Department of Biosciences and Informatics

Research Output 1987 2020

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1 Citation (Scopus)

(+)-(4aR,9aS)-O-(4-Bromobenzoyl)-N-(3-methylanthracen-9-ylidene) hydroxylamine

Ohba, S., Ishida, N., Kato, D. I., Miyamoto, K. & Ohta, H., 2006 Jun 1, In : Acta Crystallographica Section E: Structure Reports Online. 61, 6

Research output: Contribution to journalArticle

Hydroxylamine
Oximes
Crystal symmetry
Benzene
Crystal structure
2 Citations (Scopus)

(R)-1-Phenyl-1-ethylammonium (R)-2-hydroxymethyl-2-(2-naphthyl)propanoate

Ohba, S., Tsutsumi, T., Terao, Y., Miyamoto, K. & Ohta, H., 2005 May, In : Acta Crystallographica Section E: Structure Reports Online. 61, 5

Research output: Contribution to journalArticle

Phenethylamines
Propionates
Ammonium Compounds
Anions
Cations

14-3-3ϵa directs the pulsatile transport of basal factors toward the apical domain for lumen growth in tubulogenesis

Mizotani, Y., Suzuki, M., Hotta, K., Watanabe, H., Shiba, K., Inaba, K., Tashiro, E., Oka, K. & Imoto, M., 2018 Sep 18, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 38, p. E8873-E8881

Research output: Contribution to journalArticle

Notochord
Growth
Larva
Myosin Type II
Pulsatile Flow
4 Citations (Scopus)

5a-Carba-glycopyranoside primers: potential building blocks for biocombinatorial synthesis of glycosphingolipid analogues

Aoyama, H., Ogawa, S. & Sato, T., 2009 Oct 12, In : Carbohydrate Research. 344, 15, p. 2088-2092 5 p.

Research output: Contribution to journalArticle

Glycosphingolipids
Glycosides
Oligosaccharides
Galactose
Ether
19 Citations (Scopus)

5-Lipoxygenase and cysteinyl leukotriene receptor 1 regulate epidermal growth factor-induced cell migration through Tiam1 upregulation and Rac1 activation

Magi, S., Takemoto, Y., Kobayashi, H., Kasamatsu, M., Akita, T., Tanaka, A., Takano, K., Tashiro, E., Igarashi, Y. & Imoto, M., 2014, In : Cancer Science. 105, 3, p. 290-296 7 p.

Research output: Contribution to journalArticle

Arachidonate 5-Lipoxygenase
Epidermal Growth Factor
Cell Movement
Up-Regulation
Leukotriene C4
267 Citations (Scopus)

A bacterium that degrades and assimilates poly(ethylene terephthalate)

Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., Toyohara, K., Miyamoto, K., Kimura, Y. & Oda, K., 2016 Mar 11, In : Science. 351, 6278, p. 1196-1199 4 p.

Research output: Contribution to journalArticle

Polyethylene Terephthalates
Bacteria
Ethylene Glycol
Recycling
Enzymes
48 Citations (Scopus)

A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis

Takai, T., Higaki, K., Aguilar-Moncayo, M., Mena-Barragán, T., Hirano, Y., Yura, K., Yu, L., Ninomiya, H., García-Moreno, M. I., Sakakibara, Y., Ohno, K., Nanba, E., Ortiz Mellet, C., García Fernández, J. M. & Suzuki, Y., 2013 Mar, In : Molecular Therapy. 21, 3, p. 526-532 7 p.

Research output: Contribution to journalArticle

GM1 Gangliosidosis
Pharmacology
Enzymes
Mucopolysaccharidosis IV
Galactosidases
6 Citations (Scopus)

Accelerated biosynthesis of neolacto-series glycosphingolipids in differentiated mouse embryonal carcinoma F9 cells detected by using dodecyl N-acetylglucosaminide as a saccharide primer

Ogasawara, N., Katagiri, Y. U., Kiyokawa, N., Kaneko, T., Sato, B., Nakajima, H., Miyagawa, Y., Kushi, Y., Ishida, H., Kiso, M., Okita, H., Sato, T. & Fujimoto, J., 2011 Mar, In : Journal of Biochemistry. 149, 3, p. 321-330 10 p.

