Department of Biosciences and Informatics

Research Output 1987 2020

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2012
3 Citations (Scopus)

DNA display selection of peptide ligands for a full-length human G protein-coupled receptor on CHO-K1 cells

Doi, N., Yamakawa, N., Matsumoto, H., Yamamoto, Y., Nagano, T., Matsumura, N., Horisawa, K. & Yanagawa, H., 2012 Jan 10, In : PLoS One. 7, 1, e30084.

Research output: Contribution to journalArticle

Chinese hamsters
G-Protein-Coupled Receptors
Cricetulus
Peptide Library
angiotensin II
17 Citations (Scopus)

Drpiwi-1 is essential for germline cell formation during sexualization of the planarian Dugesia ryukyuensis

Nakagawa, H., Ishizu, H., Hasegawa, R., Kobayashi, K. & Matsumoto, M., 2012 Jan 1, In : Developmental Biology. 361, 1, p. 167-176 10 p.

Research output: Contribution to journalArticle

Planarians
RNA Interference
Germ Cells
Stem Cells
Gametogenesis
1 Citation (Scopus)

Erratum: Generation of 'Unnatural Natural Product' library and identification of a small molecule inhibitor of XIAP (Bioorganic and Medicinal Chemistry (2011) 19 (4377-4385))

Kawamura, T., Matsubara, K., Otaka, H., Tashiro, E., Shindo, K., Yanagita, R. C., Irie, K. & Imoto, M., 2012 Apr 1, In : Bioorganic and Medicinal Chemistry. 20, 7, p. 2479 1 p.

Research output: Contribution to journalArticle

Pharmaceutical Chemistry
Biological Products
Libraries
4 Citations (Scopus)

From microscopy data to in silico environments for in vivo-oriented simulations

Hiroi, N., Klann, M., Iba, K., Heras Ciechomski, P. D., Yamashita, S., Tabira, A., Okuhara, T., Kubojima, T., Okada, Y., Oka, K., Mange, R., Unger, M., Funahashi, A. & Koeppl, H., 2012, In : Eurasip Journal on Bioinformatics and Systems Biology. 2012, 1, 7.

Research output: Contribution to journalArticle

Microscopy
Computer Simulation
Microscopic examination
Diffusion Coefficient
Anomalous Diffusion
5 Citations (Scopus)

Glycosylation of Nα-lauryl-O-(β-d-xylopyranosyl)-l- serinamide as a saccharide primer in cells

Wang, Y., Kumazawa, T., Shiba, K., Osumi, K., Mizuno, M. & Sato, T., 2012 Nov 1, In : Carbohydrate Research. 361, p. 33-40 8 p.

Research output: Contribution to journalArticle

Glycosylation
Glycosaminoglycans
Oligosaccharides
Heparitin Sulfate
Glycoside Hydrolases
86 Citations (Scopus)

Identification of Toyocamycin, an agent cytotoxic for multiple myeloma cells, as a potent inhibitor of ER stress-induced XBP1 mRNA splicing

Ri, M., Tashiro, E., Oikawa, D., Shinjo, S., Tokuda, M., Yokouchi, Y., Narita, T., Masaki, A., Ito, A., Ding, J., Kusumoto, S., Ishida, T., Komatsu, H., Shiotsu, Y., Ueda, R., Iwawaki, T., Imoto, M. & Iida, S., 2012 Jul, In : Blood Cancer Journal. 2, 7, e79.

Research output: Contribution to journalArticle

Toyocamycin
Endoplasmic Reticulum Stress
Cytotoxins
Multiple Myeloma
Messenger RNA
4 Citations (Scopus)

Inostamycin enhanced TRAIL-induced apoptosis through DR5 upregulation on the cell surface

Yamamoto, K., Makino, M., Watanapokasin, R., Tashiro, E. & Imoto, M., 2012 Jun, In : Journal of Antibiotics. 65, 6, p. 295-300 6 p.

