Research Output 1979 2020

Conference 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

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

Ubiquitin-Protein Ligases
Binding sites
Proteins
Degradation
Substrates

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

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
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

Letter
14 Citations (Scopus)
Pyrophosphatases
DNA Repair Enzymes
Amino Acid Sequence Homology
Escherichia coli Proteins
p53 Genes
3 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

Brain-Derived Neurotrophic Factor
Heart Failure
70 Citations (Scopus)

Comparative genomic sequencing identifies novel tissue-specific enhancers and sequence elements for methylation-sensitive factors implicated in Igf2/H19 imprinting

Ishihara, K., Hatano, N., Furuumi, H., Kato, R., Iwaki, T., Miura, K., Jinno, Y. & Sasaki, H., May 1 2000, In : Genome Research. 10, 5, p. 664-671 8 p.

Research output: Contribution to journalLetter

Methylation
Endoderm
Transgenic Mice
Mothers
Genes
4 Citations (Scopus)

Co-regulation of Cxcl1 and versican in the inflammatory response to UVB induced reactive oxygen species in skin photo-tumorigenesis

Takemori, C., Kunisada, M., Yogianti, F., Oka, S., Sakumi, K., Ono, R., Nakabeppu, Y. & Nishigori, C., Feb 1 2017, In : Journal of Dermatological Science. 85, 2, p. 140-143 4 p.

Research output: Contribution to journalLetter

Neoplastic Gene Expression Regulation
Chemokine CXCL1
Radiation-Induced Neoplasms
Versicans
DNA Glycosylases
82 Citations (Scopus)

Harnessing cloud computing with Galaxy Cloud

Afgan, E., Baker, D., Coraor, N., Goto, H., Paul, I. M., Makova, K. D., Nekrutenko, A. & Taylor, J., Nov 1 2011, In : Nature Biotechnology. 29, 11, p. 972-974 3 p.

Research output: Contribution to journalLetter

Computer Storage Devices
Galaxies
Cloud computing
Mitochondrial DNA
DNA Sequence Analysis
3 Citations (Scopus)
Severity of Illness Index
Predictive Value of Tests
End Stage Liver Disease
Acute Liver Failure
ROC Curve
9 Citations (Scopus)

Identification of anti-Sez6l2 antibody in a patient with cerebellar ataxia and retinopathy

Yaguchi, H., Yabe, I., Takahashi, H., Okumura, F., Takeuchi, A., Horiuchi, K., Kano, T., Kanda, A., Saito, W., Matsumoto, M., Nakayama, K. I., Hatakeyama, S. & Sasaki, H., Jan 1 2014, In : Journal of Neurology. 261, 1, p. 224-226 3 p.

Research output: Contribution to journalLetter

Nerve Tissue Proteins
Retinal Diseases
Cerebellar Ataxia
Autoantibodies
Anti-Idiotypic Antibodies
1 Citation (Scopus)

Letter to the editor: 1H, 13C and 15N backbone resonance assignments of the N-terminal domain of Drosophila GCM protein [1]

Shimizu, M., Hiroaki, H., Kohda, D., Morita, E. H., Hotta, S. & Morikawa, K., Jul 1 2003, In : Journal of Biomolecular NMR. 26, 3, p. 277-278 2 p.

Research output: Contribution to journalLetter

15 Citations (Scopus)

PRESYMPTOMATIC DIAGNOSIS OF HETEROZYGOSITY FOR FAMILIAL AMYLOIDOTIC POLYNEUROPATHY BY RECOMBINANT DNA TECHNIQUES

Sasaki, H., Sakaki, Y., Takagi, Y., Sahashi, K., Takahashi, A., Isobe, T., Shinoda, T., Matsuo, H., Goto, I. & Kuroiwa, Y., Jan 12 1985, In : The Lancet. 325, 8420, 1 p.

Research output: Contribution to journalLetter

Heterozygote Detection
Recombinant DNA
Polyneuropathies
Peripheral Nervous System Diseases
Amyloidosis
14 Citations (Scopus)

Relationship between heat-induced fibrillogenicity and hemolytic activity of thermostable direct hemolysin and a related hemolysin of Vibrio parahaemolyticus

Ohnishi, K., Nakahira, K., Unzai, S., Mayanagi, K., Hashimoto, H., Shiraki, K., Honda, T. & Yanagihara, I., May 1 2011, In : FEMS microbiology letters. 318, 1, p. 10-17 8 p.

Research output: Contribution to journalLetter

Vibrio parahaemolyticus
Hemolysin Proteins
Hot Temperature
Amyloid
thermostable direct hemolysin

Response to the letter to the editor by Berciano J & García A

Miura, S. & Shibata, H., Jan 2018, In : European Journal of Medical Genetics. 61, 1, 1 p.

Research output: Contribution to journalLetter

2 Citations (Scopus)

TAK1 adaptor proteins, TAB2 and TAB3, link the signalosome to B-cell receptor-induced IKK activation

Shinohara, H., Yasuda, T. & Kurosaki, T., Sep 1 2016, In : FEBS Letters. 590, 18, p. 3264-3269 6 p.

Research output: Contribution to journalLetter

B-Lymphocytes
Chemical activation
Cells
Proteins
Phosphotransferases

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
Paper

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

samplers
binding sites
probability distribution
proteins
ubiquitin-protein ligase
Review article

[Mitochondrial quality control and regulation of neuronal function].

Shirane, M., 2014, In : Seikagaku. The Journal of Japanese Biochemical Society. 86, 4, p. 479-482 4 p.

