Department of Biosciences and Informatics

Research Output 1987 2020

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Article
2008
9 Citations (Scopus)
Alcaligenes
Decarboxylation
Enzymes
Substrates
Acids
45 Citations (Scopus)

Brachyury-downstream gene sets in a chordate, Ciona intestinalis: Integrating notochord specification, morphogenesis and chordate evolution

Hotta, K., Takahashi, H., Satoh, N. & Gojobori, T., 2008 Jan, In : Evolution and Development. 10, 1, p. 37-51 15 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Chordata
Notochord
morphogenesis
Morphogenesis
18 Citations (Scopus)

Ca2+ influx through P2X receptors induces actin cytoskeleton reorganization by the formation of cofilin rods in neurites

Homma, K., Niino, Y., Hotta, K. & Oka, K., 2008 Feb, In : Molecular and Cellular Neuroscience. 37, 2, p. 261-270 10 p.

Research output: Contribution to journalArticle

Actin Depolymerizing Factors
Neurites
Actin Cytoskeleton
Adenosine Triphosphate
Cytoskeleton
285 Citations (Scopus)

CellDesigner 3.5: A versatile modeling tool for biochemical networks

Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N. & Kitano, H., 2008 Aug, In : Proceedings of the IEEE. 96, 8, p. 1254-1265 12 p., 4567412.

Research output: Contribution to journalArticle

Markup languages
Graphical user interfaces
Software packages
Systems Biology
Websites
9 Citations (Scopus)

Conserved sequences of sperm-activating peptide and its receptor throughout evolution, despite speciation in the sea star Asterias amurensis and closely related species

Nakachi, M., Hoshi, M., Matsumoto, M. & Moriyama, H., 2008 Aug, In : Zygote. 16, 3, p. 229-237 9 p.

Research output: Contribution to journalArticle

Asterias
Starfish
Peptide Receptors
Conserved Sequence
Spermatozoa
2 Citations (Scopus)
Alcaligenes
Crystallization
X-Ray Diffraction
enzymes
crystallization
21 Citations (Scopus)

Dendritic design implements algorithm for synaptic extraction of sensory information

Ogawa, H., Cummins, G. I., Jacobs, G. A. & Oka, K., 2008 Apr 30, In : Journal of Neuroscience. 28, 18, p. 4592-4603 12 p.

Research output: Contribution to journalArticle

Information Storage and Retrieval
Dendrites
Interneurons
Neurons
Gryllidae
4 Citations (Scopus)

Directed acyclic graph kernels for structural RNA analysis

Sato, K., Mituyama, T., Asai, K. & Sakakibara, Y., 2008 Jul 22, In : BMC Bioinformatics. 9, 318.

Research output: Contribution to journalArticle

Untranslated RNA
Directed Acyclic Graph
RNA
kernel
Base Pairing
43 Citations (Scopus)

Discovery of incednine as a potent modulator of the anti-apoptotic function of Bcl-xL from microbial origin

Futamura, Y., Sawa, R., Umezawa, Y., Igarashi, M., Nakamura, H., Hasegawa, K., Yamasaki, M., Tashiro, E., Takahashi, Y., Akamatsu, Y. & Imoto, M., 2008 Feb 13, In : Journal of the American Chemical Society. 130, 6, p. 1822-1823 2 p.

Research output: Contribution to journalArticle

Cell death
Modulators
Tumors
Cell Death
Proteins
7 Citations (Scopus)

EEG-EMG coherence changes in postural tasks

Masakado, Y., Ushiba, J., Tsutsumi, N., Takahashi, Y., Tomita, Y., Kimura, A. & Liu, M., 2008 Jan, In : Electromyography and Clinical Neurophysiology. 48, 1, p. 27-33 7 p.