Research output: Contribution to journalArticle

Embryonal Carcinoma Stem Cells
Glycosphingolipids
Bucladesine
Biosynthesis
Tretinoin
6 Citations (Scopus)

Acceleration of discrete stochastic biochemical simulation using GPGPU

Sumiyoshi, K., Hirata, K., Hiroi, N. & Funahashi, A., 2015, In : Frontiers in Physiology. 6, FEB, 42.

Research output: Contribution to journalArticle

Costs and Cost Analysis
Transfer (Psychology)
4 Citations (Scopus)

Acceleration of Enzymatic Degradation of Poly(ethylene terephthalate) by Surface Coating with Anionic Surfactants

Furukawa, M., Kawakami, N., Oda, K. & Miyamoto, K., 2018 Dec 11, In : ChemSusChem. 11, 23, p. 4018-4025 8 p.

Research output: Contribution to journalArticle

Hydrolases
Polyethylene Terephthalates
Anionic surfactants
Polyethylene terephthalates
ethylene
23 Citations (Scopus)

Accurate identification of orthologous segments among multiple genomes

Hachiya, T., Osana, Y., Popendorf, K. & Sakakibara, Y., 2009, In : Bioinformatics. 25, 7, p. 853-860 8 p.

Research output: Contribution to journalArticle

Anchors
Genome
Genes
Bacterial Genomes
Molecular Sequence Annotation
1 Citation (Scopus)

Accurate motor mapping in awake common marmosets using micro-electrocorticographical stimulation and stochastic threshold estimation

Kosugi, A., Takemi, M., Tia, B., Castagnola, E., Ansaldo, A., Sato, K., Awiszus, F., Seki, K., Ricci, D., Fadiga, L., Iriki, A. & Ushiba, J., 2018 Apr 6, In : Journal of Neural Engineering. 15, 3, 036019.

Research output: Contribution to journalArticle

Callithrix
Implanted Electrodes
Motor Evoked Potentials
Reproducibility of Results
Computer Simulation
7 Citations (Scopus)

A chemical genomic study identifying diversity in cell migration signaling in cancer cells

Magi, S., Tashiro, E. & Imoto, M., 2012, In : Scientific Reports. 2, 823.

Research output: Contribution to journalArticle

Cell Movement
Cluster Analysis
Neoplasms
Glycogen Synthase Kinase 3
Wound Healing
1 Citation (Scopus)

A chloride ion channel in Halocynthia roretzi hemocytes is associated with PO activity but not pigmentation during the contact reaction

Miyakawa, H., Kumano, M., Hoshi, M., Takeda, N. & Matsumoto, M., 2008 Nov, In : Zoological Science. 25, 11, p. 1130-1138 9 p.

Research output: Contribution to journalArticle

Halocynthia roretzi
monophenol monooxygenase
ion channels
hemocytes
pigmentation
2 Citations (Scopus)

A comprehensive comparison of sex-inducing activity in asexual worms of the planarian Dugesia ryukyuensis: The crucial sex-inducing substance appears to be present in yolk glands in Tricladida

Nakagawa, H., Sekii, K., Maezawa, T., Kitamura, M., Miyashita, S., Abukawa, M., Matsumoto, M. & Kobayashi, K., 2018 Jun 12, In : Zoological Letters. 4, 1, 14.

Research output: Contribution to journalArticle

Tricladida
Dugesia
gender
Polycladida
Platyhelminthes
653 Citations (Scopus)

A comprehensive pathway map of epidermal growth factor receptor signaling.

Oda, K., Matsuoka, Y., Funahashi, A. & Kitano, H., 2005, In : Molecular systems biology [electronic resource].. 1

Research output: Contribution to journalArticle

Growth Factors
Epidermal Growth Factor Receptor
Receptor
Pathway
Systems Biology

Acquisition of a mental strategy to control a virtual tail via brain–computer interface

Fujisawa, A., Kasuga, S., Suzuki, T. & Ushiba, J., 2018 Jan 26, (Accepted/In press) In : Cognitive Neuroscience. p. 1-14 14 p.

