Research Center for Transomics Medicine

Research Output

A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples

Narumi, R., Murakami, T., Kuga, T., Adachi, J., Shiromizu, T., Muraoka, S., Kume, H., Kodera, Y., Matsumoto, M., Nakayama, K., Miyamoto, Y., Ishitobi, M., Inaji, H., Kato, K. & Tomonaga, T., Nov 2 2012, In : Journal of Proteome Research. 11, 11, p. 5311-5322 12 p.

Research output: Contribution to journalArticle

67 Citations (Scopus)

Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16

Hosokawa, H., Romero-Wolf, M., Yui, M. A., Ungerbäck, J., Quiloan, M. L. G., Matsumoto, M., Nakayama, K. I., Tanaka, T. & Rothenberg, E. V., Dec 1 2018, In : Nature Immunology. 19, 12, p. 1427-1440 14 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Biochemical analysis of nucleosome targeting by Tn5 transposase

Sato, S., Arimura, Y., Kujirai, T., Harada, A., Maehara, K., Nogami, J., Ohkawa, Y. & Kurumizaka, H., Aug 1 2019, In : Open Biology. 9, 8, 190116.

Research output: Contribution to journalArticle

Open Access

Biochemical and immunological characterization of a novel monoclonal antibody against mouse leukotriene B4 receptor 1

Sasaki, F., Koga, T., Saeki, K., Okuno, T., Kazuno, S., Fujimura, T., Ohkawa, Y. & Yokomizo, T., Sep 2017, In : PloS one. 12, 9, e0185133.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Biochemical characterization of CYP505D6, a self-sufficient cytochrome P450 from the white-rot fungus Phanerochaete chrysosporium

Sakai, K., Matsuzaki, F., Wise, L., Sakai, Y., Jindou, S., Ichinose, H., Takaya, N., Kato, M., Wariishi, H. & Shimizu, M., Nov 1 2018, In : Applied and environmental microbiology. 84, 22, e01091-18.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Biophysics at Kyushu University

Akiyama, R., Annaka, M., Kohda, D., Kubota, H., Maeda, Y., Matsumori, N., Mizuno, D. & Yoshida, N., Jan 1 2020, (Accepted/In press) In : Biophysical Reviews.

Research output: Contribution to journalComment/debate

1 Citation (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

157 Citations (Scopus)

Brain-derived neurotrophic factor improves limited exercise capacity in mice with heart failure

Matsumoto, J., Takada, S., Kinugawa, S., Furihata, T., Nambu, H., Kakutani, N., Tsuda, M., Fukushima, A., Yokota, T., Tanaka, S., Takahashi, H., Watanabe, M., Hatakeyama, S., Matsumoto, M., Nakayama, K. I., Otsuka, Y., Sabe, H., Tsutsui, H. & Anzai, T., Jan 1 2018, In : Circulation. 138, 18, p. 2064-2066 3 p.

Research output: Contribution to journalLetter

4 Citations (Scopus)

Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme

Witwicka, H., Nogami, J., Syed, S. A., Maehara, K., Padilla-Benavides, T., Ohkawa, Y. & Imbalzano, A. N., Oct 1 2019, In : Molecular and cellular biology. 39, 19, e00063-19.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome

Arimura, Y., Ikura, M., Fujita, R., Noda, M., Kobayashi, W., Horikoshi, N., Sun, J., Shi, L., Kusakabe, M., Harata, M., Ohkawa, Y., Tashiro, S., Kimura, H., Ikura, T. & Kurumizaka, H., Jan 1 2018, In : Nucleic acids research. 46, 19, p. 10007-10018 12 p.

Research output: Contribution to journalArticle

7 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)

Cell-autonomous and redundant roles of Hey1 and HeyL in muscle stem cells: HeyL requires HeS1 to bind diverse DNA sites

Noguchi, Y. T., Nakamura, M., Hino, N., Nogami, J., Tsuji, S., Sato, T., Zhang, L., Tsujikawa, K., Tanaka, T., Izawa, K., Okada, Y., Doi, T., Kokubo, H., Harada, A., Uezumi, A., Gessler, M., Ohkawa, Y. & Fukada, S. I., Feb 2019, In : Development (Cambridge). 146, 4, dev163618.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo

Akieda, Y., Ogamino, S., Furuie, H., Ishitani, S., Akiyoshi, R., Nogami, J., Masuda, T., Shimizu, N., Ohkawa, Y. & Ishitani, T., Dec 1 2019, In : Nature communications. 10, 1, 4710.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Cell cycle-dependent expression of mammalian E2-C regulated by the anaphase-promoting complex/cyclosome

Yamanaka, A., Hatakeyama, S., Kominami, K. I., Kitagawa, M., Matsumoto, M. & Nakayama, K. I., Jan 1 2000, In : Molecular biology of the cell. 11, 8, p. 2821-2831 11 p.

Research output: Contribution to journalArticle

44 Citations (Scopus)

Cell cycle–dependent localization of the proteasome to chromatin

Kito, Y., Matsumoto, M., Hatano, A., Takami, T., Oshikawa, K., Matsumoto, A. & Nakayama, K. I., Dec 1 2020, In : Scientific reports. 10, 1, 5801.