Research output: Contribution to journalArticle

Motor Cortex
Electroencephalography
Leg
Neurons
Muscles
54 Citations (Scopus)

Egg and sperm recognition systems during fertilization

Hirohashi, N., Kamei, N., Kubo, H., Sawada, H., Matsumoto, M. & Hoshi, M., 2008 Jun, In : Development Growth and Differentiation. 50, SUPPL. 1

Research output: Contribution to journalArticle

Fertilization
Ovum
Spermatozoa
Proteins
Sperm-Ovum Interactions

Erratum: Production of diploid and triploid offspring by inbreeding of the triploid planarian Dugesia ryukyuensis (Chromosoma 10.1007/s00412-0148-6)

Kobayashi, K., Ishizu, H., Arioka, S., Cabrera, J. P., Hoshi, M. & Matsumoto, M., 2008 Jun, In : Chromosoma. 117, 3, p. 303 1 p.

Research output: Contribution to journalArticle

Planarians
Triploidy
Inbreeding
Diploidy
13 Citations (Scopus)

Ganglioside GD1a suppresses TNFα expression via Pkn1 at the transcriptional level in mouse osteosarcoma-derived FBJ cells

Wang, L., Wang, Y., Sato, T., Yamagata, S. & Yamagata, T., 2008 Jun 27, In : Biochemical and Biophysical Research Communications. 371, 2, p. 230-235 6 p.

Research output: Contribution to journalArticle

Osteosarcoma
Matrix Metalloproteinases
Glucosylceramides
Vitronectin
rho GTP-Binding Proteins
13 Citations (Scopus)

Glycosylation of dodecyl 2-acetamido-2-deoxy-β-d-glucopyranoside and dodecyl β-d-galactopyranosyl-(1→4)-2-acetamido-2-deoxy-β-d-glucopyranoside as saccharide primers in cells

Sato, T., Takashiba, M., Hayashi, R., Zhu, X. & Yamagata, T., 2008 Apr 7, In : Carbohydrate Research. 343, 5, p. 831-838 8 p.

Research output: Contribution to journalArticle

Glycosylation
Oligosaccharides
HL-60 Cells
Serum-Free Culture Media
High performance liquid chromatography
11 Citations (Scopus)

GM3 signals regulating TNF-alpha expression are mediated by rictor and Arhgdib in mouse melanoma B16 cells

Wang, P., Yang, X., Wu, P., Zhang, J., Sato, T., Yamagata, S. & Yamagata, T., 2008 Jun, In : Oncology. 73, 5-6, p. 430-438 9 p.

Research output: Contribution to journalArticle

Guanine Nucleotide Dissociation Inhibitors
Experimental Melanomas
Phosphatidylinositol 3-Kinases
Tumor Necrosis Factor-alpha
Raptors
2 Citations (Scopus)

Hot springs and cool natural products

Kwon, H. J., Lee, C. H., Osada, H., Yoshida, M. & Imoto, M., 2008 Aug, In : Nature Chemical Biology. 4, 8, p. 444-446 3 p.

Research output: Contribution to journalArticle

Hot Springs
Biological Products
1 Citation (Scopus)

Identification and characterization of mouse type II platelet-derived growth factor receptor α transcript

Minato, Y., Nihei, Y., Kodama, Y., Tashiro, E., Kanai, M. & Imoto, M., 2008, In : Bioscience, Biotechnology and Biochemistry. 72, 3, p. 759-766 8 p.

Research output: Contribution to journalArticle

Platelet-Derived Growth Factor Receptors
Platelets
Messenger RNA
mice
5' Untranslated Regions
2 Citations (Scopus)

Identification of guanylate cyclases and related signaling proteins in sperm tail from sea stars by mass spectrometry

Nakachi, M., Matsumoto, M., Terry, P. M., Cerny, R. L. & Moriyama, H., 2008 Sep, In : Marine Biotechnology. 10, 5, p. 564-571 8 p.

Research output: Contribution to journalArticle

Starfish
Sperm Tail
guanylate cyclase
Guanylate Cyclase
Asteroidea
132 Citations (Scopus)

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: New insight into intron and operon populations

Satou, Y., Mineta, K., Ogasawara, M., Sasakura, Y., Shoguchi, E., Ueno, K., Yamada, L., Matsumoto, J., Wasserscheid, J., Dewar, K., Wiley, G. B., Macmil, S. L., Roe, B. A., Zeller, R. W., Hastings, K. E. M., Lemaire, P., Lindquist, E., Endo, T., Hotta, K. & Inaba, K., 2008 Oct 14, In : Genome Biology. 9, 10, R152.

Research output: Contribution to journalArticle

Ciona intestinalis
Chordata
genome assembly
operon
Operon
11 Citations (Scopus)

In vitro gene delivery by pDNA/chitosan complexes coated with anionic PEG derivatives that have a sugar side chain

Hashimoto, M., Koyama, Y. & Sato, T., 2008 Mar 5, In : Chemistry Letters. 37, 3, p. 266-267 2 p.

Research output: Contribution to journalArticle

Chitosan
Sugars
Polyethylene glycols
Genes
Derivatives
2 Citations (Scopus)

Lipase-catalyzed enantioselective hydrolysis of N-protected racemic non-protein amino acid esters

Kagawa, K. I., Matsubara, T. & Kawashiro, K., 2008 Jul, In : Biocatalysis and Biotransformation. 26, 3, p. 186-196 11 p.

Research output: Contribution to journalArticle

Lipases
Lipase
Amino acids
Hydrolysis
Esters
6 Citations (Scopus)

Neoblast-enriched fraction rescues eye formation in eye-defective planarian 'menashi' Dugesia ryukyuensis

Kobayashi, K., Hashiguchi, T., Ichikawa, T., Ishino, Y., Hoshi, M. & Matsumoto, M., 2008 Oct, In : Development Growth and Differentiation. 50, 8, p. 689-696 8 p.

Research output: Contribution to journalArticle

Planarians
X-Rays
Totipotent Stem Cells
Adult Stem Cells
6 Citations (Scopus)

Nitric oxide-cyclic guanosine monophosphate signaling in the local circuit of the cricket abdominal nervous system

Aonuma, H., Kitamura, Y., Niwa, K., Ogawa, H. & Oka, K., 2008 Dec 10, In : Neuroscience. 157, 4, p. 749-761 13 p.

Research output: Contribution to journalArticle

Gryllidae
Cyclic GMP
Nervous System
Nitric Oxide
Ganglia
6 Citations (Scopus)

Production of diploid and triploid offspring by inbreeding of the triploid planarian Dugesia ryukyuensis

Kobayashi, K., Ishizu, H., Arioka, S., Cabrera, J. P., Hoshi, M. & Matsumoto, M., 2008 Jun, In : Chromosoma. 117, 3, p. 289-296 8 p.

Research output: Contribution to journalArticle

Planarians
Triploidy
Inbreeding
Diploidy
Tetraploidy
15 Citations (Scopus)

Protease-catalyzed dipeptide synthesis from N-protected amino acid carbamoylmethyl esters and free amino acids in frozen aqueous solutions

Salam, S. M. A., Kagawa, K. I., Matsubara, T. & Kawashiro, K., 2008 Dec 10, In : Enzyme and Microbial Technology. 43, 7, p. 537-543 7 p.

Research output: Contribution to journalArticle

Dipeptides
Papain
Amino acids
Esters
Peptide Hydrolases
4 Citations (Scopus)

PSSMTS: Position specific scoring matrices on tree structures

Sato, K., Morita, K. & Sakakibara, Y., 2008 Jan, In : Journal of Mathematical Biology. 56, 1-2, p. 201-214 14 p.

Research output: Contribution to journalArticle

Position-Specific Scoring Matrices
Tree Structure
RNA
Scoring
Untranslated RNA
18 Citations (Scopus)
Brevibacterium
Phenylethyl Alcohol
Purification
Enzymes
NAD
11 Citations (Scopus)

Regulation of the starfish sperm acrosome reaction by cGMP, pH, cAMP and Ca2+

Matsumoto, M., Kawase, O., Islam, M. S., Naruse, M., Watanabe, S. N., Ishikawa, R. & Hoshi, M., 2008, In : International Journal of Developmental Biology. 52, 5-6, p. 523-526 4 p.

Research output: Contribution to journalArticle

Starfish
Acrosome Reaction
Spermatozoa
Asterias
Eggs
17 Citations (Scopus)
Rifabutin
Fermentation
Thapsigargin
Streptomyces
HeLa Cells
15 Citations (Scopus)
Rifabutin
Macrocyclic Lactams
Streptomyces
quinotrierixin
11 Citations (Scopus)

Screening, cloning, expression, and purification of an acidic arylmalonate decarboxylase from Enterobacter cloacae KU1313

Yatake, Y., Miyamoto, K. & Ohta, H., 2008 Apr, In : Applied Microbiology and Biotechnology. 78, 5, p. 793-799 7 p.