Research output: Contribution to journalArticle

Up-Regulation
Apoptosis
Neoplasms
HCT116 Cells
Caspases
1 Citation (Scopus)

Intricate recognition of glycolipid-like compounds by HIV-1 envelope proteins evaluated with surface plasmon resonance imaging

Okada, T., Kimura, A., Miura, H., Nishiyama, T., Mori, M., Suzuki, J., Ogiso, M., Matsuoka, K., Sato, T., Hatanaka, K. & Minoura, N., 2012 Sep 1, In : Journal of Carbohydrate Chemistry. 31, 7, p. 584-592 9 p.

Research output: Contribution to journalArticle

Human Immunodeficiency Virus env Gene Products
Surface Plasmon Resonance
Glycolipids
Surface plasmon resonance
Cell membranes
16 Citations (Scopus)

In vitro selection of fab fragments by mRNA display and gene-linking emulsion PCR

Sumida, T., Yanagawa, H. & Doi, N., 2012, In : Journal of Nucleic Acids. 2012, 371379.

Research output: Contribution to journalArticle

Immunoglobulin Fab Fragments
Emulsions
Genes
Display devices
Polymerase Chain Reaction
4 Citations (Scopus)

Isolation of 9-hydroxy-10E,12Z-octadecadienoic acid, an inhibitor of fat accumulation from Valeriana fauriei

Yuki, K., Ikeda, M., Miyamoto, K., Ohno, O., Yamada, K. & Uemura, D., 2012, In : Bioscience, Biotechnology and Biochemistry. 76, 6, p. 1233-1235 3 p.

Research output: Contribution to journalArticle

Valerian
Fats
Conjugated Linoleic Acids
Adipocytes
Derivatives
5 Citations (Scopus)

Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms In Vivo

Takizawa, H., Hiroi, N. & Funahashi, A., 2012 Dec 20, In : PLoS One. 7, 12, e51000.

Research output: Contribution to journalArticle

synapse
Synapses
Signal transduction
mathematical models
Actins
320 Citations (Scopus)

MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y., 2012 Nov, In : Nucleic Acids Research. 40, 20

Research output: Contribution to journalArticle

Metagenome
Genome
Metagenomics
38 Citations (Scopus)

Modulation of event-related desynchronization during motor imagery with transcranial direct current stimulation (tDCS) in patients with chronic hemiparetic stroke

Kasashima, Y., Fujiwara, T., Matsushika, Y., Tsuji, T., Hase, K., Ushiyama, J., Ushiba, J. & Liu, M., 2012 Sep, In : Experimental Brain Research. 221, 3, p. 263-268 6 p.

Research output: Contribution to journalArticle

Imagery (Psychotherapy)
Stroke
Brain-Computer Interfaces
Motor Cortex
Paresis
3 Citations (Scopus)

Napyradiomycin A1, an inhibitor of mitochondrial complexes i and II

Yamamoto, K., Tashiro, E., Motohashi, K., Seto, H. & Imoto, M., 2012 Apr, In : Journal of Antibiotics. 65, 4, p. 211-214 4 p.

Research output: Contribution to journalArticle

Electron Transport Complex II
Electron Transport Complex I
Naphthoquinones
Tumor Cell Line
Cell Survival
9 Citations (Scopus)

Newer challenges to restore hemiparetic upper extremity after stroke: HANDS therapy and BMI neurorehabilitation

Liu, M., Fujiwara, T., Shindo, K., Kasashima, Y., Otaka, Y., Tsuji, T. & Ushiba, J., 2012 Dec, In : Hong Kong Physiotherapy Journal. 30, 2, p. 83-92 10 p.

Research output: Contribution to journalArticle

Upper Extremity
Electromyography
Stroke
Fingers
Hand
1 Citation (Scopus)

Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments

Hiroi, N., Okuhara, T., Kubojima, T., Iba, K., Tabira, A., Yamashita, S., Okada, Y., Kobayashi, T. J. & Funahashi, A., 2012, In : Frontiers in Physiology. 3 JUL, Article 293.