Research output: Contribution to journalArticle

Open Access

Characterization of the mouse gene for the U-box-type ubiquitin ligase UFD2a

Kaneko, C., Hatakeyama, S., Matsumoto, M., Yada, M., Nakayama, K. & Nakayama, K., Jan 10 2003, In : Biochemical and Biophysical Research Communications. 300, 2, p. 297-304 8 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)

Chd2 interacts with H3.3 to determine myogenic cell fate

Harada, A., Okada, S., Konno, D., Odawara, J., Yoshimi, T., Yoshimura, S., Kumamaru, H., Saiwai, H., Tsubota, T., Kurumizaka, H., Akashi, K., Tachibana, T., Imbalzano, A. N. & Ohkawa, Y., Jul 4 2012, In : EMBO Journal. 31, 13, p. 2994-3007 14 p.

Research output: Contribution to journalArticle

69 Citations (Scopus)

Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells

Semba, Y., Harada, A., Maehara, K., Oki, S., Meno, C., Ueda, J., Yamagata, K., Suzuki, A., Onimaru, M., Nogami, J., Okada, S., Akashi, K. & Ohkawa, Y., Sep 1 2017, In : Nucleic acids research. 45, 15, p. 8758-8772 15 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2

Hayashi, M., Maehara, K., Harada, A., Semba, Y., Kudo, K., Takahashi, H., Oki, S., Meno, C., Ichiyanagi, K., Akashi, K. & Ohkawa, Y., Mar 2016, In : Journal of Cellular Biochemistry. 117, 3, p. 780-792 13 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

CHD8 haploinsufficiency results in autistic-like phenotypes in mice

Katayama, Y., Nishiyama, M., Shoji, H., Ohkawa, Y., Kawamura, A., Sato, T., Suyama, M., Takumi, T., Miyakawa, T. & Nakayama, K. I., Jan 1 2016, In : Nature. 537, 7622, p. 675-679 5 p.

Research output: Contribution to journalArticle

86 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

22 Citations (Scopus)

Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing

Kobayashi, W., Takaku, M., Machida, S., Tachiwana, H., Maehara, K., Ohkawa, Y. & Kurumizaka, H., Apr 7 2016, In : Scientific reports. 6, 24228.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells

Oka, M., Mura, S., Otani, M., Miyamoto, Y., Nogami, J., Maehara, K., Harada, A., Tachibana, T., Yoneda, Y. & Ohkawa, Y., Nov 2019, In : eLife. 8, e46667.

Research output: Contribution to journalArticle

Open Access

Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes

Oka, M., Mura, S., Yamada, K., Sangel, P., Hirata, S., Maehara, K., Kawakami, K., Tachibana, T., Ohkawa, Y., Kimura, H. & Yoneda, Y., Jan 7 2016, In : eLife. 5, JANUARY2016, e09540.

Research output: Contribution to journalArticle

15 Citations (Scopus)

CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors

Miki, M., Oono, T., Fujimori, N., Takaoka, T., Kawabe, K., Miyasaka, Y., Ohtsuka, T., Saito, D., Nakamura, M., Ohkawa, Y., Oda, Y., Suyama, M., Ito, T. & Ogawa, Y., Jul 2019, In : Cancer Medicine. 8, 8, p. 3748-3760 13 p.

Research output: Contribution to journalArticle

Open Access
2 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

15 Citations (Scopus)
Open Access
2 Citations (Scopus)

Comparison of sequential derivatization with concurrent methods for GC/MS-based metabolomics

Miyagawa, H. & Bamba, T., Feb 2019, In : Journal of Bioscience and Bioengineering. 127, 2, p. 160-168 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis

Hirano, A., Umeno, J., Okamoto, Y., Shibata, H., Ogura, Y., Moriyama, T., Torisu, T., Fujioka, S., Fuyuno, Y., Kawarabayasi, Y., Matsumoto, T., Kitazono, T. & Esaki, M., Sep 2018, In : Journal of Gastroenterology and Hepatology (Australia). 33, 9, p. 1590-1597 8 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Comprehensive identification of substrates for f-box proteins by differential proteomics analysis

Yumimoto, K., Matsumoto, M., Oyamada, K., Moroishi, T. & Nakayama, K. I., Jun 1 2012, In : Journal of Proteome Research. 11, 6, p. 3175-3185 11 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Comprehensive study of protein ubiquitylation sites by conjugation of engineered lysine-less ubiquitin

Oshikawa, K., Matsumoto, M. & Nakayama, K. I., Dec 1 2012, In : Seikagaku. 84, 6, p. 479-487 9 p.

