Research Output 1979 2020

Letter

X-ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation

Abe, Y., Shioi, S., Kita, S., Nakata, H., Maenaka, K., Kohda, D., Katayama, T. & Ueda, T., Nov 2017, In : FEBS Letters. 591, 22, p. 3805-3816 12 p.

Research output: Contribution to journalLetter

Crystal structure
X-Rays
X rays
Heat-Shock Proteins
Proteins
Foreword/postscript

Preface

Lodhi, H. & Yamanishi, Y., Dec 1 2010, Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques. IGI Global, p. xv-xvi

Research output: Chapter in Book/Report/Conference proceedingForeword/postscript

Editorial
7 Citations (Scopus)

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

beta Catenin
Phosphotransferases
6 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

Pneumocystis
C-Type Lectins
Innate Immunity
Pneumocystis carinii
Pathogens

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

Molecular Evolution
Germ-Line Mutation
Mutagenesis

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

Molecules
Proteins
Conference contribution
6 Citations (Scopus)

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

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

Binding sites
Binding Sites
Proteins
Substrates
Probability distributions

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

Screening
Throughput
Microfluidics
Biological fuel cells
Sorting

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

Protein-protein Interaction
Distance Matrix
False Positive
Proteins
Mirrors
51 Citations (Scopus)

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

Semi-supervised Learning
Conjugate gradient method
Supervised learning
Learning algorithms
Tensors

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

Nonlinear Estimation
Function Estimation
Autoregressive Model
Nonlinear Function
Nonlinear Model

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

Recovery
Signal transduction
Systems Biology
17 Citations (Scopus)

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

Pairwise
kernel
Collaborative filtering
Alternatives
Cartesian
122 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

DNA Damage
Mitochondria
DNA Glycosylases
Proteins
Nucleotides
15 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

Osteoclasts
Caspase 3
Apoptosis
Proteins
Chemical activation

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

Signal transduction
Molecular interactions
Factorization
Genes
Proteins
4 Citations (Scopus)

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

Amyloid beta-Protein Precursor
Amyloid beta-Peptides
Genes
28 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

Supervised learning
Hilbert spaces
Topology
Proteins

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

Conference article
56 Citations (Scopus)

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

Mitochondria
DNA Glycosylases
Nucleic Acids
Reactive Oxygen Species
Neurodegenerative diseases
180 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

DNA Glycosylases
Mutagenesis
Nucleic Acids
Carcinogenesis
Genes

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

Corpus Striatum
Genome
Brain
Mitochondrial DNA
Parkinson Disease
1 Citation (Scopus)

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

DNA Mutational Analysis
Bromates
Neoplastic Cell Transformation
Radiation-Induced Neoplasms
DNA Repair-Deficiency Disorders
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

DNA Breaks
Immunoglobulin Isotypes
Genetic Recombination
Biomedical Research

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., Jan 1 2020, (Accepted/In press) In : Cell Research.

Research output: Contribution to journalComment/debate

Open Access
Carcinogenesis
Israel
Sarcoma
Connective Tissue
Pathology

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

CD30 Ligand
Autoimmunity
Central Nervous System
Therapeutics

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

Immunological Synapses
Biomedical Research
Actins
Emotions

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

Cell Biology
Molecular Biology
Phosphorylation
Cell Proliferation
4 Citations (Scopus)
75 Citations (Scopus)
Histone Code
Toxoplasmosis
DNA Methylation
Drug Discovery
Drug Delivery Systems

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., Jan 1 2015, In : American Journal of Pathology. 185, 10, 1 p., 2145.

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

1 Citation (Scopus)
Western Blotting
Insulin
Liver

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

3 Citations (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

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

Cell Aging
Carcinogenesis
Non-Receptor Type 6 Protein Tyrosine Phosphatase
Dendritic Cells
Macrophages
Pathology

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

Heterochromatin
DNA Methylation
Stem Cells

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

F-Box Proteins
Ligases
Ubiquitin

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: 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

Chromosomes, Human, Pair 1
Nucleic Acids
Research
1 Citation (Scopus)
Alkylating Agents
DNA Repair
Genes

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

Medical Genetics
Molecular Biology
Proteins
Ataxin-2
RNA-Binding Motifs