Research Output

Book

Diabetes Mellitus, A risk factor for Alzheimer's Disease

Nakabeppu, Y. (ed.) & Ninomiya, T. (ed.), May 7 2019, Singapore: Springer. 248 p. (Advances in Experimental Medicine and Biology)

Research output: Book/ReportBook

Chapter

An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure in samples of limited cell number

Ohkawa, Y., Mallappa, C., Vallaster, C. S. D. & Imbalzano, A. N., Jan 2 2012, Myogenesis: Methods and Protocols. DiMario, J. (ed.). p. 531-542 12 p. (Methods in Molecular Biology; vol. 798).

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)

Context-dependent bidirectional modulation of Wnt/β-catenin signaling

Ishitani, T., Nov 1 2014, New Principles in Developmental Processes. Springer Japan, Vol. 9784431546344. p. 213-225 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Replication and Transcription

Nakabeppu, Y., Maki, H. & Sekiguchi, M., 2007, Genomics and Genetics: From Molecular Details to Analysis and Techniques. Meyers, R. A. (ed.). Weinheim, Germany: Wiley-VCH, Vol. 1. p. 47-74 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Replication and Transcription

Nakabeppu, Y., Maki, H. & Mutsuo, S., 1995, Molecular Biology and Biotechnology: A comprehensive Desk Reference. Meyers, R. A. (ed.). New York, NY, USA: VCH Publishers, p. 234-238 5 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Replication and Transcription

Maki, H., Nakabeppu, Y. & Mutsuo, S., 1996, Molecular Biology and Biotechnology: A comprehensive Desk Reference. Meyers, R. A. (ed.). New York, NY, USA: VCH Publishers, p. 86-96 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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)

Knockout Mouse Models Provide Insight into the Biological Functions of CRL1 Components

Nakagawa, T., Nakayama, K. & Nakayama, K. I., Jan 1 2020, Advances in Experimental Medicine and Biology. Springer, p. 147-171 25 p. (Advances in Experimental Medicine and Biology; vol. 1217).

Research output: Chapter in Book/Report/Conference proceedingChapter

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)

Molecular pathophysiology of insulin depletion, mitochondrial dysfunction, and oxidative stress in Alzheimer’s disease brain

Nakabeppu, Y., May 7 2019, Advances in Experimental Medicine and Biology. Springer, p. 27-44 18 p. (Advances in Experimental Medicine and Biology; vol. 1128).

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Neurodegeneration caused by accumulation of an oxidized base lesion, 8-oxoguanine, in nuclear and mitochondrial DNA: from animal models to human diseases.

Nakabeppu, Y., Apr 1 2017, The Base Excision Repair Pathway: Molecular Mechanisms and Role in Disease Development and Therapeutic Design . World Scientific Publishing Co. Pte Ltd, p. 523-556 34 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Origins of brain insulin and its function

Nakabeppu, Y., May 7 2019, Advances in Experimental Medicine and Biology. Springer, p. 1-11 11 p. (Advances in Experimental Medicine and Biology; vol. 1128).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Pathogen-sensing by mincle: Function and molecular aspects

Nagata, M., Omahdi, Z. & Yamasaki, S., Jan 1 2016, C-Type Lectin Receptors in Immunity. Springer Japan, p. 15-34 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

Polar Lipid Profiling by Supercritical Fluid Chromatography/Mass Spectrometry Method

Yamada, T., Nagasawa, Y., Taguchi, K., Fukusaki, E. & Bamba, T., Apr 15 2015, Polar Lipids: Biology, Chemistry, and Technology. Elsevier Inc., p. 439-462 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Post-translational modification of Tcf/Lef: New insights into the regulation of Wnt/β-catenin signaling

Ishitani, T., Sep 2 2015, Protein Modifications in Pathogenic Dysregulation of Signaling. Springer Japan, p. 327-342 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Prediction of compound-protein interactions with machine learning methods

Yamanishi, Y. & Kashima, H., Dec 1 2010, Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques. IGI Global, p. 304-317 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Prevention of the Mutagenecity and Cytotoxicity of Oxidized Purine Nucleotides