Research output: Contribution to journalArticle

Enterobacter cloacae
Cloning
Purification
Organism Cloning
Screening
18 Citations (Scopus)

Selection of a carbohydrate-binding domain with a helix-loop-helix structure

Matsubara, T., Iida, M., Tsumuraya, T., Fujii, I. & Sato, T., 2008 Jul 1, In : Biochemistry. 47, 26, p. 6745-6751 7 p.

Research output: Contribution to journalArticle

Peptide Library
Carbohydrates
Bacteriophages
Peptides
Surface Plasmon Resonance
6 Citations (Scopus)

Synthesis and antitumor activity of combretastatin D-4

Uno, K., Tanabe, T., Ogamino, T., Okada, R., Imoto, M. & Nishiyama, S., 2008 Feb 1, In : Heterocycles. 75, 2, p. 291-296 6 p.

Research output: Contribution to journalArticle

Dimerization
Phenols
Anodic oxidation
Phenol
Biological Assay

The 57th FCCA seminar/Forum and Annual Meeting for Young Glycoscientists 2008

Higashi, N., Nihira, T., Amano, M., Ida, M., Kobayashi, A., Matsubara, T., Miura, Y. & Mizuno, M., 2008 Dec, In : Trends in Glycoscience and Glycotechnology. 20, 116, p. 399-401 3 p.

Research output: Contribution to journalArticle

Technical presentations
37 Citations (Scopus)

The green and effective oxidation of alcohols to carboxylic acids with molecular oxygen via biocatalytic reaction

Hirano, J. I., Miyamoto, K. & Ohta, H., 2008 Feb 11, In : Tetrahedron Letters. 49, 7, p. 1217-1219 3 p.

Research output: Contribution to journalArticle

Molecular oxygen
Carboxylic Acids
Alcohols
Oxygen
Oxidation
96 Citations (Scopus)

The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I

Kawatani, M., Okumura, H., Honda, K., Kanoh, N., Muroi, M., Dohmae, N., Takami, M., Kitagawa, M., Futamura, Y., Imoto, M. & Osada, H., 2008 Aug 19, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 33, p. 11691-11696 6 p.

Research output: Contribution to journalArticle

Lactoylglutathione Lyase
Osteogenesis
Osteoclasts
Bone Density Conservation Agents
Pyruvaldehyde
7 Citations (Scopus)

Use of cDNA Tiling Arrays for Identifying Protein Interactions Selected by In Vitro Display Technologies

Horisawa, K., Doi, N. & Yanagawa, H., 2008, In : PLoS One. 3, 2, e0001646.

Research output: Contribution to journalArticle

Oligonucleotide Array Sequence Analysis
Complementary DNA
Display devices
Technology
Messenger RNA
2007
5 Citations (Scopus)

A simple two-transition model for loss of infectivity of phages on exposure to organic solvent

Matsubara, T., Emoto, W. & Kawashiro, K., 2007 Jun, In : Biomolecular Engineering. 24, 2, p. 269-271 3 p.

Research output: Contribution to journalArticle

Bacteriophages
Organic solvents
Peptide Library
Peptides
Kinetics
145 Citations (Scopus)

A web-based interactive developmental table for the Ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva

Hotta, K., Mitsuhara, K., Takahashi, H., Inaba, K., Oka, K., Gojobori, T. & Ikeo, K., 2007 Jul, In : Developmental Dynamics. 236, 7, p. 1790-1805 16 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Urochordata
Computer-Assisted Image Processing
Zygote
Chordata
27 Citations (Scopus)

Brachyury-downstream notochord genes and convergent extension in Ciona intestinalis embryos

Hotta, K., Yamada, S., Ueno, N., Satoh, N. & Takahashi, H., 2007 Jun, In : Development Growth and Differentiation. 49, 5, p. 373-382 10 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Notochord
Embryonic Structures
Genes
Chordata
6 Citations (Scopus)

Characterization of novel genes expressed specifically in the sexual organs of the planarian Dugesia ryukyuensis

Hase, S., Kashiwagi, E., Kobayashi, K., Hoshi, M. & Matsumoto, M., 2007, In : International Journal of Developmental Biology. 51, 4, p. 345-349 5 p.

