Research Center for Transomics Medicine

Research Output

Quantification of coffee blends for authentication of Asian palm civet coffee (Kopi Luwak) via metabolomics: A proof of concept

Jumhawan, U., Putri, S. P., Yusianto, Bamba, T. & Fukusaki, E., Jul 1 2016, In : Journal of Bioscience and Bioengineering. 122, 1, p. 79-84 6 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Quantitative target analysis and kinetic profiling of acyl-CoAs reveal the rate-limiting step in cyanobacterial 1-butanol production

Noguchi, S., Putri, S. P., Lan, E. I., Laviña, W. A., Dempo, Y., Bamba, T., Liao, J. C. & Fukusaki, E., Feb 1 2016, In : Metabolomics. 12, 2, p. 1-10 10 p., 26.

Research output: Contribution to journalArticle

18 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

5 Citations (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

1 Citation (Scopus)
12 Citations (Scopus)

Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data

Kawata, K., Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K. I. & Kuroda, S., Jan 2019, In : Genes to Cells. 24, 1, p. 82-93 12 p.

Research output: Contribution to journalArticle

Reconstruction of insulin signal flow from phosphoproteome and metabolome data

Yugi, K., Kubota, H., Toyoshima, Y., Noguchi, R., Kawata, K., Komori, Y., Uda, S., Kunida, K., Tomizawa, Y., Funato, Y., Miki, H., Matsumoto, M., Nakayama, K. I., Kashikura, K., Endo, K., Ikeda, K., Soga, T. & Kuroda, S., Aug 21 2014, In : Cell Reports. 8, 4, p. 1171-1183 13 p.

Research output: Contribution to journalArticle

40 Citations (Scopus)

Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1

Sorida, M., Hirauchi, T., Ishizaki, H., Kaito, W., Shimada, A., Mori, C., Chikashige, Y., Hiraoka, Y., Suzuki, Y., Ohkawa, Y., Kato, H., Takahata, S. & Murakami, Y., Jun 2019, In : PLoS genetics. 15, 6, e1008129.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Regulation of RNA polymerase II activation by histone acetylation in single living cells

Stasevich, T. J., Hayashi-Takanaka, Y., Sato, Y., Maehara, K., Ohkawa, Y., Sakata-Sogawa, K., Tokunaga, M., Nagase, T., Nozaki, N., McNally, J. G. & Kimura, H., Dec 11 2014, In : Nature. 516, 7530, p. 272-275 4 p.

Research output: Contribution to journalArticle

113 Citations (Scopus)

Relationship between 3-methyl-2,4-nonanedione concentration and intensity of light-induced off-odor in soy bean oil

Sano, T., Iwahashi, M., Imagi, J., Sato, T., Yamashita, T., Fukusaki, E. & Bamba, T., May 1 2016, In : Journal of oleo science. 65, 5, p. 447-450 4 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Relationship between the risk for a shrimp allergy and freshness or cooking

Usui, M., Harada, A., Yasumoto, S., Sugiura, Y., Nishidai, A., Ikarashi, M., Takaba, H., Miyasaki, T., Azakami, H. & Kondo, M., Jan 1 2015, In : Bioscience, Biotechnology and Biochemistry. 79, 10, p. 1698-1701 4 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Response to the letter to the editor by Berciano J & García A

Miura, S. & Shibata, H., Jan 2018, In : European Journal of Medical Genetics. 61, 1, 1 p.

Research output: Contribution to journalLetter

Reversible interconversion and maintenance of mammary epithelial cell characteristics by the ligand-regulated EGFR system

Fukuda, S., Nishida-Fukuda, H., Nanba, D., Nakashiro, K. I., Nakayama, H., Kubota, H. & Higashiyama, S., Feb 2 2016, In : Scientific reports. 6, 20209.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Ribophorin ii is involved in the tissue factor expression mediated by phosphatidylserinedependent antiprothrombin antibody on monocytes

Fujieda, Y., Amengual, O., Matsumoto, M., Kuroki, K., Takahashi, H., Kono, M., Kurita, T., Otomo, K., Kato, M., Oku, K., Bohgaki, T., Horita, T., Yasuda, S., Maenaka, K., Hatakeyama, S., Nakayama, K. & Atsumi, T., Jun 1 2016, In : Rheumatology (United Kingdom). 55, 6, p. 1117-1126 10 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

RNA-primed PCR

Shibata, H., Tahira, T. & Hayashi, K., Nov 1 1995, In : Genome Research. 5, 4, p. 400-403 4 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Role of Ad4-binding protein/steroidogenic factor 1 in regulating NADPH production in adrenocortical Y-1 cells

