Department of Biosciences and Informatics

Research Output 1987 2020

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2011
8 Citations (Scopus)

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

Saito, Y., Sato, K. & Sakakibara, Y., 2011 Feb 15, In : BMC Bioinformatics. 12, SUPPL. 1, S48.

Research output: Contribution to journalArticle

Untranslated RNA
Sequence Alignment
Secondary Structure
RNA
Cluster Analysis
4 Citations (Scopus)

Fragmin/protamine microparticles (F/P MPs) as cell carriers enhance the formation and growth of tumors In Vivo

Kumano, I., Kishimoto, S., Nakamura, S., Hattori, H., Tanaka, Y., Nakata, M., Sato, T., Fujita, M., Maehara, T. & Ishihara, M., 2011 Sep, In : Cellular and Molecular Bioengineering. 4, 3, p. 476-483 8 p.

Research output: Contribution to journalArticle

Dalteparin
Protamines
Tumors
Tumor
Cells
6 Citations (Scopus)

Ganglioside GD1a negatively regulates hepatocyte growth factor expression through caveolin-1 at the transcriptional level in murine osteosarcoma cells

Zhang, L., Wang, Y., Wang, L., Cao, T., Hyuga, S., Sato, T., Wu, Y., Yamagata, S. & Yamagata, T., 2011 Aug, In : Biochimica et Biophysica Acta - General Subjects. 1810, 8, p. 759-768 10 p.

Research output: Contribution to journalArticle

Caveolin 1
Hepatocyte Growth Factor
Osteosarcoma
(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase
Phosphorylation
22 Citations (Scopus)

Generation of 'Unnatural Natural Product' library and identification of a small molecule inhibitor of XIAP

Kawamura, T., Matsubara, K., Otaka, H., Tashiro, E., Shindo, K., Yanagita, R. C., Irie, K. & Imoto, M., 2011 Jul 15, In : Bioorganic and Medicinal Chemistry. 19, 14, p. 4377-4385 9 p.

Research output: Contribution to journalArticle

Biological Products
Libraries
Metabolites
Molecules
Small Molecule Libraries
5 Citations (Scopus)

GM3 suppresses anchorage-independent growth via Rho GDP dissociation inhibitor beta in melanoma B16 cells

Wang, P., Xu, S., Wang, Y., Wu, P., Zhang, J., Sato, T., Yamagata, S. & Yamagata, T., 2011 Aug, In : Cancer Science. 102, 8, p. 1476-1485 10 p.

Research output: Contribution to journalArticle

rho Guanine Nucleotide Dissociation Inhibitor beta
Guanine Nucleotide Dissociation Inhibitors
Experimental Melanomas
Raptors
Growth

Improved measurements of RNA structure conservation with generalized centroid estimators

Okada, Y., Saito, Y., Sato, K. & Sakakibara, Y., 2011, In : Frontiers in Genetics. 2, AUG, Article 54.

Research output: Contribution to journalArticle

Untranslated RNA
RNA
Base Pairing
Genome
Computational Biology
33 Citations (Scopus)

Inhibition of amyloid β aggregation and cytotoxicity by photodegradation using a designed fullerene derivative

Ishida, Y., Fujii, T., Oka, K., Takahashi, D. & Toshima, K., 2011 Sep 5, In : Chemistry - An Asian Journal. 6, 9, p. 2312-2315 4 p.

Research output: Contribution to journalArticle

Fullerenes
Photolysis
PC12 Cells
Photodegradation
Cytotoxicity
31 Citations (Scopus)

Involvement of 14-3-3 proteins in the second epidermal growth factor-induced wave of Rac1 activation in the process of cell migration

Kobayashi, H., Ogura, Y., Sawada, M., Nakayama, R., Takano, K., Minato, Y., Takemoto, Y., Tashiro, E., Watanabe, H. & Imoto, M., 2011 Nov 11, In : Journal of Biological Chemistry. 286, 45, p. 39259-39268 10 p.

Research output: Contribution to journalArticle

14-3-3 Proteins
Epidermal Growth Factor
Cell Movement
Chemical activation
Monomeric GTP-Binding Proteins
5 Citations (Scopus)

Melanin biosynthesis inhibitors from tarragon Artemisia dracunculus

Yamada, M., Nakamura, K., Watabe, T., Ohno, O., Kawagoshi, M., Maru, N., Uotsu, N., Chiba, T., Yamaguchi, K. & Uemura, D., 2011, In : Bioscience, Biotechnology and Biochemistry. 75, 8, p. 1628-1630 3 p.