Research output: Contribution to journalArticle

Tail
Buttocks
Haplorhini
Electroencephalography
Healthy Volunteers
4 Citations (Scopus)

Acrosome reaction in starfish: Signal molecules in the jelly coat and their receptors

Hoshi, M., Nishigaki, T., Kawamura, M., Ikeda, M., Gunaratne, J., Ueno, S., Ogiso, M., Moriyama, H. & Matsumoto, M., 2000, In : Zygote. 8, SUPPL.

Research output: Contribution to journalArticle

Molecular Sequence Data
Carbohydrate Sequence
Starfish
Acrosome Reaction
Species Specificity
12 Citations (Scopus)

Acrosome reaction is subfamily specific in sea star fertilization

Nakachi, M., Moriyama, H., Hoshi, M. & Matsumoto, M., 2006 Oct 15, In : Developmental Biology. 298, 2, p. 597-604 8 p.

Research output: Contribution to journalArticle

Starfish
Acrosome Reaction
Fertilization
Asterias
Spermatozoa
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
14 Citations (Scopus)

A cumulative sum test for a peri-stimulus time histogram using the Monte Carlo method

Ushiba, J., Tomita, Y., Masakado, Y. & Komune, Y., 2002 Aug 30, In : Journal of Neuroscience Methods. 118, 2, p. 207-214 8 p.

Research output: Contribution to journalArticle

Monte Carlo Method
Noise
Confidence Intervals
2 Citations (Scopus)
Computational Model
Enzymes
DNA
Restriction
Parsing
1 Citation (Scopus)

A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator

Aye, S. L., Fujiwara, K. & Doi, N., 2018 Nov 1, In : Journal of Biochemistry. 164, 5, p. 341-348 8 p.

Research output: Contribution to journalArticle

Arsenic
Synthetic Biology
Genetic Engineering
Networks (circuits)
Biosensing Techniques
29 Citations (Scopus)

Affinity selection of DNA-binding protein complexes using mRNA display

Tateyama, S., Horisawa, K., Takashima, H., Miyamoto-Sato, E., Doi, N. & Yanagawa, H., 2006, In : Nucleic Acids Research. 34, 3, e27.

Research output: Contribution to journalArticle

DNA-Binding Proteins
jun Genes
Messenger RNA
DNA
Transcription Factors
9 Citations (Scopus)
Sea Urchins
Fertilization
Peptides
Proteins
Dextrans
82 Citations (Scopus)
G(M1) Ganglioside
Amyloidogenic Proteins
Presynaptic Terminals
Cluster Analysis
Alzheimer Disease
3 Citations (Scopus)

Age-related differences in cognitive function for interlimb coordination during split-belt walking: A pilot study

Saito, M., Hyodo, M., Masakado, Y., Tomita, Y. & Ushiba, J., 2013, In : Somatosensory and Motor Research. 30, 1, p. 56-63 8 p.

Research output: Contribution to journalArticle

Cognition
Walking
4 Citations (Scopus)

Algebraic method for the analysis of signaling crosstalk

Matsubara, Y., Kikuchi, S., Sugimoto, M., Oka, K. & Tomita, M., 2008 Dec, In : Artificial Life. 14, 1, p. 81-94 14 p.

Research output: Contribution to journalArticle

Signal transduction
Signal Transduction
Long-Term Potentiation
Algebraic Methods
Crosstalk

Alteration of a motor learning rule under mirror-reversal transformation does not depend on the amplitude of visual error

Kasuga, S., Kurata, M., Liu, M. & Ushiba, J., 2015 May 1, In : Neuroscience Research. 94, p. 62-69 8 p.

Research output: Contribution to journalArticle

Sensory Feedback
Learning
9 Citations (Scopus)

Altered expression of Mg2+ transport proteins during Parkinson's disease-like dopaminergic cell degeneration in PC12 cells

Shindo, Y., Yamanaka, R., Suzuki, K., Hotta, K. & Oka, K., 2016 Aug 1, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1863, 8, p. 1979-1984 6 p.