Research output: Contribution to journalArticle

Space Simulation
Fractals
18 Citations (Scopus)
Peptide Library
Carbohydrates
Peptides
Derivatives
Vaccination
3 Citations (Scopus)
Planarians
Ovary
Pluripotent Stem Cells
Chimerism
Transplantation
7 Citations (Scopus)

Rtips: Fast and accurate tools for RNA 2D structure prediction using integer programming

Kato, Y., Sato, K., Asai, K. & Akutsu, T., 2012 Jul, In : Nucleic Acids Research. 40, W1

Research output: Contribution to journalArticle

RNA
6 Citations (Scopus)

SAMSCOPE: An opengl-based real-time interactive scale-free SAM viewer

Popendorf, K. & Sakakibara, Y., 2012 May, In : Bioinformatics. 28, 9, p. 1276-1277 2 p., bts122.

Research output: Contribution to journalArticle

OpenGL
Genome
Visualization
Genes
Real-time
43 Citations (Scopus)

Software support for SBGN maps: SBGN-ML and LibSBGN

Van Iersel, M. P., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S. L., Kitano, H., Le novère, N. & Schreiber, F., 2012 Aug, In : Bioinformatics. 28, 15, p. 2016-2021 6 p., bts270.

Research output: Contribution to journalArticle

Systems Biology
Notation
Software
Libraries
Bioinformatics
24 Citations (Scopus)

Specialized motor-driven dusp1 expression in the song systems of multiple lineages of vocal learning birds

Horita, H., Kobayashi, M., Liu, W. C., Oka, K., Jarvis, E. D. & Wada, K., 2012 Aug 2, In : PLoS One. 7, 8, e42173.

Research output: Contribution to journalArticle

Dual Specificity Phosphatase 1
Birds
Music
animal communication
learning
5 Citations (Scopus)

Starfish ApDOCK protein essentially functions in larval defense system operated by mesenchyme cells

Furukawa, R., Funabashi, H., Matsumoto, M. & Kaneko, H., 2012 Nov, In : Immunology and Cell Biology. 90, 10, p. 955-965 11 p.

Research output: Contribution to journalArticle

Starfish
Mesoderm
Larva
Proteins
Oils
5 Citations (Scopus)

Stem cells from innate sexual but not acquired sexual planarians have the capability to form a sexual individual

Nodono, H., Ishino, Y., Hoshi, M. & Matsumoto, M., 2012 Nov, In : Molecular Reproduction and Development. 79, 11, p. 757-766 10 p.

Research output: Contribution to journalArticle

Planarians
Stem Cells
Population
Fertilization
Sexual Behavior
12 Citations (Scopus)

Structure of acrosome reaction-inducing substance in the jelly coat of starfish eggs: A mini review

Hoshi, M., Moriyama, H. & Matsumoto, M., 2012 Aug 31, In : Biochemical and Biophysical Research Communications. 425, 3, p. 595-598 4 p.

Research output: Contribution to journalArticle

Starfish
Acrosome Reaction
Eggs
Polysaccharides
Genes
23 Citations (Scopus)

Synthesis and assignment of the absolute configuration of indenotryptoline bisindole alkaloid BE-54017

Kimura, T., Kanagaki, S., Matsui, Y., Imoto, M., Watanabe, T. & Shibasaki, M., 2012 Sep 7, In : Organic Letters. 14, 17, p. 4418-4421 4 p.

Research output: Contribution to journalArticle

alkaloids
stereochemistry
Alkaloids
Stereochemistry
osmium
20 Citations (Scopus)

Target identification of bioactive compounds

Tashiro, E. & Imoto, M., 2012 Mar 15, In : Bioorganic and Medicinal Chemistry. 20, 6, p. 1910-1921 12 p.

Research output: Contribution to journalArticle

Proteins
Functional analysis
Assays
Technology
Genetics
4 Citations (Scopus)

The comparison of motor learning performance with and without feedback

Orand, A., Ushiba, J., Tomita, Y. & Honda, S., 2012 Sep, In : Somatosensory and Motor Research. 29, 3, p. 103-110 8 p.

Research output: Contribution to journalArticle

Imagery (Psychotherapy)
Learning
Sensory Feedback
Electroencephalography
Hand
18 Citations (Scopus)

The correlation between motor impairments and event-related desynchronization during motor imagery in ALS patients

Kasahara, T., Terasaki, K., Ogawa, Y., Ushiba, J., Aramaki, H. & Masakado, Y., 2012 Jun 15, In : BMC Neuroscience. 13, 1, 66.

