Research Center for Transomics Medicine

Research Output

Interaction of reactive astrocytes with type i collagen induces astrocytic scar formation through the integrin-N-cadherin pathway after spinal cord injury

Hara, M., Kobayakawa, K., Ohkawa, Y., Kumamaru, H., Yokota, K., Saito, T., Kijima, K., Yoshizaki, S., Harimaya, K., Nakashima, Y. & Okada, S., Jul 1 2017, In : Nature medicine. 23, 7, p. 818-828 11 p.

Research output: Contribution to journalArticle

89 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

70 Citations (Scopus)

Inter-laboratory comparison of metabolite measurements for metabolomics data integration

Izumi, Y., Matsuda, F., Hirayama, A., Ikeda, K., Kita, Y., Horie, K., Saigusa, D., Saito, K., Sawada, Y., Nakanishi, H., Okahashi, N., Takahashi, M., Nakao, M., Hata, K., Hoshi, Y., Morihara, M., Tanabe, K., Bamba, T. & Oda, Y., Nov 2019, In : Metabolites. 9, 11, 257.

Research output: Contribution to journalArticle

Open Access

Interleukin-10-producing plasmablasts exert regulatory function in autoimmune inflammation

Matsumoto, M., Baba, A., Yokota, T., Nishikawa, H., Ohkawa, Y., Kayama, H., Kallies, A., Nutt, S. L., Sakaguchi, S., Takeda, K., Kurosaki, T. & Baba, Y., Dec 18 2014, In : Immunity. 41, 6, p. 1040-1051 12 p.

Research output: Contribution to journalArticle

205 Citations (Scopus)

Intracellular metabolite β-glucosylceramide is an endogenous Mincle ligand possessing immunostimulatory activity

Nagata, M., Izumi, Y., Ishikawa, E., Kiyotake, R., Doi, R., Iwai, S., Omahdi, Z., Yamaji, T., Miyamoto, T., Bamba, T. & Yamasaki, S., Apr 18 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 16, p. E3285-E3294

Research output: Contribution to journalArticle

33 Citations (Scopus)

In vitro steroid profiling system for the evaluation of endocrine disruptors

Nakano, Y., Yamashita, T., Okuno, M., Fukusaki, E. & Bamba, T., Sep 1 2016, In : Journal of Bioscience and Bioengineering. 122, 3, p. 370-377 8 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver

Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y. & Kuroda, S., Jul 25 2018, In : Cell Systems. 7, 1, p. 118-128.e3

Research output: Contribution to journalArticle

5 Citations (Scopus)

Isolation and characterization of Fetal Leydig progenitor cells of male mice

Inoue, M., Shima, Y., Miyabayashi, K., Tokunaga, K., Sato, T., Baba, T., Ohkawa, Y., Akiyama, H., Suyama, M. & Morohashi, K. I., Mar 2016, In : Endocrinology. 157, 3, p. 1222-1233 12 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays

Ohkawa, Y., Mallappa, C., Vallaster, C. S. D. & Imbalzano, A. N., Jan 2 2012, Myogenesis: Methods and Protocols. DiMario, J. (ed.). p. 517-530 14 p. (Methods in Molecular Biology; vol. 798).

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Citations (Scopus)

JPOSTrepo: An international standard data repository for proteomes

Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. & Ishihama, Y., Jan 1 2017, In : Nucleic acids research. 45, D1, p. D1107-D1111

Research output: Contribution to journalArticle

81 Citations (Scopus)

Kupffer cells induce Notch-mediated hepatocyte conversion in a common mouse model of intrahepatic cholangiocarcinoma

Terada, M., Horisawa, K., Miura, S., Takashima, Y., Ohkawa, Y., Sekiya, S., Matsuda-Ito, K. & Suzuki, A., Oct 4 2016, In : Scientific reports. 6, 34691.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction

Kudo, T., Uda, S., Tsuchiya, T., Wada, T., Karasawa, Y., Fujii, M., Saito, T. H. & Kuroda, S., Aug 2016, In : PloS one. 11, 8, e0160548.

Research output: Contribution to journalArticle

1 Citation (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

145 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

43 Citations (Scopus)

LATS2 positively regulates polycomb repressive complex 2

Torigata, K., Daisuke, O., Mukai, S., Hatanaka, A., Ohka, F., Motooka, D., Nakamura, S., Ohkawa, Y., Yabuta, N., Kondo, Y. & Nojima, H., Jul 1 2016, In : PloS one. 11, 7, e0158562.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Lipidomic analysis of cells and extracellular vesicles from high-and low-metastatic triple-negative breast cancer

Nishida-Aoki, N., Izumi, Y., Takeda, H., Takahashi, M., Ochiya, T. & Bamba, T., Feb 2020, In : Metabolites. 10, 2, 67.