Li, B., Baba, T., Miyabayashi, K., Sato, T., Shima, Y., Ichinose, T., Miura, D., Ohkawa, Y., Suyama, M. & Morohashi, K. I., Jan 1 2017, In : Endocrine Journal. 64, 3, p. 315-324 10 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Role of apolipoprotein B100 and oxidized low-density lipoprotein in the monocyte tissue factor induction mediated by anti-β2 glycoprotein i antibodies

Otomo, K., Amengual, O., Fujieda, Y., Nakagawa, H., Kato, M., Oku, K., Horita, T., Yasuda, S., Matsumoto, M., Nakayama, K. I., Hatakeyama, S., Koike, T. & Atsumi, T., Oct 1 2016, In : Lupus. 25, 12, p. 1288-1298 11 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Roles of histone H3.5 in human spermatogenesis and spermatogenic disorders

Shiraishi, K., Shindo, A., Harada, A., Kurumizaka, H., Kimura, H., Ohkawa, Y. & Matsuyama, H., Jan 2018, In : Andrology. 6, 1, p. 158-165 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin

Sano, T., Kawata, K., Ohno, S., Yugi, K., Kakuda, H., Kubota, H., Uda, S., Fujii, M., Kunida, K., Hoshino, D., Hatano, A., Ito, Y., Sato, M., Suzuki, Y. & Kuroda, S., Nov 22 2016, In : Science Signaling. 9, 455, ra112.

Research output: Contribution to journalArticle

7 Citations (Scopus)
55 Citations (Scopus)

Sensitive detection of fluorescence in western blotting by merging images

Kondo, Y., Higa, S., Iwasaki, T., Matsumoto, T., Maehara, K., Harada, A., Baba, Y., Fujita, M. & Ohkawa, Y., Jan 2018, In : PloS one. 13, 1, e0191532.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Separation of Lipids

Yamada, T., Taguchi, K. & Bamba, T., Feb 20 2017, Supercritical Fluid Chromatography: Handbooks in Separation Science. Elsevier Inc., p. 419-438 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi

Kajitani, T., Kato, H., Chikashige, Y., Tsutsumi, C., Hiraoka, Y., Kimura, H., Ohkawa, Y., Obuse, C., Hermand, D. & Murakami, Y., Dec 26 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 52, p. E11208-E11217

Research output: Contribution to journalArticle

4 Citations (Scopus)

Sez6l2 regulates phosphorylation of ADD and neuritogenesis

Yaguchi, H., Yabe, I., Takahashi, H., Watanabe, M., Nomura, T., Kano, T., Matsumoto, M., Nakayama, K. I., Watanabe, M. & Hatakeyama, S., Dec 9 2017, In : Biochemical and Biophysical Research Communications. 494, 1-2, p. 234-241 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Silica-based hybrid porous layers to enhance the retention and efficiency of open tubular capillary columns with a 5 μm inner diame9ter

Hara, T., Izumi, Y., Nakao, M., Hata, K., Baron, G. V., Bamba, T. & Desmet, G., Dec 14 2018, In : Journal of Chromatography A. 1580, p. 63-71 9 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Simultaneous profiling of 17 steroid hormones for the evaluation of endocrine-disrupting chemicals in H295R cells

Jumhawan, U., Yamashita, T., Ishida, K., Fukusaki, E. & Bamba, T., Jan 2017, In : Bioanalysis. 9, 1, p. 67-79 13 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Small Nucleolar Noncoding RNA SNORA23, Up-Regulated in Human Pancreatic Ductal Adenocarcinoma, Regulates Expression of Spectrin Repeat-Containing Nuclear Envelope 2 to Promote Growth and Metastasis of Xenograft Tumors in Mice

Cui, L., Nakano, K., Obchoei, S., Setoguchi, K., Matsumoto, M., Yamamoto, T., Obika, S., Shimada, K. & Hiraoka, N., Jul 2017, In : Gastroenterology. 153, 1, p. 292-306.e2

Research output: Contribution to journalArticle

14 Citations (Scopus)

Solid-phase analytical derivatization for gas-chromatography–mass-spectrometry-based metabolomics

Takeo, E., Sasano, R., Shimma, S., Bamba, T. & Fukusaki, E., Dec 2017, In : Journal of Bioscience and Bioengineering. 124, 6, p. 700-706 7 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Sparse Gaussian graphical model with missing values

Uda, S. & Kubota, H., Jan 8 2018, Proceedings of the 21st Conference of Open Innovations Association, FRUCT 2017. IEEE Computer Society, p. 336-343 8 p.

