Research Output

Erratum: Regulation of SV40 large T-Antigen stability by reversible acetylation (Oncogene (2006) 25 (7391-7400) DOI: 10.1038/sj.onc.1209731)

Shimazu, T., Komatsu, Y., Nakayama, K. I., Fukazawa, H., Horinouchi, S. & Yoshida, M., Jul 17 2014, In : Oncogene. 33, 29, 1 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Erratum: The Skp2-SCF E3 ligase regulates akt ubiquitination, glycolysis, herceptin sensitivity, and tumorigenesis (Cell (2012) 149 (1098-1111))

Chan, C. H., Li, C. F., Yang, W. L., Gao, Y., Lee, S. W., Feng, Z., Huang, H. Y., Tsai, K. K. C., Flores, L. G., Shao, Y., Hazle, J. D., Yu, D., Wei, W., Sarbassov, D., Hung, M. C., Nakayama, K. I. & Lin, H. K., Nov 9 2012, In : Cell. 151, 4, p. 913-914 2 p.

Research output: Contribution to journalComment/debate

4 Citations (Scopus)

Erratum: Identification and Characterization of a Novel Small-Molecule Inhibitor of β-Catenin Signaling ((2014) 184 (2111-2122) DOI: 10.1016/j.ajpath.2014.04.002)

Delgado, E. R., Yang, J., So, J., Fanti, M., Leimgruber, S., Kahn, M., Ishitani, T., Shin, D., Wilson, G. M. & Monga, S. P., Oct 2015, In : American Journal of Pathology. 185, 10, 1 p., 2145.

Research output: Contribution to journalComment/debate

Erratum: FosB-null mice display impaired adult hippocampal neurogenesis and spontaneous epilepsy with depressive behavior (Neuropsychopharmacology (2013) 38 (1374-1375) DOI: 10.1038/npp.2013.56)

Yutsudo, N., Kamada, T., Kajitani, K., Nomaru, H., Katogi, A., Ohnishi, Y. H., Ohnishi, Y. N., Takase, K. I., Sakumi, K., Shigeto, H. & Nakabeppu, Y., Jun 1 2013, In : Neuropsychopharmacology. 38, 7, p. 1374-1375 2 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Erratum: Human Oggl, a protein involved in the repair of 8-oxoguanine, is inhibited by nitric oxide (Cancer Research (September 1, 2001) (6388-6393))

Jaiswal, M., LaRusso, N. F., Nishioka, K., Nakabeppu, Y. & Gores, G. J., Oct 15 2001, In : Cancer Research. 61, 20, 1 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Erratum: Hyperactive mTOR signals in the proopiomelanocortin-expressing hippocampal neurons cause age-dependent epilepsy and premature death in mice (Scientific Reports (2016) 6 (22991) DOI: 10.1038/srep22991)

Matsushita, Y., Sakai, Y., Shimmura, M., Shigeto, H., Nishio, M., Akamine, S., Sanefuji, M., Ishizaki, Y., Torisu, H., Nakabeppu, Y., Suzuki, A., Takada, H. & Hara, T., Jun 10 2016, In : Scientific reports. 6, 27164.

Research output: Contribution to journalComment/debate

Erratum: Identification of human MutY homolog (hMYH) as a repair enzyme for 2-hydroxyadenine in DNA and detection of multiple forms of hMYH located in nuclei and mitochondria (Nucleic Acids Res. (2000) 28 (1355-64))

Ohtsubo, T., Nishioka, K., Imaiso, Y., Iwai, S., Shimokawa, H., Oda, H., Fujiwara, T. & Nakabeppu, Y., Mar 23 2015, In : Nucleic acids research. 43, 7, p. 3870-3871 2 p.