Research output: Contribution to journalReview article

Tacrolimus Binding Proteins
Mitochondria
Molecular Chaperones
Neurons
Quality control

[Studies of T cells for better understanding of immunity and allergy].

Yoshikai, Y., Jun 2011, In : Nihon Jibiinkoka Gakkai kaiho. 114, 6, p. 539-546 8 p.

Research output: Contribution to journalReview article

Immunity
Hypersensitivity
T-Lymphocytes
8 Citations (Scopus)

A comprehensive screening system for damaged nucleotide-binding proteins

Tsuchimoto, D., Iyama, T., Nonaka, M., Abolhassani, N., Ohta, E., Sakumi, K. & Nakabeppu, Y., Nov 28 2010, In : Mutation Research - Genetic Toxicology and Environmental Mutagenesis. 703, 1, p. 37-42 6 p.

Research output: Contribution to journalReview article

Inosine Triphosphate
Carrier Proteins
Nucleotides
Inosine Monophosphate
Adenosine Triphosphate

A critical role of the CDM family molecule DOCK2 in lymphocyte migration

Fukui, Y., Jan 1 2002, In : Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 47, 16 Suppl, p. 2194-2199 6 p.

Research output: Contribution to journalReview article

rac1 GTP-Binding Protein
rac GTP-Binding Proteins
GTPase-Activating Proteins
Cytoskeleton
Cell Movement
84 Citations (Scopus)

Acute myeloid leukemia with the 8q22;21q22 translocation: Secondary mutational events and alternative t(8;21) transcripts

Peterson, L. F., Boyapati, A., Ahn, E. Y., Biggs, J. R., Akiko, J. O., Lo, M. C., Yan, M. & Zhang, D. E., Aug 1 2007, In : Blood. 110, 3, p. 799-805 7 p.

Research output: Contribution to journalReview article

Genetic Translocation
Chromosomes
Acute Myeloid Leukemia
Genes
Chromosomes, Human, Pair 21
12 Citations (Scopus)

Analysis of cellular signal transduction from an information theoretic approach

Uda, S. & Kuroda, S., Mar 1 2016, In : Seminars in Cell and Developmental Biology. 51, p. 24-31 8 p.

Research output: Contribution to journalReview article

Signal Transduction
Information Theory
Cell Differentiation
Cell Death
Cell Proliferation
14 Citations (Scopus)

Application of supercritical fluid carbon dioxide to the extraction and analysis of lipids

Lee, J. W., Fukusaki, E. & Bamba, T., Oct 1 2012, In : Bioanalysis. 4, 19, p. 2413-2422 10 p.

Research output: Contribution to journalReview article

Supercritical Fluid Chromatography
Supercritical fluids
Carbon Dioxide
Lipids
Environmental Pollution
5 Citations (Scopus)

Artificial induction and disease-related conversion of the hepatic fate

Suzuki, A., Oct 1 2013, In : Current Opinion in Genetics and Development. 23, 5, p. 579-584 6 p.

Research output: Contribution to journalReview article

Hepatocytes
Liver
Liver Diseases
Transcription Factors
Tissue Transplantation
4 Citations (Scopus)

Brief summary of the current protocols for generating intestinal organoids

Miura, S. & Suzuki, A., Aug 2018, In : Development Growth and Differentiation. 60, 6, p. 387-392 6 p.

Research output: Contribution to journalReview article

Organoids
Intestinal Diseases
Epithelial Cells
Intestines
Food
253 Citations (Scopus)

Calcium signaling in lymphocytes

Oh-hora, M. & Rao, A., Jun 1 2008, In : Current Opinion in Immunology. 20, 3, p. 250-258 9 p.

Research output: Contribution to journalReview article

Calcium Signaling
Lymphocytes
T-Lymphocytes
Mast Cells
Antigen-Presenting Cells
103 Citations (Scopus)

Calcium signaling in the development and function of T-lineage cells

Oh-Hora, M., Sep 1 2009, In : Immunological Reviews. 231, 1, p. 210-224 15 p.

Research output: Contribution to journalReview article

Calcium Signaling
NFATC Transcription Factors
Calcineurin
Cell Lineage
Lymphocytes
1 Citation (Scopus)

Cell fate modification toward the hepatic lineage by extrinsic factors

Kawamata, M. & Suzuki, A., Jul 1 2017, In : Journal of biochemistry. 162, 1, p. 11-16 6 p.

Research output: Contribution to journalReview article

Stem cells
Liver
Hepatocytes
Induced Pluripotent Stem Cells
Fibroblasts
81 Citations (Scopus)
nucleotides
DNA Glycosylases
Nucleotides
Cell Survival
Carcinogenesis
170 Citations (Scopus)

Cip/Kip cyclin-dependent kinase inhibitors: Brakes of the cell cycle engine during development

Nakayama, K. & Nakayama, K., Jan 1 1998, In : BioEssays. 20, 12, p. 1020-1029 10 p.

Research output: Contribution to journalReview article

Cyclin-Dependent Kinases
Brakes
Cell Cycle
Cells
Engines
12 Citations (Scopus)

Close link between development and function of gamma-delta T cells

Shibata, K., Apr 1 2012, In : MICROBIOLOGY and IMMUNOLOGY. 56, 4, p. 217-227 11 p.

Research output: Contribution to journalReview article

Somatostatin-Secreting Cells
T-Lymphocytes
Thymus Gland
Interleukin-17
T-Lymphocyte Subsets