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

Spatial re-organization of myogenic regulatory sequences temporally controls gene expression

Harada, A., Mallappa, C., Okada, S., Butler, J. T., Baker, S. P., Lawrence, J. B., Ohkawa, Y. & Imbalzano, A. N., Feb 27 2015, In : Nucleic acids research. 43, 4, p. 2008-2021 14 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

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)

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

18 Citations (Scopus)

Spinocerebellar ataxia 27 with a novel nonsense variant (Lys177X) in FGF14

Miura, S., Kosaka, K., Fujioka, R., Uchiyama, Y., Shimojo, T., Morikawa, T., Irie, A., Taniwaki, T. & Shibata, H., Mar 2019, In : European Journal of Medical Genetics. 62, 3, p. 172-176 5 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data

Oki, S., Maehara, K., Ohkawa, Y. & Meno, C., Dec 1 2014, In : Genes to Cells. 19, 12, p. 919-926 8 p.

Research output: Contribution to journalArticle

14 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

11 Citations (Scopus)

Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus

Fujinami, D., Matsumoto, M., Noguchi, T., Sonomoto, K. & Kohda, D., Mar 31 2014, In : Carbohydrate Research. 387, 1, p. 30-36 7 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Structure and evolution of the filaggrin gene repeated region in primates

Romero, V., Hosomichi, K., Nakaoka, H., Shibata, H. & Inoue, I., Jan 11 2017, In : BMC Evolutionary Biology. 17, 1, p. 1-13 13 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Structure and function of human histone H3.Y nucleosome

Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Jul 27 2016, In : Nucleic acids research. 44, 13, p. 6127-6141 15 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Structure and polymorphisms of the human metabotropic glutamate receptor type 2 gene (GRM2): Analysis of association with schizophrenia

Joo, A., Shibata, H., Ninomiya, H., Kawasaki, H., Tashiro, N. & Fukumaki, Y., Mar 14 2001, In : Molecular Psychiatry. 6, 2, p. 186-192 7 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

Supercritical Fluid Chromatography

Jumhawan, U. & Bamba, T., Mar 22 2017, The Application of Green Solvents in Separation Processes. Elsevier Inc., p. 483-516 34 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 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

20 Citations (Scopus)

Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle

Fukuda, S., Kaneshige, A., Kaji, T., Noguchi, Y. T., Takemoto, Y., Zhang, L., Tsujikawa, K., Kokubo, H., Uezumi, A., Maehara, K., Harada, A., Ohkawa, Y. & Fukada, S. I., Sep 2019, In : eLife. 8, e48284.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies

Kawaguchi, T., Tanigawa, A., Naganuma, T., Ohkawa, Y., Souquere, S., Pierron, G., Hirose, T. & Steitz, J. A., Apr 7 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 14, p. 4304-4309 6 p.

Research output: Contribution to journalArticle

57 Citations (Scopus)
11 Citations (Scopus)

Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production

Honjo, H., Iwasaki, K., Soma, Y., Tsuruno, K., Hamada, H. & Hanai, T., Sep 2019, In : Metabolic Engineering. 55, p. 268-275 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Synthetic quorum sensing as a tunable cell density sensor-regulator for dynamic metabolic engineering

Hanai, T. & Soma, Y., Jan 1 2016, Metabolic Engineering 11. AIChE, p. 181-182 2 p. (Metabolic Engineering 11).

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

System identification of signaling dependent gene expression with different time-scale data

Tsuchiya, T., Fujii, M., Matsuda, N., Kunida, K., Uda, S., Kubota, H., Konishi, K. & Kuroda, S., Dec 2017, In : PLoS Computational Biology. 13, 12, e1005913.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Targeted disruption of Skp2 results in accumulation of cyclin E and p27 (Kip1), polyploidy and centrosome overduplication

Nakayama, K., Nagahama, H., Minamishima, Y. A., Matsumoto, M., Nakamichi, I., Kitagawa, K., Shirane, M., Tsunematsu, R., Tsukiyama, T., Ishida, N., Kitagawa, M., Nakayama, K. I. & Hatakeyama, S., May 2 2000, In : EMBO Journal. 19, 9, p. 2069-2081 13 p.

Research output: Contribution to journalArticle

597 Citations (Scopus)

TDRKH is a candidate gene for an autosomal dominant distal hereditary motor neuropathy

Miura, S., Kosaka, K., Nomura, T., Nagata, S., Shimojo, T., Morikawa, T., Fujioka, R., Harada, M., Taniwaki, T. & Shibata, H., Dec 2019, In : European Journal of Medical Genetics. 62, 12, 103594.

Research output: Contribution to journalArticle

Temporal coding of insulin signaling

Kubota, H. & Kuroda, S., Sep 2 2015, Protein Modifications in Pathogenic Dysregulation of Signaling. Springer Japan, p. 95-109 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter