Research Center for Transomics Medicine

Research Output

2016

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)

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)

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)

Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling

Hatano, A., Matsumoto, M. & Nakayama, K. I., Oct 1 2016, In : Genes to Cells. 21, 10, p. 1095-1112 18 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Prediction of periodontal inflammation via metabolic profiling of saliva

Kuboniwa, M., Sakanaka, A., Hashino, E., Bamba, T., Fukusaki, E. & Amano, A., Nov 1 2016, In : Journal of Dental Research. 95, 12, p. 1381-1386 6 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Protection of stromal cell-derived factor 2 by heat shock protein 72 prevents oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells

Takahashi, K., Tanaka, M., Yashiro, M., Matsumoto, M., Ohtsuka, A., Nakayama, K. I., Izumi, Y., Nagayama, K., Miura, K., Iwao, H. & Shiota, M., Aug 1 2016, In : Cancer Letters. 378, 1, p. 8-15 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

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)

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)

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)

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)

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)

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)

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

The novel heart-specific RING finger protein 207 is involved in energy metabolism in cardiomyocytes

Mizushima, W., Takahashi, H., Watanabe, M., Kinugawa, S., Matsushima, S., Takada, S., Yokota, T., Furihata, T., Matsumoto, J., Tsuda, M., Chiba, I., Nagashima, S., Yanagi, S., Matsumoto, M., Nakayama, K. I., Tsutsui, H. & Hatakeyama, S., Nov 1 2016, In : Journal of Molecular and Cellular Cardiology. 100, p. 43-53 11 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands

Shibata, H., Chijiwa, T., Hattori, S., Terada, K., Ohno, M. & Fukumaki, Y., Aug 1 2016, In : Molecular Phylogenetics and Evolution. 101, p. 91-100 10 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Yugi, K., Kubota, H., Hatano, A. & Kuroda, S., Apr 1 2016, In : Trends in biotechnology. 34, 4, p. 276-290 15 p.

Research output: Contribution to journalReview article

94 Citations (Scopus)

Truncation mutants of ASXL1 observed in myeloid malignancies are expressed at detectable protein levels

Inoue, D., Matsumoto, M., Nagase, R., Saika, M., Fujino, T., Nakayama, K. I. & Kitamura, T., Mar 1 2016, In : Experimental Hematology. 44, 3, p. 172-176.e1

Research output: Contribution to journalArticle

24 Citations (Scopus)

UV damage-induced phosphorylation of HBO1 triggers CRL4DDB2-mediated degradation to regulate cell proliferation

Matsunuma, R., Niida, H., Ohhata, T., Kitagawa, K., Sakai, S., Uchida, C., Shiotani, B., Matsumoto, M., Nakayama, K. I., Ogura, H., Shiiya, N. & Kitagawa, M., Jan 1 2016, In : Molecular and cellular biology. 36, 3, p. 394-406 13 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)
2015

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation

Tomita, S., Abdalla, M. O. A., Fujiwara, S., Matsumori, H., Maehara, K., Ohkawa, Y., Iwase, H., Saitoh, N. & Nakao, M., Apr 29 2015, In : Nature communications. 6, 6966.

Research output: Contribution to journalArticle

28 Citations (Scopus)

A genome-wide analysis identifies a Notch-RBP-Jk-IL-7Ra axis that controls IL-17-Producing γδ T cell homeostasis in mice

Nakamura, M., Shibata, K., Hatano, S., Sato, T., Ohkawa, Y., Yamada, H., Ikuta, K. & Yoshikai, Y., Jan 1 2015, In : Journal of Immunology. 194, 1, p. 243-251 9 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Agplus: A rapid and flexible tool for aggregation plots

Maehara, K. & Ohkawa, Y., Jul 31 2015, In : Bioinformatics. 31, 18, p. 3046-3047 2 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

An optogenetic system for interrogating the temporal dynamics of Akt

Katsura, Y., Kubota, H., Kunida, K., Kanno, A., Kuroda, S. & Ozawa, T., Oct 1 2015, In : Scientific reports. 5, 14589.

Research output: Contribution to journalArticle

27 Citations (Scopus)

A novel missense mutation of RYR1 in familial idiopathic hyper CK-emia

Sano, K., Miura, S., Fujiwara, T., Fujioka, R., Yorita, A., Noda, K., Kida, H., Azuma, K., Kaieda, S., Yamamoto, K., Taniwaki, T., Fukumaki, Y. & Shibata, H., Sep 15 2015, In : Journal of the Neurological Sciences. 356, 1-2, p. 142-147 6 p., 13864.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture

Sugimoto, N., Maehara, K., Yoshida, K., Yasukouchi, S., Osano, S., Watanabe, S., Aizawa, M., Yugawa, T., Kiyono, T., Kurumizaka, H., Ohkawa, Y. & Fujita, M., Jan 1 2015, In : Nucleic acids research. 43, 12, p. 5898-5911 14 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies

Hayashi-Takanaka, Y., Maehara, K., Harada, A., Umehara, T., Yokoyama, S., Obuse, C., Ohkawa, Y., Nozaki, N. & Kimura, H., Dec 1 2015, In : Chromosome Research. 23, 4, p. 753-766 14 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis

Kubo, N., Toh, H., Shirane, K., Shirakawa, T., Kobayashi, H., Sato, T., Sone, H., Sato, Y., Tomizawa, S. I., Tsurusaki, Y., Shibata, H., Saitsu, H., Suzuki, Y., Matsumoto, N., Suyama, M., Kono, T., Ohbo, K. & Sasaki, H., Aug 20 2015, In : BMC genomics. 16, 1, 624.

Research output: Contribution to journalArticle

53 Citations (Scopus)

Engrafted Neural Stem/Progenitor Cells Promote Functional Recovery through Synapse Reorganization with Spared Host Neurons after Spinal Cord Injury

Yokota, K., Kobayakawa, K., Kubota, K., Miyawaki, A., Okano, H., Ohkawa, Y., Iwamoto, Y. & Okada, S., Jan 1 2015, In : Stem Cell Reports. 5, 2, p. 264-277 14 p.

Research output: Contribution to journalArticle

30 Citations (Scopus)

Erratum: PSMC5, a 19S proteasomal ATPase, regulates cocaine action in the nucleus accumbens (PLoS ONE (2015) 10:5 (e0126710) DOI: 10.1371/journal.pone.0126710)

Ohnishi, Y. H., Ohnishi, Y. N., Nakamura, T., Ohno, M., Kennedy, P. J., Ohkawa, Y., Nishi, A., Neve, R., Tsuzuki, T. & Nestler, E. J., Jun 25 2015, In : PloS one. 10, 6, e0131263.

Research output: Contribution to journalComment/debate

Foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka

Nishimura, T., Sato, T., Yamamoto, Y., Watakabe, I., Ohkawa, Y., Suyama, M., Kobayashi, S. & Tanaka, M., Jul 17 2015, In : Science. 349, 6245, p. 328-331 4 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)

Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis

Shimaji, K., Konishi, T., Tanaka, S., Yoshida, H., Kato, Y., Ohkawa, Y., Sato, T., Suyama, M., Kimura, H. & Yamaguchi, M., Nov 2015, In : Genes to Cells. 20, 11, p. 902-914 13 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

Hatanaka, Y., Inoue, K., Oikawa, M., Kamimura, S., Ogonuki, N., Kodama, E. N., Ohkawa, Y., Tsukada, Y. I. & Ogura, A., Nov 24 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 47, p. 14641-14646 6 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)

Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle

Harada, A., Maehara, K., Sato, Y., Konno, D., Tachibana, T., Kimura, H. & Ohkawa, Y., Jan 30 2015, In : Nucleic acids research. 43, 2, p. 775-786 12 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA

Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y. & Kurumizaka, H., Oct 7 2015, In : Open Biology. 5, 10, 150128.

Research output: Contribution to journalArticle

12 Citations (Scopus)

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)

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

25 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)

Opposing calcium-dependent signalling pathways control skeletal muscle differentiation by regulating a chromatin remodelling enzyme

Nasipak, B. T., Padilla-Benavides, T., Green, K. M., Leszyk, J. D., Mao, W., Konda, S., Sif, S., Shaffer, S. A., Ohkawa, Y. & Imbalzano, A. N., Jun 17 2015, In : Nature communications. 6, 7441.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Overexpression of Ephrin A2 receptors in cancer stromal cells is a prognostic factor for the relapse of gastric cancer

Kikuchi, S., Kaibe, N., Morimoto, K., Fukui, H., Niwa, H., Maeyama, Y., Takemura, M., Matsumoto, M., Nakamori, S., Miwa, H., Hirota, S. & Sasako, M., Jul 27 2015, In : Gastric Cancer. 18, 3, p. 485-494 10 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Planteose as a storage carbohydrate required for early stage of germination of Orobanche minor and its metabolism as a possible target for selective control

Wakabayashi, T., Joseph, B., Yasumoto, S., Akashi, T., Aoki, T., Harada, K., Muranaka, S., Bamba, T., Fukusaki, E., Takeuchi, Y., Yoneyama, K., Muranaka, T., Sugimoto, Y. & Okazawa, A., Jun 1 2015, In : Journal of Experimental Botany. 66, 11, p. 3085-3097 13 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
5 Citations (Scopus)

PSMC5, a 19S proteasomal ATPase, regulates cocaine action in the nucleus accumbens

Ohnishi, Y. H., Ohnishi, Y. N., Nakamura, T., Ohno, M., Kennedy, P. J., Yasuyuki, O., Nishi, A., Neve, R., Tsuzuki, T. & Nestler, E. J., May 11 2015, In : PloS one. 10, 5, e0126710.

Research output: Contribution to journalArticle

3 Citations (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)
55 Citations (Scopus)

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)

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)

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

Tissue-specific expression of histone H3 variants diversified after species separation

Maehara, K., Harada, A., Sato, Y., Matsumoto, M., Nakayama, K. I., Kimura, H. & Ohkawa, Y., Sep 17 2015, In : Epigenetics and Chromatin. 8, 1, 35.

Research output: Contribution to journalArticle

19 Citations (Scopus)
2014

Acute hyperglycemia impairs functional improvement after spinal cord injury in mice and humans

Kobayakawa, K., Kumamaru, H., Saiwai, H., Kubota, K., Ohkawa, Y., Kishimoto, J., Yokota, K., Ideta, R., Shiba, K., Tozaki-Saitoh, H., Inoue, K., Iwamoto, Y. & Okada, S., Oct 1 2014, In : Science Translational Medicine. 6, 256, 256ra137.

Research output: Contribution to journalArticle

22 Citations (Scopus)