Research output: Contribution to journalComment/debate

2 Citations (Scopus)

Generation of human oogonia from induced pluripotent stem cells in vitro

Yamashiro, C., Sasaki, K., Yabuta, Y., Kojima, Y., Nakamura, T., Okamoto, I., Yokobayashi, S., Murase, Y., Ishikura, Y., Shirane, K., Sasaki, H., Yamamoto, T. & Saitou, M., Mar 1 2019, In : Obstetrical and Gynecological Survey. 74, 3, p. 158-159 2 p.

Research output: Contribution to journalComment/debate

Genomic organization of the human-amyloid beta-protein precursor gene

Yoshikai, S. I., Sasaki, H., Doh-ura, K., Furuya, H. & Sakaki, Y., Jun 30 1991, In : Gene. 102, 2, p. 291-292 2 p.

Research output: Contribution to journalComment/debate

15 Citations (Scopus)

Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development (Genome Research (2011) 21 (2058-2066))

Ichiyanagi, K., Li, Y., Watanabe, T., Ichiyanagi, T., Fukuda, K., Kitayama, J., Yamamoto, Y., Kuramochi-Miyagawa, S., Nakano, T., Yabuta, Y., Seki, Y., Saitou, M. & Sasaki, H., Apr 1 2012, In : Genome Research. 22, 4, 1 p.

Research output: Contribution to journalComment/debate

Mutual regulation of protein-tyrosine phosphatase 20 and protein-tyrosine kinase Tec activities by tyrosine phosphorylation and dephosphorylation (Journal of Biological Chemistry (2004) 279, (10765-10775))

Aoki, N., Ueno, S., Mano, H., Yamasaki, S., Shiota, M., Miyazaki, H., Yamaguchi-Aoki, Y., Matsuda, T. & Ullrich, A., Oct 15 2010, In : Journal of Biological Chemistry. 285, 42, 1 p.

Research output: Contribution to journalComment/debate

Novel methods for the treatment of liver fibrosis using in vivo direct reprogramming technology

Goya, T. & Suzuki, A., Jan 1 2016, In : Stem Cell Investigation. 2016, DEC, 92.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Phosphorylation of p27Kip1on serine 10 is required for its binding to CRM1 and nuclear export

Ishida, N., Hara, T., Kamura, T., Yoshida, M., Nakayama, K. & Nakayama, K. I., Mar 13 2015, In : Journal of Biological Chemistry. 290, 11, 1 p.

Research output: Contribution to journalComment/debate

3 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)

Sendai virus pneumonia: Evidence for the early recruitment of γδ T cells during the disease course

Ogasawara, T., Emoto, M., Kiyotani, K., Shimokata, K., Yoshida, T., Nagai, Y. & Yoshikai, Y., Jan 1 1994, In : Journal of virology. 68, 6, p. 4022-4027 6 p.

Research output: Contribution to journalComment/debate

23 Citations (Scopus)

The anti-apoptotic ubiquitin conjugating enzyme BIRC6/BRUCE regulates autophagosome-lysosome fusion

Ikeda, F., Jul 3 2018, In : Autophagy. 14, 7, p. 1283-1284 2 p.

Research output: Contribution to journalComment/debate

Open Access
2 Citations (Scopus)