Research output: Contribution to journalArticle

Planarians
Oviparity
Genes
Testis
Spermatocytes
9 Citations (Scopus)

Conversion of α-methyltropate to optically active α-phenylpropionate by tropate-degrading Rhodococcus sp. KU1314

Miyamoto, K., Hirokawa, S. & Ohta, H., 2007 May 2, In : Journal of Molecular Catalysis B: Enzymatic. 46, 1-4, p. 14-19 6 p.

Research output: Contribution to journalArticle

Phenylpropionates
Rhodococcus
Enantiomers
Microorganisms
Propionates

Cyclic AMP-dependent PKA phosphorylates starfish sperm proteins during acrosome reaction

Islam, M. S., Hoshi, M. & Matsumoto, M., 2007 Mar, In : Central European Journal of Biology. 2, 1, p. 109-121 13 p.

Research output: Contribution to journalArticle

Starfish
Acrosome Reaction
acrosome reaction
cAMP-dependent protein kinase
Asteroidea
7 Citations (Scopus)

Deduction of intracellular sub-systems from a topological description of the network

Nordling, T. E. M., Hiroi, N., Funahashi, A. & Kitano, H., 2007, In : Molecular BioSystems. 3, 8, p. 523-529 7 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Information Storage and Retrieval
Metabolic Networks and Pathways
Linearization
Molecules
5 Citations (Scopus)

Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes

Sakakibara, Y., Osana, Y. & Popendorf, K., 2007, In : Japanese Journal of Leprosy. 76, 3, p. 251-256 6 p.

Research output: Contribution to journalArticle

Mycobacterium
Genome
Chromosomes, Human, X
Mammals
Chromosomes
35 Citations (Scopus)

Flagella facilitate escape of Salmonella from oncotic macrophages

Sano, G. I., Takada, Y., Goto, S., Maruyama, K., Shindo, Y., Oka, K., Matsui, H. & Matsuo, K., 2007 Nov, In : Journal of Bacteriology. 189, 22, p. 8224-8232 9 p.

Research output: Contribution to journalArticle

Flagella
Salmonella
Macrophages
Bacillus
Salmonella enterica
182 Citations (Scopus)

Functions of cyclin D1 as an oncogene and regulation of cyclin D1 expression

Tashiro, E., Tsuchiya, A. & Imoto, M., 2007 May, In : Cancer Science. 98, 5, p. 629-635 7 p.

Research output: Contribution to journalArticle

Cyclin D1
Oncogenes
bcl-1 Genes
Neoplasms
Fibroblasts
12 Citations (Scopus)

Ganglioside GD1a negatively regulates matrix metalloproteinase-9 expression in mouse FBJ cell lines at the transcriptional level

Hu, D., Man, Z., Wang, P., Tan, X., Wang, X., Takaku, S., Hyuga, S., Sato, T., Yao, X., Yamagata, S. & Yamagata, T., 2007 Jul, In : Connective Tissue Research. 48, 4, p. 198-205 8 p.

Research output: Contribution to journalArticle

Matrix Metalloproteinase 9
Cells
Cell Line
Caveolin 1
GD1a ganglioside
1 Citation (Scopus)

Guest editorial to the special issue on grammatical inference

Paliouras, G. & Sakakibara, Y., 2007 Jan, In : Machine Learning. 66, 1, p. 3-5 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

High-throughput fluorescence labelling of full-length cDNA products based on a reconstituted translation system

Kawahashi, Y., Doi, N., Oishi, Y., Tsuda, C., Takashima, H., Baba, T., Mori, H., Ito, T. & Yanagawa, H., 2007 Jan, In : Journal of Biochemistry. 141, 1, p. 19-24 6 p.

Research output: Contribution to journalArticle

Labeling
Complementary DNA
Fluorescence
Throughput
Proteins