Research output: Contribution to journalArticle

Open Access

Lipidomic analysis of plasma lipoprotein fractions in myocardial infarction-prone rabbits

Takeda, H., Koike, T., Izumi, Y., Yamada, T., Yoshida, M., Shiomi, M., Fukusaki, E. & Bamba, T., Oct 1 2015, In : Journal of Bioscience and Bioengineering. 120, 4, p. 476-482 7 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Lipid profiling by supercritical fluid chromatography/mass spectrometry

Yamada, T. & Bamba, T., Mar 1 2017, Neuromethods. Humana Press Inc., p. 109-131 23 p. (Neuromethods; vol. 125).

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)

Lipophagy maintains energy homeostasis in the kidney proximal tubule during prolonged starvation

Minami, S., Yamamoto, T., Takabatake, Y., Takahashi, A., Namba, T., Matsuda, J., Kimura, T., Kaimori, J. Y., Matsui, I., Hamano, T., Takeda, H., Takahashi, M., Izumi, Y., Bamba, T., Matsusaka, T., Niimura, F. & Isaka, Y., Oct 3 2017, In : Autophagy. 13, 10, p. 1629-1647 19 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Lipoprotein profiling methodology based on determination of apolipoprotein concentration

Takeda, H., Izumi, Y., Tomita, A., Koike, T., Shiomi, M., Fukusaki, E., Matsuda, F. & Bamba, T., Jan 2017, In : Bioanalysis. 9, 1, p. 9-19 11 p.

Research output: Contribution to journalArticle

Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection

Kobayakawa, K., DePetro, K. A., Zhong, H., Pham, B., Hara, M., Harada, A., Nogami, J., Ohkawa, Y. & Edgerton, V. R., Jan 1 2019, In : Neurorehabilitation and Neural Repair.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans

Fujii, M., Murakami, Y., Karasawa, Y., Sumitomo, Y., Fujita, S., Koyama, M., Uda, S., Kubota, H., Inoue, H., Konishi, K., Oba, S., Ishii, S. & Kuroda, S., Dec 1 2019, In : npj Systems Biology and Applications. 5, 1, 31.

Research output: Contribution to journalArticle

Open Access
55 Citations (Scopus)

Macrophage centripetal migration drives spontaneous healing process after spinal cord injury

Kobayakawa, K., Ohkawa, Y., Yoshizaki, S., Tamaru, T., Saito, T., Kijima, K., Yokota, K., Hara, M., Kubota, K., Matsumoto, Y., Harimaya, K., Ozato, K., Masuda, T., Tsuda, M., Tamura, T., Inoue, K., Reggie Edgerton, V., Iwamoto, Y., Nakashima, Y. & Okada, S., May 15 2019, In : Science Advances. 5, 5, eaav5086.

Research output: Contribution to journalArticle

Open Access
2 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

44 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

8 Citations (Scopus)

Matrix rank minimization approach to signal recovery and nonlinear function estimation for nonlinear ARX model with input nonlinearity

Konishi, K., Fujii, M., Kunida, K., Uda, S. & Kuroda, S., Feb 8 2018, Control Conference (ASCC), 2017 11th Asian. IEEE

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

Matrix rank minimization approach to signal recovery and nonlinear function estimation for nonlinear ARX model with input nonlinearity

Konishi, K., Fujii, M., Kunida, K., Uda, S. & Kuroda, S., Feb 7 2018, 2017 Asian Control Conference, ASCC 2017. Institute of Electrical and Electronics Engineers Inc., p. 1428-1431 4 p. (2017 Asian Control Conference, ASCC 2017; vol. 2018-January).

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

MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex

Takahashi, H., Takigawa, I., Watanabe, M., Anwar, D., Shibata, M., Tomomori-Sato, C., Sato, S., Ranjan, A., Seidel, C. W., Tsukiyama, T., Mizushima, W., Hayashi, M., Ohkawa, Y., Conaway, J. W., Conaway, R. C. & Hatakeyama, S., Jan 9 2015, In : Nature communications. 6, 5941.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Metabolic distance estimation based on principle component analysis of metabolic turnover

Nakayama, Y., Putri, S. P., Bamba, T. & Fukusaki, E., Sep 2014, In : Journal of Bioscience and Bioengineering. 118, 3, p. 350-355 6 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Metabolic effects of RUBCN/Rubicon deficiency in kidney proximal tubular epithelial cells

Matsuda, J., Takahashi, A., Takabatake, Y., Sakai, S., Minami, S., Yamamoto, T., Fujimura, R., Namba-Hamano, T., Yonishi, H., Nakamura, J., Kimura, T., Kaimori, J. Y., Matsui, I., Takahashi, M., Nakao, M., Izumi, Y., Bamba, T., Matsusaka, T., Niimura, F., Yanagita, M. & 2 others, Yoshimori, T. & Isaka, Y., Jan 1 2020, (Accepted/In press) In : Autophagy.