Research output: Contribution to journalArticle

Imagery (Psychotherapy)
Upper Extremity
Electroencephalography
Healthy Volunteers
Hand
14 Citations (Scopus)

The Dr-nanos gene is essential for germ cell specification in the planarian Dugesia ryukyuensis

Nakagawa, H., Ishizu, H., Chinone, A., Kobayashi, K. & Matsumoto, M., 2012, In : International Journal of Developmental Biology. 56, 1-3, p. 165-171 7 p.

Research output: Contribution to journalArticle

Planarians
Essential Genes
Germ Cells
Testis
Ovary
32 Citations (Scopus)

The effects of coating pDNA/chitosan complexes with chondroitin sulfate on physicochemical characteristics and cell transfection

Hagiwara, K., Nakata, M., Koyama, Y. & Sato, T., 2012 Oct, In : Biomaterials. 33, 29, p. 7251-7260 10 p.

Research output: Contribution to journalArticle

Chondroitin Sulfates
Chitosan
Transfection
Coatings
Viscosity
25 Citations (Scopus)

Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution

Nakamura, M. J., Terai, J., Okubo, R., Hotta, K. & Oka, K., 2012 Dec 15, In : Developmental Biology. 372, 2, p. 274-284 11 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Anatomy
Embryonic Structures
Chordata
Tail
8 Citations (Scopus)

Three-dimensional expansion using plasma-medium gel with fragmin/protamine nanoparticles and FGF-2 to stimulate adipose-derived stromal cells and bone marrow-derived mesenchymal stem cells

Kishimoto, S., Ishihara, M., Mori, Y., Takikawa, M., Sumi, Y., Nakamura, S., Sato, T. & Kiyosawa, T., 2012 Dec 1, In : BioResearch Open Access. 1, 6, p. 314-323 10 p.

Research output: Contribution to journalArticle

Dalteparin
Plasma (human)
Protamines
Fibroblast Growth Factor 2
Eagles
41 Citations (Scopus)

Tuning glycosidase inhibition through aglycone interactions: Pharmacological chaperones for Fabry disease and GM 1 gangliosidosis

Aguilar-Moncayo, M., Takai, T., Higaki, K., Mena-Barragán, T., Hirano, Y., Yura, K., Li, L., Yu, Y., Ninomiya, H., García-Moreno, M. I., Ishii, S., Sakakibara, Y., Ohno, K., Nanba, E., Ortiz Mellet, C., García Fernández, J. M. & Suzuki, Y., 2012 Jul 4, In : Chemical Communications. 48, 52, p. 6514-6516 3 p.

Research output: Contribution to journalArticle

Galactosidases
Glycoside Hydrolases
Tuning
38 Citations (Scopus)

Xanthohumol impairs autophagosome maturation through direct inhibition of valosin-containing protein

Sasazawa, Y., Kanagaki, S., Tashiro, E., Nogawa, T., Muroi, M., Kondoh, Y., Osada, H. & Imoto, M., 2012 May 18, In : ACS Chemical Biology. 7, 5, p. 892-900 9 p.

Research output: Contribution to journalArticle

Autophagy
Humulus
Neurodegenerative diseases
Chalcone
Autophagosomes
2011
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
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
37 Citations (Scopus)

Between-subject variance in the magnitude of corticomuscular coherence during tonic isometric contraction of the tibialis anterior muscle in healthy young adults

Ushiyama, J., Suzuki, T., Masakado, Y., Hase, K., Kimura, A., Liu, M. & Ushiba, J., 2011 Sep, In : Journal of Neurophysiology. 106, 3, p. 1379-1388 10 p.

Research output: Contribution to journalArticle

Isometric Contraction
Electromyography
Young Adult
Electroencephalography
Muscles
44 Citations (Scopus)

Biocatalytic strategies for the asymmetric synthesis of profens - Recent trends and developments

Kourist, R., Domínguez De María, P. & Miyamoto, K., 2011 Oct, In : Green Chemistry. 13, 10, p. 2607-2618 12 p.