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Stunnenberg, H. G., Abrignani, S., Adams, D., de Almeida, M., Altucci, L., Amin, V., Amit, I., Antonarakis, S. E., Aparicio, S., Arima, T., Arrigoni, L., Arts, R., Asnafi, V., Badosa, M. E., Bae, J. B., Bassler, K., Beck, S., Berkman, B., Bernstein, B. E., Bilenky, M. & 210 others, Bird, A., Bock, C., Boehm, B., Bourque, G., Breeze, C. E., Brors, B., Bujold, D., Burren, O., Bussemakers, M. J., Butterworth, A., Campo, E., Carrillo-de-Santa-Pau, E., Chadwick, L., Chan, K. M., Chen, W., Cheung, T. H., Chiapperino, L., Choi, N. H., Chung, H. R., Clarke, L., Connors, J. M., Cronet, P., Danesh, J., Dermitzakis, M., Drewes, G., Durek, P., Dyke, S., Dylag, T., Eaves, C. J., Ebert, P., Eils, R., Eils, J., Ennis, C. A., Enver, T., Feingold, E. A., Felder, B., Ferguson-Smith, A., Fitzgibbon, J., Flicek, P., Foo, R. S. Y., Fraser, P., Frontini, M., Furlong, E., Gakkhar, S., Gasparoni, N., Gasparoni, G., Geschwind, D. H., Glažar, P., Graf, T., Grosveld, F., Guan, X. Y., Guigo, R., Gut, I. G., Hamann, A., Han, B. G., Harris, R. A., Heath, S., Helin, K., Hengstler, J. G., Heravi-Moussavi, A., Herrup, K., Hill, S., Hilton, J. A., Hitz, B. C., Horsthemke, B., Hu, M., Hwang, J. Y., Ip, N. Y., Ito, T., Javierre, B. M., Jenko, S., Jenuwein, T., Joly, Y., Jones, S. J. M., Kanai, Y., Kang, H. G., Karsan, A., Kiemer, A. K., Kim, S. C., Kim, B. J., Kim, H. H., Kimura, H., Kinkley, S., Klironomos, F., Koh, I. U., Kostadima, M., Kressler, C., Kreuzhuber, R., Kundaje, A., Küppers, R., Larabell, C., Lasko, P., Lathrop, M., Lee, D. H. S., Lee, S., Lehrach, H., Leitão, E., Lengauer, T., Lernmark, Å., Leslie, R. D., Leung, G. K. K., Leung, D., Loeffler, M., Ma, Y., Mai, A., Manke, T., Marcotte, E. R., Marra, M. A., Martens, J. H. A., Martin-Subero, J. I., Maschke, K., Merten, C., Milosavljevic, A., Minucci, S., Mitsuyama, T., Moore, R. A., Müller, F., Mungall, A. J., Netea, M. G., Nordström, K., Norstedt, I., Okae, H., Onuchic, V., Ouellette, F., Ouwehand, W., Pagani, M., Pancaldi, V., Pap, T., Pastinen, T., Patel, R., Paul, D. S., Pazin, M. J., Pelicci, P. G., Phillips, A. G., Polansky, J., Porse, B., Pospisilik, J. A., Prabhakar, S., Procaccini, D. C., Radbruch, A., Rajewsky, N., Rakyan, V., Reik, W., Ren, B., Richardson, D., Richter, A., Rico, D., Roberts, D. J., Rosenstiel, P., Rothstein, M., Salhab, A., Sasaki, H., Satterlee, J. S., Sauer, S., Schacht, C., Schmidt, F., Schmitz, G., Schreiber, S., Schröder, C., Schübeler, D., Schultze, J. L., Schulyer, R. P., Schulz, M., Seifert, M., Shirahige, K., Siebert, R., Sierocinski, T., Siminoff, L., Sinha, A., Soranzo, N., Spicuglia, S., Spivakov, M., Steidl, C., Strattan, J. S., Stratton, M., Südbeck, P., Sun, H., Suzuki, N., Suzuki, Y., Tanay, A., Torrents, D., Tyson, F. L., Ulas, T., Ullrich, S., Ushijima, T., Valencia, A., Vellenga, E., Vingron, M., Wallace, C., Wallner, S., Walter, J., Wang, H., Weber, S., Weiler, N., Weller, A., Weng, A., Wilder, S., Wiseman, S. M., Wu, A. R., Wu, Z., Xiong, J., Yamashita, Y., Yang, X., Yap, D. Y., Yip, K. Y., Yip, S., Yoo, J. I., Zerbino, D., Zipprich, G. & Hirst, M., Nov 17 2016, In : Cell. 167, 5, p. 1145-1149 5 p.