Nakabeppu, Y., Behmanesh, M., Ymaguchi, H., Tsuchimoto, D. & Kunihiko, S., 2007, Oxidative Damage to Nucleic Acids. Evans, MD. & Cooke, MS. (eds.). Landes Bioscience, Springer Science+Business Media, p. 40-53

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein-ligand interactions studied by NMR

Hiroaki, H. & Kohda, D., Nov 23 2017, Experimental Approaches of NMR Spectroscopy: Methodology and Application to Life Science and Materials Science. Springer Singapore, p. 579-600 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Sensing necrotic cells

Miyake, Y. & Yamasaki, S., Apr 23 2012, Self and Nonself. p. 144-152 9 p. (Advances in Experimental Medicine and Biology; vol. 738).

Research output: Chapter in Book/Report/Conference proceedingChapter

50 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)

Structural basis of protein asn-glycosylation by oligosaccharyltransferases

Kohda, D., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 171-199 29 p. (Advances in Experimental Medicine and Biology; vol. 1104).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Structural biology of oligosaccharyltransferase (ost)

Matsumoto, S., Nyirenda, J. & Kohda, D., Jan 1 2015, Glycoscience: Biology and Medicine. Springer Japan, p. 437-445 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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)

Supervised Inference of Metabolic Networks from the Integration of Genomic Data and Chemical Information

Yamanishi, Y., Apr 19 2010, Elements of Computational Systems Biology. John Wiley and Sons, p. 189-211 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

5 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

What have we learned from cultured adult dorsal root ganglion neurons?

Sango, K., Niimi, N., Tsukamoto, M., Utsunomiya, K., Sakumi, K., Nakabeppu, Y., Kadoya, T. & Horie, H., Jan 1 2014, Ganglion Cells: Morphology, Functional Development and Role in Disease. Nova Science Publishers, Inc., p. 125-148 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Chapter (peer-reviewed)

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)

Comment/debate

APE1- and APE2-dependent DNA breaks in immunoglobulin class switch recombination (Journal of Experimental Medicine (November 26, 2007) 204: 12 (3017-3026))

Guikema, J. E. J., Linehan, E. K., Tsuchimoto, D., Nakabeppu, Y., Strauss, P. R., Stavnezer, J. & Schrader, C. E., Dec 24 2007, In : Journal of Experimental Medicine. 204, 13, 1 p.

Research output: Contribution to journalComment/debate

Author Correction: Intragenic antagonistic roles of protein and circRNA in tumorigenesis (Cell Research, (2019), 29, 8, (628-640), 10.1038/s41422-019-0192-1)

Guarnerio, J., Zhang, Y., Cheloni, G., Panella, R., Katon, J. M., Simpson, M., Matsumoto, A., Papa, A., Loretelli, C., Petri, A., Kauppinen, S., Garbutt, C., Nielsen, G. P., Deshpande, V., Castillo-Martin, M., Cordon-Cardo, C., Spentzos, D., Clohessy, J. G., Batish, M. & Pandolfi, P. P., Feb 1 2020, In : Cell Research. 30, 2, 1 p.

Research output: Contribution to journalComment/debate

Open Access

CD30 ligand could be a new therapeutic target for central nervous system autoimmunity

Shinoda, K. & Yoshikai, Y., May 1 2015, In : Clinical and Experimental Neuroimmunology. 6, 2, p. 111-112 2 p.

Research output: Contribution to journalComment/debate

Correction: Co-stimulation with LFA-1 triggers apoptosis in γδ T cells on T cell receptor engagement (European Journal of Immunology (1994) 24 (10))

Matsumoto, Y., Hiromatsu, K., Saki, T., Kobayashi, Y., Kimura, Y., Usami, J., Shinzato, T., Maeda, K. & Yoshikai, Y., Nov 23 1994, In : European Journal of Immunology. 24, 11, 1 p.

Research output: Contribution to journalComment/debate

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

Correction: Annular PIP3 accumulation controls actin architecture and modulates cytotoxicity at the immunological synapse [The Journal of Experimental Medicine, 210, 12, November 18, (2013) 2721-2737]doi 10.1084/jem.20131324

Le Floc'h, A., Tanaka, Y., Bantilan, N. S., Voisinne, G., Altan-Bonnet, G., Fukui, Y. & Huse, M., Apr 1 2017, In : Journal of Experimental Medicine. 214, 4, 1 p.