Research output: Contribution to journalReview article

1 Citation (Scopus)

Construction and analysis of EST libraries of the trans-polyisoprene producing plant, Eucommia ulmoides Oliver

Suzuki, N., Uefuji, H., Nishikawa, T., Mukai, Y., Yamashita, A., Hattori, M., Ogasawara, N., Bamba, T., Fukusaki, E. I., Kobayashi, A., Ogata, Y., Sakurai, N., Suzuki, H., Shibata, D. & Nakazawa, Y., Oct 1 2012, In : Planta. 236, 5, p. 1405-1417 13 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Control of tissue size and development by a regulatory element in the yorkie 3'UTR

Umegawachi, T., Yoshida, H., Koshida, H., Yamada, M., Ohkawa, Y., Sato, T., Suyama, M., Krause, H. M. & Yamaguchi, M., Jan 1 2017, In : American Journal of Cancer Research. 7, 3, p. 673-687 15 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Correction: "UV damage-induced phosphorylation of HBO1 triggers CRL4DDB2-mediated degradation to regulate cell proliferation" [Molecular and Cellular Biology 36, 3, (2016) (394-406)] doi 10.1128/MCB.00809-15

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., Apr 1 2018, In : Molecular and cellular biology. 38, 7, e00572-17.

Research output: Contribution to journalComment/debate

Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation

Nakagome, S., Mano, S., Kozlowski, L., Bujnicki, J. M., Shibata, H., Fukumaki, Y., Kidd, J. R., Kidd, K. K., Kawamura, S. & Oota, H., Jun 1 2012, In : Molecular Biology and Evolution. 29, 6, p. 1569-1585 17 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence

Takizawa, Y., Tanaka, H., Machida, S., Koyama, M., Maehara, K., Ohkawa, Y., Wade, P. A., Wolf, M. & Kurumizaka, H., Jan 1 2018, In : Open Biology. 8, 3, 170255.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Apr 25 2017, In : Biochemistry. 56, 16, p. 2184-2196 13 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Crystal structure of the c-terminal globular domain of oligosaccharyltransferase from archaeoglobus fulgidus at 1.75 Åresolution

Matsumoto, S., Igura, M., Nyirenda, J., Matsumoto, M., Yuzawa, S., Noda, N., Inagaki, F. & Kohda, D., May 22 2012, In : Biochemistry. 51, 20, p. 4157-4166 10 p.

Research output: Contribution to journalArticle

32 Citations (Scopus)

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Kato, D., Osakabe, A., Arimura, Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi, S., Nishimura, Y., Park, S. Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M. & Kurumizaka, H., Apr 14 2017, In : Science. 356, 6334, p. 205-208 4 p., 356.

Research output: Contribution to journalArticle

28 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

320 Citations (Scopus)

Defective cortex glia plasma membrane structure underlies light-induced epilepsy in cpes mutants

Kunduri, G., Turner-Evans, D., Konya, Y., Izumi, Y., Nagashima, K., Lockett, S., Holthuis, J., Bamba, T., Acharya, U. & Acharya, J. K., Sep 18 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 38, p. E8919-E8928

Research output: Contribution to journalArticle

7 Citations (Scopus)

DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites

Maruyama, O. & Matsuzaki, F., Dec 6 2018, Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc., p. 1-9 9 p. 8567448. (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018).

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

DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites

Maruyama, O. & Matsuzaki, F., Dec 10 2018, p. 1-9. 9 p.

Research output: Contribution to conferencePaper

DegSampler3: Pairwise dependency model in degradation motif site prediction of substrate protein sequences

Maruyama, O. & Matsuzaki, F., Oct 2019, Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019. Institute of Electrical and Electronics Engineers Inc., p. 11-17 7 p. 8941973. (Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019).

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

12 Citations (Scopus)

Development of a practical online supercritical fluid extraction–supercritical fluid chromatography/mass spectrometry system with an integrated split-flow method

Sakai, M., Hayakawa, Y., Funada, Y., Ando, T., Fukusaki, E. & Bamba, T., May 10 2019, In : Journal of Chromatography A. 1592, p. 161-172 12 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Development of a split-flow system for high precision variable sample introduction in supercritical fluid chromatography

Sakai, M., Hayakawa, Y., Funada, Y., Ando, T., Fukusaki, E. & Bamba, T., Sep 15 2017, In : Journal of Chromatography A. 1515, p. 218-231 14 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Dietary Intake of Curcumin Improves eIF2 Signaling and Reduces Lipid Levels in the White Adipose Tissue of Obese Mice

Kobori, M., Takahashi, Y., Takeda, H., Takahashi, M., Izumi, Y., Akimoto, Y., Sakurai, M., Oike, H., Nakagawa, T., Itoh, M., Bamba, T. & Kimura, T., Dec 1 2018, In : Scientific reports. 8, 1, 9081.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells

Shishido, Y., Baba, T., Sato, T., Shima, Y., Miyabayashi, K., Inoue, M., Akiyama, H., Kimura, H., Kanai, Y., Ishihara, Y., Haraguchi, S., Miyazaki, A., Rozman, D., Yamazaki, T., Choi, M. H., Ohkawa, Y., Suyama, M. & Morohashi, K. I., Jan 1 2017, In : Scientific reports. 7, 41912.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells

Kumamaru, H., Ohkawa, Y., Saiwai, H., Yamada, H., Kubota, K., Kobayakawa, K., Akashi, K., Okano, H., Iwamoto, Y. & Okada, S., Nov 26 2012, In : Nature communications. 3, 1140.

Research output: Contribution to journalArticle

41 Citations (Scopus)