Research output: Contribution to journalComment/debate

100 Citations (Scopus)

USP19 deubiquitinating enzyme supports cell proliferation by stabilizing KPC1, a ubiquitin ligase for p27Kip1 (Molecular and Cellular Biology (2009) 29, 2, (547-558))

Lu, Y., Adegoke, O. A. J., Nepveu, A., Nakayama, K. I., Bedard, N., Cheng, D., Peng, J. & Wing, S. S., Jun 1 2009, In : Molecular and cellular biology. 29, 11, 1 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)
Conference article

Biological significance of the defense mechanisms against oxidative damage in nucleic acids caused by reactive oxygen species: From mitochondria to nuclei

Nakabeppu, Y., Tsuchimoto, D., Ichinoe, A., Ohno, M., Ide, Y., Hirano, S., Yoshimura, D., Tominaga, Y., Furuichi, M. & Sakumi, K., Jan 1 2004, In : Annals of the New York Academy of Sciences. 1011, p. 101-111 11 p.

Research output: Contribution to journalConference article

56 Citations (Scopus)

Mutagenesis and carcinogenesis caused by the oxidation of nucleic acids.

Nakabeppu, Y., Kunihiko, S., Sakamoto, K., Tsuchimoto, D., Tsuzuki, T. & Nakatsu, Y., Jan 1 2006, In : Biological chemistry. 387, 4, p. 373-379 7 p.

Research output: Contribution to journalConference article

182 Citations (Scopus)

Oxidative damage in brain genome and neuroprotection

Nakabeppu, Y., Sheng, Z. & Oka, S., Jul 8 2010, In : Hirosaki Medical Journal. 61, SUPPL., p. S70-S79

Research output: Contribution to journalConference article

Oxidative stress-induced tumorigenesis in the small intestines of DNA repair-deficient mice.

Tsuzuki, T., Piao, J. S., Isoda, T., Sakumi, K., Nakabeppu, Y. & Nakatsu, Y., Mar 1 2011, In : Health physics. 100, 3, p. 293-294 2 p.

Research output: Contribution to journalConference article

1 Citation (Scopus)
Conference contribution

A BP-Based Algorithm for Performing Bayesian Inference in Large Perceptron-Type Networks

Kabashima, Y. & Uda, S., 2004, International Conference on Algorithmic Learning Theory. p. 479-493

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

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

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

Development of μtas for high-throughput screening of nad(p)-dependent oxidoreductases

Shimokihara, S., Shitara, S., Oyobiki, R., Watanabe, T., Einaga, Y., Matsumoto, Y., Fujiwara, K., Horisawa, K. & Doi, N., Jan 1 2015, MicroTAS 2015 - 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences. Chemical and Biological Microsystems Society, p. 1302-1304 3 p. (MicroTAS 2015 - 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences).

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

2 Citations (Scopus)

Inference of protein-protein interactions by using co-evolutionary information

Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M. & Toh, H., 2007, Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS. p. 322-333 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4545 LNCS).

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

Link propagation: A fast semi-supervised learning algorithm for link prediction

Kashima, H., Kato, T., Yamanishi, Y., Sugiyama, M. & Tsuda, K., Dec 1 2009, Society for Industrial and Applied Mathematics - 9th SIAM International Conference on Data Mining 2009, Proceedings in Applied Mathematics 133. p. 1093-1104 12 p. (Society for Industrial and Applied Mathematics - 9th SIAM International Conference on Data Mining 2009, Proceedings in Applied Mathematics; vol. 3).

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

52 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

On pairwise kernels: An efficient alternative and generalization analysis

Kashima, H., Oyama, S., Yamanishi, Y. & Tsuda, K., Jul 23 2009, 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2009. p. 1030-1037 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5476 LNAI).