Research output: Contribution to journalArticle

Artemisia
Biosynthesis
Melanins
Melanocyte-Stimulating Hormones
Experimental Melanomas
10 Citations (Scopus)

Modulation of event-related desynchronization during motor imagery with transcranial direct current stimulation in a patient with severe hemiparetic stroke: A case report

Tohyama, T., Fujiwara, T., Matsumoto, J., Honaga, K., Ushiba, J., Tsuji, T., Hase, K. & Liu, M., 2011 Dec, In : Keio Journal of Medicine. 60, 4, p. 114-118 5 p.

Research output: Contribution to journalArticle

Imagery (Psychotherapy)
Brain-Computer Interfaces
Stroke
Electroencephalography
Motor Cortex
11 Citations (Scopus)

Molecular design, chemical synthesis, and biological evaluation of agents that selectively photo-degrade the transcription factor estrogen receptor-α

Tsumura, K., Suzuki, A., Tsuzuki, T., Tanimoto, S., Kaneko, H., Matsumura, S., Imoto, M., Umezawa, K., Takahashi, D. & Toshima, K., 2011 Sep 21, In : Organic and Biomolecular Chemistry. 9, 18, p. 6357-6366 10 p.

Research output: Contribution to journalArticle

estrogens
Biological Factors
Estrogen Receptors
Transcription Factors
Irradiation
16 Citations (Scopus)

mRNA display selection of an optimized MDM2-binding peptide that potently inhibits MDM2-p53 interaction

Shiheido, H., Takashima, H., Doi, N. & Yanagawa, H., 2011, In : PLoS One. 6, 3, e17898.

Research output: Contribution to journalArticle

Display devices
peptides
Messenger RNA
Peptides
peptide libraries
33 Citations (Scopus)
Muscle Fatigue
Isometric Contraction
Electromyography
Electroencephalography
Muscles
10 Citations (Scopus)

Mycotrienin II, a translation inhibitor that prevents ICAM-1 expression induced by pro-inflammatory cytokines

Yamada, Y., Tashiro, E., Taketani, S., Imoto, M. & Kataoka, T., 2011 May, In : Journal of Antibiotics. 64, 5, p. 361-366 6 p.

Research output: Contribution to journalArticle

Intercellular Adhesion Molecule-1
Cytokines
Interleukin-1
Rifabutin
Tumor Necrosis Factor-alpha
40 Citations (Scopus)

Newly developed Mg 2+-selective fluorescent probe enables visualization of Mg 2+ dynamics in mitochondria

Shindo, Y., Fujii, T., Komatsu, H., Citterio, D., Hotta, K., Suzuki, K. & Oka, K., 2011, In : PLoS One. 6, 8, e23684.

Research output: Contribution to journalArticle

Mitochondria
Fluorescent Dyes
mitochondria
Visualization
cytosol
6 Citations (Scopus)

Novel conserved structural domains of acrosome reaction-inducing substance are widespread in invertebrates

Naruse, M., Ishikawa, R., Sakaya, H., Moriyama, H., Hoshi, M. & Matsumoto, M., 2011 Jan, In : Molecular Reproduction and Development. 78, 1, p. 57-66 10 p.

Research output: Contribution to journalArticle

Acrosome Reaction
Invertebrates
Spermatozoa
Ctenophora
Proteins
26 Citations (Scopus)

Peptidomic analysis of the central nervous system of the protochordate, Ciona intestinalis: Homologs and prototypes of vertebrate peptides and novel peptides

Kawada, T., Ogasawara, M., Sekiguchi, T., Aoyama, M., Hotta, K., Oka, K. & Satake, H., 2011 Jun, In : Endocrinology. 152, 6, p. 2416-2427 12 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Vertebrates
Central Nervous System
Peptides
Urochordata
3 Citations (Scopus)

Physicochemical properties of pDNA/chitosan complexes as gene delivery systems

Hagiwara, K., Anastasia, R., Nakata, M. & Sato, T., 2011 Dec, In : Current Drug Discovery Technologies. 8, 4, p. 329-339 11 p.

Research output: Contribution to journalArticle

Gene Transfer Techniques
Chitosan
Genes
Genetic Therapy
7 Citations (Scopus)

Physiological environment induces quick response - slow exhaustion reactions

Hiroi, N., Lu, J., Iba, K., Tabira, A., Yamashita, S., Okada, Y., Flamm, C., Oka, K., Köhler, G. & Funahashi, A., 2011, In : Frontiers in Physiology. 2 SEP, Article 50.

Research output: Contribution to journalArticle

Fluorescence Spectrometry
Fractals
Transmission Electron Microscopy
4 Citations (Scopus)

Positive afferent feedback to the human soleus muscle during quiet standing

van Doornik, J., Azevedo Coste, C., Ushiba, J. & Sinkjær, T., 2011 May, In : Muscle and Nerve. 43, 5, p. 726-732 7 p.

Research output: Contribution to journalArticle

Ankle
Skeletal Muscle
Ischemia
Achilles Tendon
Electromyography

Possibility of brain-computer interface in neurorehabilitation

Ushiba, J., 2011, In : Clinical Neurology. 51, 11, p. 927 1 p.

Research output: Contribution to journalArticle

Man-Machine Systems
Brain-Computer Interfaces
Hemiplegia
Upper Extremity
Stroke
10 Citations (Scopus)
Messenger RNA
Unfolded Protein Response
Proteins
Protein Synthesis Inhibitors
Genes
3 Citations (Scopus)

Selective expansion of CD34+ cells from mouse bone marrow cultured on LH/P MP-coated plates with adequate cytokines

Kishimoto, S., Ishihara, M., Kanatani, Y., Nambu, M., Takikawa, M., Sumi, Y., Nakamura, S., Mori, Y., Hattori, H., Tanaka, Y. & Sato, T., 2011, In : Journal of Tissue Engineering. 2, 1, p. 1-8 8 p.

Research output: Contribution to journalArticle

Protamines
Low Molecular Weight Heparin
Bone Marrow Cells
Bone
Molecular weight
17 Citations (Scopus)

Synthesis and anti-migrative evaluation of moverastin derivatives

Sawada, M., Kubo, S. I., Matsumura, K., Takemoto, Y., Kobayashi, H., Tashiro, E., Kitahara, T., Watanabe, H. & Imoto, M., 2011 Mar 1, In : Bioorganic and Medicinal Chemistry Letters. 21, 5, p. 1385-1389 5 p.

Research output: Contribution to journalArticle

Tumors
Cell Movement
Farnesyltranstransferase
Derivatives
Cells
18 Citations (Scopus)

Transcranial direct current stimulation modulates the spinal plasticity induced with patterned electrical stimulation

Fujiwara, T., Tsuji, T., Honaga, K., Hase, K., Ushiba, J. & Liu, M., 2011 Sep, In : Clinical Neurophysiology. 122, 9, p. 1834-1837 4 p.

Research output: Contribution to journalArticle

Electric Stimulation
Motor Cortex
H-Reflex
Peroneal Nerve
Electrodes
6 Citations (Scopus)

Uneven distribution pattern and increasing numbers of mesenchyme cells during development in the starfish, Asterina pectinifera

Hamanaka, G., Hosaka, E., Kuraishi, R., Hosoya, N., Matsumoto, M. & Kaneko, H., 2011 Apr, In : Development Growth and Differentiation. 53, 3, p. 440-449 10 p.

Research output: Contribution to journalArticle

Asterina
Starfish
Mesoderm
Cell Count
Larva
6 Citations (Scopus)

Using binding profiles to predict binding sites of target RNAs

Poolsap, U., Kato, Y., Sato, K. & Akutsu, T., 2011 Dec, In : Journal of Bioinformatics and Computational Biology. 9, 6, p. 697-713 17 p.

Research output: Contribution to journalArticle

Antisense RNA
Binding sites
RNA
Binding Sites
Small Untranslated RNA
2010
13 Citations (Scopus)

Acrosome reaction-related steroidal saponin, Co-ARIS, from the starfish induces structural changes in microdomains

Naruse, M., Suetomo, H., Matsubara, T., Sato, T., Yanagawa, H., Hoshi, M. & Matsumoto, M., 2010 Nov 1, In : Developmental Biology. 347, 1, p. 147-153 7 p.

Research output: Contribution to journalArticle

Starfish
Acrosome Reaction
Saponins
Spermatozoa
Caveolae
7 Citations (Scopus)

A non-parametric bayesian approach for predicting rna secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2010 Aug, In : Journal of Bioinformatics and Computational Biology. 8, 4, p. 727-742 16 p.

Research output: Contribution to journalArticle

Bayes Theorem
RNA
Stochastic Processes
Context free grammars
Bioinformatics
2 Citations (Scopus)

Automatic pipeline construction focused on similarity of rate law functions for an FPGA-based biochemical simulator

Yamada, H., Ogawa, Y., Ooya, T., Ishimori, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2010, In : IPSJ Transactions on System LSI Design Methodology. 3, p. 244-256 13 p.

Research output: Contribution to journalArticle

Field programmable gate arrays (FPGA)
Pipelines
Simulators
Hardware
Costs
22 Citations (Scopus)

Bioactive secondary metabolites from symbiotic marine dinoflagellates: Symbiodinolide and durinskiols

Kita, M., Ohno, O., Han, C. & Uemura, D., 2010 Apr, In : Chemical Record. 10, 2, p. 57-69 13 p.

Research output: Contribution to journalArticle

Dinoflagellida
Polyols
Metabolites
Aquatic ecosystems
Alkenes
22 Citations (Scopus)

Blue fluorescent cGMP sensor for multiparameter fluorescence imaging

Niino, Y., Hotta, K. & Oka, K., 2010 Feb 11, In : PLoS One. 5, 2, e9164.

Research output: Contribution to journalArticle

cyclic GMP
Fluorescence Resonance Energy Transfer
Optical Imaging
Cyclic GMP
sensors (equipment)
8 Citations (Scopus)

Brain-machine interface - Current status and future prospects

Ushiba, J., 2010 Feb, In : Brain and Nerve. 62, 2, p. 101-111 11 p.

Research output: Contribution to journalArticle

Brain-Computer Interfaces
Electrodes
Needles
Electroencephalography
Hemiplegia
32 Citations (Scopus)

Change in brain activity through virtual reality-based brain-machine communication in a chronic tetraplegic subject with muscular dystrophy

Hashimoto, Y., Ushiba, J., Kimura, A., Liu, M. & Tomita, Y., 2010 Sep 16, In : BMC Neuroscience. 11, 117.

Research output: Contribution to journalArticle

Brain-Computer Interfaces
Muscular Dystrophies
Communication
Brain
Electroencephalography
87 Citations (Scopus)

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

Shang, W. H., Hori, T., Toyoda, A., Kato, J., Popendorf, K., Sakakibara, Y., Fujiyama, A. & Fukagawa, T., 2010 Sep, In : Genome Research. 20, 9, p. 1219-1228 10 p.

Research output: Contribution to journalArticle

Centromere
Nucleic Acid Repetitive Sequences
Microsatellite Repeats
Chickens
Kinetochores
20 Citations (Scopus)

Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

Tanaka, J., Doi, N., Takashima, H. & Yanagawa, H., 2010 Apr, In : Protein Science. 19, 4, p. 786-795 10 p.

Research output: Contribution to journalArticle

Amino Acids
Libraries
Proteins
Solubility
Chemical Evolution
10 Citations (Scopus)

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. & Kiga, D., 2010 Dec 2, In : BMC Genomics. 11, SUPPL. 4, S16.

Research output: Contribution to journalArticle

operator regions
Logic gates
Nucleic Acid Regulatory Sequences
Gene expression
Plasmids
35 Citations (Scopus)

Correlation between EEG-EMG coherence during isometric contraction and its imaginary execution

Hashimoto, Y., Ushiba, J., Kimura, A., Liu, M. & Tomita, Y., 2010, In : Acta Neurobiologiae Experimentalis. 70, 1, p. 76-85 10 p.

Research output: Contribution to journalArticle

Isometric Contraction
Electromyography
Electroencephalography
Imagery (Psychotherapy)
Muscle Contraction
4 Citations (Scopus)

Dinohydrazides a and b, novel hydrazides from a symbiotic marine dinoflagellate

Maru, N., Ohno, O., Yamada, K. & Uemura, D., 2010, In : Chemistry Letters. 39, 6, p. 596-597 2 p.

Research output: Contribution to journalArticle

Cells
25 Citations (Scopus)

Distinct subcellular localization in the cytosol and apicoplast, unexpected dimerization and inhibition of Plasmodium falciparum glyoxalases

Urscher, M., Przyborski, J. M., Imoto, M. & Deponte, M., 2010, In : Molecular Microbiology. 76, 1, p. 92-103 12 p.

Research output: Contribution to journalArticle

Apicoplasts
Lactoylglutathione Lyase
Dimerization
Plasmodium falciparum
hydroxyacylglutathione hydrolase
18 Citations (Scopus)

Distribution and structural diversity of cilia in tadpole larvae of the ascidian Ciona intestinalis

Konno, A., Kaizu, M., Hotta, K., Horie, T., Sasakura, Y., Ikeo, K. & Inaba, K., 2010 Jan 1, In : Developmental Biology. 337, 1, p. 42-62 21 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Urochordata
Cilia
Larva
Chordata
27 Citations (Scopus)

Electrochemical detection of tyrosine derivatives and protein tyrosine kinase activity using boron-doped diamond electrodes

Chiku, M., Horisawa, K., Doi, N., Yanagawa, H. & Einaga, Y., 2010 Sep, In : Biosensors and Bioelectronics. 26, 1, p. 235-240 6 p.

Research output: Contribution to journalArticle

Diamond
Boron
Protein-Tyrosine Kinases
Tyrosine
Diamonds
58 Citations (Scopus)

Encapsulation of glucose oxidase (GOD) in polyelectrolyte complexes of chitosan-carrageenan

Briones, A. V. & Sato, T., 2010 Jan, In : Reactive and Functional Polymers. 70, 1, p. 19-27 9 p.

Research output: Contribution to journalArticle

carrageenan
Glucose Oxidase
Glucose oxidase
encapsulation
Carrageenan
4 Citations (Scopus)

Ganglioside GD1a suppression of NOS2 expression via ERK1 pathway in mouse osteosarcoma FBJ cells

Cao, T., Zhang, T., Wang, L., Zhang, L., Adachi, T., Sato, T., Yamagata, S. & Yamagata, T., 2010 Aug 1, In : Journal of Cellular Biochemistry. 110, 5, p. 1165-1174 10 p.

Research output: Contribution to journalArticle

Osteosarcoma
(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase
Tumors
Phosphorylation
Gangliosides
22 Citations (Scopus)

Glutamate-induced calcium increase mediates magnesium release from mitochondria in rat hippocampal neurons

Shindo, Y., Fujimoto, A., Hotta, K., Suzuki, K. & Oka, K., 2010 Nov 1, In : Journal of Neuroscience Research. 88, 14, p. 3125-3132 8 p.

Research output: Contribution to journalArticle

Magnesium
Glutamic Acid
Mitochondria
Calcium
Neurons
34 Citations (Scopus)

Glyoxalase-I is a novel target against Bcr-Abl leukemic cells acquiring stem-like characteristics in a hypoxic environment

Takeuchi, M., Kimura, S., Kuroda, J., Ashihara, E., Kawatani, M., Osada, H., Umezawa, K., Yasui, E., Imoto, M., Tsuruo, T., Yokota, A., Tanaka, R., Nagao, R., Nakahata, T., Fujiyama, Y. & Maekawa, T., 2010 Jul, In : Cell Death and Differentiation. 17, 7, p. 1211-1220 10 p.

Research output: Contribution to journalArticle

Lactoylglutathione Lyase
Stem Cells
Protein-Tyrosine Kinases
Leukemia
Pyruvaldehyde
26 Citations (Scopus)

Inhibitory effects of bakuchiol, bavachin, and isobavachalcone isolated from piper longum on melanin production in b16 mouse melanoma cells

Ohno, O., Watabe, T., Nakamura, K., Kawagoshi, M., Uotsu, N., Chiba, T., Yamada, M., Yamaguchi, K., Yamada, K., Miyamoto, K. & Uemura, D., 2010, In : Bioscience, Biotechnology and Biochemistry. 74, 7, p. 1504-1506 3 p.

Research output: Contribution to journalArticle

Sulfalene
Piper
Experimental Melanomas
Melanins
Fruits
14 Citations (Scopus)

Isolation and structure elucidation of a novel androgen antagonist, arabilin, produced by Streptomyces sp. MK756-CF1

Kawamura, T., Fujimaki, T., Hamanaka, N., Torii, K., Kobayashi, H., Takahashi, Y., Igarashi, M., Kinoshita, N., Nishimura, Y., Tashiro, E. & Imoto, M., 2010 Oct, In : Journal of Antibiotics. 63, 10, p. 601-605 5 p.

Research output: Contribution to journalArticle

Androgen Antagonists
Streptomyces
Androgens
Androgen Receptor Antagonists
Pyrones
2 Citations (Scopus)

Mesenchyme cells can function to induce epithelial cell proliferation in starfish embryos

Hamanaka, G., Matsumoto, M., Imoto, M. & Kaneko, H., 2010 Mar, In : Developmental Dynamics. 239, 3, p. 818-827 10 p.

Research output: Contribution to journalArticle

Starfish
Mesoderm
Embryonic Structures
Epithelial Cells
Cell Proliferation