y., Nakamura, M. & Tachibana, T., Jun 1 2010, In : Hybridoma. 29, 3, p. 255-258 4 p.

Research output: Contribution to journalArticle

Skeletal Muscle
Monoclonal Antibodies
Helix-Loop-Helix Motifs
Myogenic Regulatory Factors
Myoblasts
1 Citation (Scopus)

Rat monoclonal antibody specific for the chromatin remodeling factor, CHD1

Yoshimura, S., Harada, A., Odawara, J., Azuma, M., Okada, S., Nakamura, M., Ohkawa, Y. & Tachibana, T., Jun 1 2010, In : Hybridoma. 29, 3, p. 237-240 4 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
Monoclonal Antibodies
Mammals
Chromatin
Adenosine Triphosphate
97 Citations (Scopus)

The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury

Saiwai, H., Ohkawa, Y., Yamada, H., Kumamaru, H., Harada, A., Okano, H., Yokomizo, T., Iwamoto, Y. & Okada, S., May 2010, In : American Journal of Pathology. 176, 5, p. 2352-2366 15 p.

Research output: Contribution to journalArticle

Leukotriene B4
Neutrophil Infiltration
Spinal Cord Injuries
Leukotriene B4 Receptors
Leukocytes
2009
6 Citations (Scopus)

An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites

Oishi, T., Tanaka, K. I., Hashimoto, T., Shinbo, Y., Jumtee, K., Bamba, T., Fukusaki, E., Suzuki, H., Shibata, D., Takahashi, H., Asahi, H., Kurokawa, K., Nakamura, Y., Hirai, A., Nakamura, K., Altaf-Ul-Amin, M. & Kanaya, S., 2009, In : Plant Biotechnology. 26, 1, p. 167-174 8 p.

Research output: Contribution to journalArticle

Metabolomics
Databases
metabolites
metabolomics
prediction
8 Citations (Scopus)

Association analysis of the glutamic acid decarboxylase 2 and the glutamine synthetase genes (GAD2, GLUL) with schizophrenia

Arai, S., Shibata, H., Sakai, M., Ninomiya, H., Lwata, N., Ozaki, N. & Fukumaki, Y., Feb 1 2009, In : Psychiatric Genetics. 19, 1, p. 6-13 8 p.

Research output: Contribution to journalArticle

Glutamate Decarboxylase
Schizophrenia
Genes
Single Nucleotide Polymorphism
Haplotypes
93 Citations (Scopus)
Electrospray ionization
Plant Growth Regulators
Liquid chromatography
Liquid Chromatography
quantitative analysis
22 Citations (Scopus)

Does ossification of the posterior longitudinal ligament affect the neurological outcome after traumatic cervical cord injury?

Okada, S., Maeda, T., Ohkawa, Y., Harimaya, K., Saiwai, H., Kumamaru, H., Matsumoto, Y., Doi, T., Ueta, T., Shiba, K. & Iwamoto, Y., May 15 2009, In : Spine. 34, 11, p. 1148-1152 5 p.

Research output: Contribution to journalArticle

Ossification of Posterior Longitudinal Ligament
Nervous System
Wounds and Injuries
Spinal Cord Injuries
Spinal Injuries
65 Citations (Scopus)

Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development

Saiga, T., Fukuda, T., Matsumoto, M., Tada, H., Okano, H. J., Okano, H. & Nakayama, K. I., Jul 1 2009, In : Molecular and cellular biology. 29, 13, p. 3529-3543 15 p.

Research output: Contribution to journalArticle

Ligases
Ubiquitin
F-Box Proteins
Neuromuscular Junction
Consensus Sequence
6 Citations (Scopus)

Generation of a rat monoclonal antibody specific for Brm

Okada, S., Harada, A., Saiwai, H., Nakamura, M. & Ohkawa, Y., Dec 1 2009, In : Hybridoma. 28, 6, p. 455-458 4 p.

Research output: Contribution to journalArticle

Monoclonal Antibodies
Myoblasts
DNA Repair
Adenosine Triphosphatases
Skeletal Muscle