Research output: Contribution to journalArticle

PC12 Cells
Parkinson Disease
Carrier Proteins
Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone
Messenger RNA
7 Citations (Scopus)
Mass Spectrometry
Tandem Mass Spectrometry
Sequencing
Mass spectrometry
Polysaccharides
2 Citations (Scopus)
RNA
Thermodynamics
Learning systems
Benchmarking
Computational Biology
23 Citations (Scopus)

A method for selective ablation of neurons in C. elegans using the phototoxic fluorescent protein, KillerRed

Kobayashi, J., Shidara, H., Morisawa, Y., Kawakami, M., Tanahashi, Y., Hotta, K. & Oka, K., 2013 Aug 26, In : Neuroscience Letters. 548, p. 261-264 4 p.

Research output: Contribution to journalArticle

Sensory Receptor Cells
Neurons
Methyl Green
Diacetyl
Proteins
5 Citations (Scopus)

AMPA glutamate receptors are required for sensory-organ formation and morphogenesis in the basal chordate

Hirai, S., Hotta, K., Kubo, Y., Nishino, A., Okabe, S., Okamura, Y. & Okado, H., 2017 Apr 11, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 15, p. 3939-3944 6 p.

Research output: Contribution to journalArticle

Chordata
Urochordata
AMPA Receptors
Glutamate Receptors
Morphogenesis
5 Citations (Scopus)

Amyloid- fibrils assembled on ganglioside-enriched membranes contain both parallel -sheets and turns

Matsubara, T., Yasumori, H., Ito, K., Shimoaka, T., Hasegawa, T. & Sato, T., 2018 Jan 1, In : Journal of Biological Chemistry. 293, 36, p. 14146-14154 9 p.

Research output: Contribution to journalArticle

Gangliosides
Nanoclusters
Amyloid
Membranes
Alzheimer Disease
2 Citations (Scopus)

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data

Kato, Y., Mori, T., Sato, K., Maegawa, S., Hosokawa, H. & Akutsu, T., 2017 Jan 15, In : Bioinformatics. 33, 2, p. 202-209 8 p.

Research output: Contribution to journalArticle

RNA
Accessibility
Prediction
Interaction
Prediction Model
7 Citations (Scopus)
Efficient Algorithms
Testing
DNA sequences
Secondary Structure
DNA Sequence
10 Citations (Scopus)

An Anilinoquinazoline Derivative Inhibits Tumor Growth through Interaction with hCAP-G2, a Subunit of Condensin II

Shiheido, H., Naito, Y., Kimura, H., Genma, H., Takashima, H., Tokunaga, M., Ono, T., Hirano, T., Du, W., Yamada, T., Doi, N., Iijima, S., Hattori, Y. & Yanagawa, H., 2012 Sep 13, In : PLoS One. 7, 9, e44889.

Research output: Contribution to journalArticle

myeloma
Chromosomes
Tumors
chemical derivatives
Cells
1 Citation (Scopus)

An Artificial Reaction Promoter Modulates Mitochondrial Functions via Chemically Promoting Protein Acetylation

Shindo, Y., Komatsu, H., Hotta, K., Ariga, K. & Oka, K., 2016 Jul 4, In : Scientific Reports. 6, 29224.

Research output: Contribution to journalArticle

Acetyl Coenzyme A
Acetylation
Mitochondria
Adenosine Triphosphate
Mitochondrial Proteins
72 Citations (Scopus)

A near-infrared fluorescent calcium probe: A new tool for intracellular multicolour Ca 2+ imaging

Matsui, A., Umezawa, K., Shindo, Y., Fujii, T., Citterio, D., Oka, K. & Suzuki, K., 2011 Oct 7, In : Chemical Communications. 47, 37, p. 10407-10409 3 p.

Research output: Contribution to journalArticle

Fluorophores
Calcium
Optical properties
Fluorescence
Color
4 Citations (Scopus)

A new, convenient cell-based screening method for small-molecule glycolytic inhibitors

Kitagawa, M., Misawa, M., Ogawa, S., Tashiro, E. & Imoto, M., 2011, In : Bioscience, Biotechnology and Biochemistry. 75, 2, p. 367-369 3 p.