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

17 Citations (Scopus)

Regulation of intracellular localization of human MTH1, OGG1, and MYH proteins for repair of oxidative DNA damage

Nakabeppu, Y., Dec 1 2001, Progress in Nucleic Acid Research and Molecular Biology: Base Excsion Repair. Moldave, K. (ed.). San Dieg, CA, USA: Academic Press Inc., p. 75-94 20 p.

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

123 Citations (Scopus)

Regulation of osteoclast apoptosis by bcl-2 family protein bim and caspase-3

Tanaka, S., Wakeyama, H., Akiyama, T., Takahashi, K., Amano, H., Nakayama, K. I. & Nakamura, K., Dec 1 2010, Osteoimmunology: Interactions of the Immune and Skeletal Systems II. Choi, Y. (ed.). p. 111-116 6 p. (Advances in Experimental Medicine and Biology; vol. 658).

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

15 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

Structure and expression of Alzheimer's amyloid β-protein precursor gene

Sasaki, H., Yoshikai, S. I., Izumi, R., Yamada, T., Furuya, H., Doh-Ura, K., Goto, I. & Sakaki, Y., Jan 1 1990, Molecular biology and genetics of Alzheimer's disease: proceedings of the International Symposium on Dementia: Molecular Biology and Genetics of Alzheimer's Disease. ICS884. Miyatake, T., Selkoe, D. J., Ihara, Y., Miyatake, T., Selkoe, D. J. & Ihara, Y. (eds.). Elsevier Science Publishers B.V., p. 105-112 8 p. (Molecular biology and genetics of Alzheimer's disease: proceedings of the International Symposium on Dementia: Molecular Biology and Genetics of Alzheimer's Disease. ICS884).

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

4 Citations (Scopus)

Supervised bipartite graph inference

Yamanishi, Y., Dec 1 2009, Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. p. 1841-1848 8 p. (Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference).

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

29 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 genes involved in the repair of alkylated DNA in Escherichia coli K-12

Yamamoto, Y., Kataoka, H., Nakabeppu, Y., Tsuzuki, T. & Mutsuo, S., 1983, Cellular Responses to DNA Damage . Friedberg, EC. & Bridges, BR. (eds.). New York, NY, USA: Alan R. Liss, Inc., p. 271-278

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

Transcription Factors Induced by Growth-Stimulating Agents

Nathans, D., Christy, BA., DuBois, RA., Lanahan, A., Sanders, LK. & Nakabeppu, Y., 1991, Origins of Human Cancer: A Comprehensive Review. Brugge, J., Curran, T., Harlow, E. & McCormick, F. (eds.). Plainview, New York: Cold Spring Harbor Laboratory Press, p. 353-364 12 p.

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

Editorial

Context-dependent dual and opposite roles of nemo-like kinase in the Wnt/β-catenin signaling

Ishitani, T., May 1 2012, In : Cell Cycle. 11, 9, p. 1743-1745 3 p.

Research output: Contribution to journalEditorial

7 Citations (Scopus)

Dectin-2 is a C-type lectin receptor that recognizes pneumocystis and participates in innate immune responses

Kottom, T. J., Hebrink, D. M., Jenson, P. E., Marsolek, P. L., Wüthrich, M., Wang, H., Klein, B., Yamasaki, S. & Limper, A. H., Feb 2018, In : American journal of respiratory cell and molecular biology. 58, 2, p. 232-240 9 p.

Research output: Contribution to journalEditorial

7 Citations (Scopus)

International symposium on “germline mutagenesis and Biodiversification”

Uchimura, A., Hara, Y., Gondo, Y. & Nakabeppu, Y., Sep 1 2014, In : Genes and Genetic Systems. 89, 2, p. 93-95 3 p.

Research output: Contribution to journalEditorial

Preface to the special issue on novel measurement techniques for visualizing ‘live’ protein molecules at work

Nishida, N., Tsukazaki, T. & Kohda, D., Feb 2020, In : Biochimica et Biophysica Acta - General Subjects. 1864, 2, 129421.

Research output: Contribution to journalEditorial