Research output: Contribution to journalComment/debate

5 Citations (Scopus)

Erratum: New Insight into the Role of the Calvin Cycle: Reutilization of CO2 Emitted through Sugar Degradation (Scientific Reports 5 (2016) (11617) DOI: 10.1038/srep11617)

Shimizu, R., Dempo, Y., Nakayama, Y., Nakamura, S., Bamba, T., Fukusaki, E. & Fukui, T., Jun 20 2016, In : Scientific reports. 6, 27961.

Research output: Contribution to journalComment/debate

Erratum: Skp2 targeting suppresses tumorigenesis by Arf-p53-independent cellular senescence (Nature (2010) 464 (374-379))

Lin, H. K., Chen, Z., Wang, G., Nardella, C., Lee, S. W., Chan, C. H., Yang, W. L., Wang, J., Egia, A., Nakayama, K. I., Cordon-Cardo, C., Teruya-Feldstein, J. & Pandolfi, P. P., Jul 15 2010, In : Nature. 466, 7304, 1 p.

Research output: Contribution to journalComment/debate

3 Citations (Scopus)
1 Citation (Scopus)
1 Citation (Scopus)

Erratum: Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, MethylRO (Stem Cell Reports (2014) 2 (910-924))

Ueda, J., Maehara, K., Mashiko, D., Ichinose, T., Yao, T., Hori, M., Sato, Y., Kimura, H., Ohkawa, Y. & Yamagata, K., Jul 8 2014, In : Stem Cell Reports. 3, 1, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome (Nature Communications (2015) 6 (7870) DOI: 10.1038/ncomms8870)

Thijssen, P. E., Ito, Y., Grillo, G., Wang, J., Velasco, G., Nitta, H., Unoki, M., Yoshihara, M., Suyama, M., Sun, Y., Lemmers, R. J. L. F., De Greef, J. C., Gennery, A., Picco, P., Kloeckener-Gruissem, B., Güngör, T., Reisli, I., Picard, C., Kebaili, K., Roquelaure, B. & 9 others, Iwai, T., Kondo, I., Kubota, T., Van Ostaijen-Ten Dam, M. M., Van Tol, M. J. D., Weemaes, C., Francastel, C., Van Der Maarel, S. M. & Sasaki, H., Jun 22 2016, In : Nature communications. 7, 12003.

Research output: Contribution to journalComment/debate

Erratum: Ubiquitin-dependent degradation of IκBα is mediated by a ubiquitin ligase Skp1/Cul1/F-box protein FWD1 (Proceedings of the National Academy of Sciences of the United States America (March 30, 1999) 96:7 (3859- 3863))

Hatakeyama, S., Kitagawa, M., Nakayama, K., Shirane, M., Matsumoto, M., Hattori, K., Higashi, H., Nakano, H., Okumura, K., Onoe, K., Good, R. A. & Nakayama, K. I., Jan 1 1999, In : Proceedings of the National Academy of Sciences of the United States of America. 96, 11, 1 p.

Research output: Contribution to journalComment/debate

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

Erratum: Structure and function of human histone H3.Y nucleosome (Nucleic acids research (2016) 44 13 (6127-6141))

Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Apr 7 2017, In : Nucleic acids research. 45, 6, 1 p.

Research output: Contribution to journalComment/debate

1 Citation (Scopus)

Erratum: A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip (Nucleic Acids Research (2010) 38:15 (4929-4945)) DOI:10.1093/nar/gkq200)

Hiura, H., Sugawara, A., Ogawa, H., John, R. M., Miyauchi, N., Miyanari, Y., Horiike, T., Li, Y., Yaegashi, N., Sasaki, H., Kono, T. & Arima, T., Sep 15 2014, In : Nucleic acids research. 42, 16, 1 p.

Research output: Contribution to journalComment/debate

Erratum: A novel protein with RNA-binding motifs interacts with ataxin-2 (Human Molecular Genetics (2000) vol.9 (1303-1313))

Shibata, H., Huynh, D. P. & Pulst, S. M., Aug 17 2000, In : Human Molecular Genetics. 9, 12, 1 p.

Research output: Contribution to journalComment/debate