Research output: Contribution to journalArticle

Glycolysis
Screening
Molecules
Carbasugars
Tumors
10 Citations (Scopus)

A new therapeutic application of brain-machine interface (BMI) training followed by hybrid assistive neuromuscular dynamic stimulation (HANDS) therapy for patients with severe hemiparetic stroke: A proof of concept study

Kawakami, M., Fujiwara, T., Ushiba, J., Nishimoto, A., Abe, K., Honaga, K., Nishimura, A., Mizuno, K., Kodama, M., Masakado, Y. & Liu, M., 2016, In : Restorative Neurology and Neuroscience. 34, 5, p. 789-797 9 p.

Research output: Contribution to journalArticle

Brain-Computer Interfaces
Stroke
Fingers
Paresis
Therapeutics
6 Citations (Scopus)

An extended genovo metagenomic assembler by incorporating paired-end information

Afiahayati, Sato, K. & Sakakibara, Y., 2013, In : PeerJ. 2013, 1, e196.

Research output: Contribution to journalArticle

Metagenomics
Metagenome
Genes
Genome
Restaurants
3 Citations (Scopus)

Anomalous exciton spectra of laser-driven semiconductor superlattices

Yashima, K., Oka, K., Hino, K. I., Maeshima, N. & Tong, X. M., 2009 Jun, In : Solid State Communications. 149, 21-22, p. 823-826 4 p.

Research output: Contribution to journalArticle

Semiconductor superlattices
Excitons
superlattices
excitons
replicas
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
82 Citations (Scopus)

A novel action of terpendole E on the motor activity of mitotic kinesin Eg5

Nakazawa, J., Yajima, J., Usui, T., Ueki, M., Takatsuki, A., Imoto, M., Toyoshima, Y. Y. & Osada, H., 2003 Feb 1, In : Chemistry and Biology. 10, 2, p. 131-137 7 p.

Research output: Contribution to journalArticle

Kinesin
Motor Activity
Cell Division
Sterol O-Acyltransferase
Microtubules
37 Citations (Scopus)

A novel biological role of tachykinins as an up-regulator of oocyte growth: Identification of an evolutionary origin of tachykininergic functions in the ovary of the ascidian, Ciona intestinalis

Aoyama, M., Kawada, T., Fujie, M., Hotta, K., Sakai, T., Sekiguchi, T., Oka, K., Satoh, N. & Satake, H., 2008 Sep, In : Endocrinology. 149, 9, p. 4346-4356 11 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Tachykinins
Urochordata
Oocytes
Ovary
7 Citations (Scopus)

A novel cyclic lipoundecapeptide, pholipeptin, isolated from Pseudomonas sp.

Ui, H., Miyake, T., Iinuma, H., Imoto, M., Hattori, S., Hamada, M., Takeuchi, T., Umezawa, S. & Umezawa, K., 1995 Oct 9, In : Tetrahedron Letters. 36, 41, p. 7479-7480 2 p.

Research output: Contribution to journalArticle

Phosphoinositide Phospholipase C
Trifluoroacetic Acid
Pseudomonas
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
38 Citations (Scopus)

A novel thermostable esterase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7

Suzuki, Y., Miyamoto, K. & Ohta, H., 2004 Jul 1, In : FEMS Microbiology Letters. 236, 1, p. 97-102 6 p.

Research output: Contribution to journalArticle

Sulfolobus
Archaea
Esterases
Esters
Caprylates
5 Citations (Scopus)

Antarlides: A New Type of Androgen Receptor (AR) Antagonist that Overcomes Resistance to AR-Targeted Therapy

Saito, S., Fujimaki, T., Panbangred, W., Igarashi, Y. & Imoto, M., 2016 Feb 18, In : Angewandte Chemie - International Edition. 55, 8, p. 2728-2732 5 p.

Research output: Contribution to journalArticle

Androgen Receptor Antagonists
Androgen Receptors
propylene glycol methyl ether
Chemical modification
Androgens