Research output: Contribution to journalArticle

Metabolic engineering of oleaginous fungus Mortierella alpina for high production of oleic and linoleic acids

Sakamoto, T., Sakuradani, E., Okuda, T., Kikukawa, H., Ando, A., Kishino, S., Izumi, Y., Bamba, T., Shima, J. & Ogawa, J., Dec 1 2017, In : Bioresource Technology. 245, p. 1610-1615 6 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch

Soma, Y., Tsuruno, K., Wada, M., Yokota, A. & Hanai, T., May 2014, In : Metabolic Engineering. 23, p. 175-184 10 p.

Research output: Contribution to journalArticle

90 Citations (Scopus)
51 Citations (Scopus)

Metabolome analysis reveals the effect of carbon catabolite control on the poly(γ-glutamic acid) biosynthesis of Bacillus licheniformis ATCC 9945

Mitsunaga, H., Meissner, L., Palmen, T., Bamba, T., Büchs, J. & Fukusaki, E., Apr 1 2016, In : Journal of Bioscience and Bioengineering. 121, 4, p. 413-419 7 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Metabolomic analysis to discover candidate therapeutic agents against acute pancreatitis

Sakai, A., Nishiumi, S., Shiomi, Y., Kobayashi, T., Izumi, Y., Kutsumi, H., Hayakumo, T., Azuma, T. & Yoshida, M., Jun 15 2012, In : Archives of Biochemistry and Biophysics. 522, 2, p. 107-120 14 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Metabolomics approach to reduce the Crabtree effect in continuous culture of Saccharomyces cerevisiae

Imura, M., Iwakiri, R., Bamba, T. & Fukusaki, E., Aug 2018, In : Journal of Bioscience and Bioengineering. 126, 2, p. 183-188 6 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Methylation of Gata3 protein at Arg-261 regulates transactivation of the Il5 gene in T helper 2 cells

Hosokawa, H., Kato, M., Tohyama, H., Tamaki, Y., Endo, Y., Kimura, M. Y., Tumes, D. J., Motohashi, S., Matsumoto, M., Nakayama, K. I., Tanaka, T. & Nakayama, T., May 22 2015, In : Journal of Biological Chemistry. 290, 21, p. 13095-13103 9 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Microbe participation in aroma production during soy sauce fermentation

Harada, R., Yuzuki, M., Ito, K., Shiga, K., Bamba, T. & Fukusaki, E., Jun 2018, In : Journal of Bioscience and Bioengineering. 125, 6, p. 688-694 7 p.

Research output: Contribution to journalArticle

10 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

6 Citations (Scopus)

miR-124 dosage regulates prefrontal cortex function by dopaminergic modulation

Kozuka, T., Omori, Y., Watanabe, S., Tarusawa, E., Yamamoto, H., Chaya, T., Furuhashi, M., Morita, M., Sato, T., Hirose, S., Ohkawa, Y., Yoshimura, Y., Hikida, T. & Furukawa, T., Dec 1 2019, In : Scientific reports. 9, 1, 3445.

Research output: Contribution to journalArticle

1 Citation (Scopus)

MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast

Luo, D., Kato, D., Nogami, J., Ohkawa, Y., Kurumizaka, H. & Kono, H., Jan 1 2018, In : Nucleic acids research. 46, 14, p. 7124-7137 14 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Molecular analysis of α-thalassemia in Nepal: Correlation with malaria endemicity

Sakai, Y., Kobayashi, S., Shibata, H., Furuumi, H., Endo, T., Fucharoen, S., Hamano, S., Acharya, G. P., Kawasaki, T. & Fukumaki, Y., Jan 1 2000, In : Journal of Human Genetics. 45, 3, p. 127-132 6 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)
50 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

113 Citations (Scopus)

Molecular dissection of the interactions among IκBα, FWD1, and Skp1 required for ubiquitin-mediated proteolysis of IκBα

Hattori, K., Hatakeyama, S., Shirane, M., Matsumoto, M. & Nakayama, K. I., Oct 15 1999, In : Journal of Biological Chemistry. 274, 42, p. 29641-29647 7 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Molecular evolution of the 5′-flanking regions of the duplicated Amy genes in Drosophila melanogaster species subgroup

Okuyama, E., Shibata, H., Tachida, H. & Yamazaki, T., Apr 1996, In : Molecular Biology and Evolution. 13, 4, p. 574-583 10 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)
64 Citations (Scopus)

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 6D2 and 8H3 against mouse Chd2

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

Research output: Contribution to journalShort survey