Research output: Contribution to journalArticle

Enantioselectivity
Sustainable development
drug
Enzymes
Proteins
11 Citations (Scopus)

BioPAX support in CellDesigner

Mi, H., Muruganujan, A., Demir, E., Matsuoka, Y., Funahashi, A., Kitano, H. & Thomas, P. D., 2011 Dec, In : Bioinformatics. 27, 24, p. 3437-3438 2 p., btr586.

Research output: Contribution to journalArticle

Pathway
Software
Databases
Biological Phenomena
Information Storage and Retrieval
252 Citations (Scopus)

Caffeine induces apoptosis by enhancement of autophagy via PI3K/Akt/mTOR/p70S6K inhibition

Saiki, S., Sasazawa, Y., Imamichi, Y., Kawajiri, S., Fujimaki, T., Tanida, I., Kobayashi, H., Sato, F., Sato, S., Ishikawa, K. I., Imoto, M. & Hattori, N., 2011 Feb, In : Autophagy. 7, 2, p. 176-187 12 p.

Research output: Contribution to journalArticle

70-kDa Ribosomal Protein S6 Kinases
Autophagy
Caffeine
Phosphatidylinositol 3-Kinases
Apoptosis
36 Citations (Scopus)

Chemical chaperone therapy: Chaperone effect on mutant enzyme and cellular pathophysiology in β-galactosidase deficiency

Higaki, K., Li, L., Bahrudin, U., Okuzawa, S., Takamuram, A., Yamamoto, K., Adachi, K., Paraguison, R. C., Takai, T., Ikehata, H., Tominaga, L., Hisatome, I., Iida, M., Ogawa, S., Matsuda, J., Ninomiya, H., Sakakibara, Y., Ohno, K., Suzuki, Y. & Nanba, E., 2011 Jul, In : Human Mutation. 32, 7, p. 843-852 10 p.

Research output: Contribution to journalArticle

Galactosidases
Enzymes
Therapeutics
Mutant Proteins
Mutation
7 Citations (Scopus)

Chromatophore activity during natural pattern expression by the squid Sepioteuthis lessoniana: Contributions of miniature oscillation

Suzuki, M., Kimura, T., Ogawa, H., Hotta, K. & Oka, K., 2011, In : PLoS One. 6, 4, e18244.

Research output: Contribution to journalArticle

Chromatophores
chromatophores
Decapodiformes
squid
oscillation
24 Citations (Scopus)

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

Endo, T., Ueno, K., Yonezawa, K., Mineta, K., Hotta, K., Satou, Y., Yamada, L., Ogasawara, M., Takahashi, H., Nakajima, A., Nakachi, M., Nomura, M., Yaguchi, J., Sasakura, Y., Yamasaki, C., Sera, M., Yoshizawa, A. C., Imanishi, T., Taniguchi, H. & Inaba, K., 2011 Jan, In : Nucleic Acids Research. 39, SUPPL. 1

Research output: Contribution to journalArticle

Ciona intestinalis
Protein Databases
Computational Biology
Databases
Molecular Sequence Annotation
12 Citations (Scopus)

Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display

Tanaka, J., Yanagawa, H. & Doi, N., 2011, In : PLoS One. 6, 3, e18034.

Research output: Contribution to journalArticle

src Homology Domains
Display devices
Amino Acids
Messenger RNA
amino acids
20 Citations (Scopus)

Dramatically improved catalytic activity of an artificial (S)-selective arylmalonate decarboxylase by structure-guided directed evolution

Miyauchi, Y., Kourist, R., Uemura, D. & Miyamoto, K., 2011 Jul 14, In : Chemical Communications. 47, 26, p. 7503-7505 3 p.

Research output: Contribution to journalArticle

Naproxen
Enantioselectivity
Catalyst activity
malonate decarboxylase
6 Citations (Scopus)

Effects of 17β-estradiol and bisphenol a on the formation of reproductive organs in planarians

Miyashita, H., Nakagawa, H., Kobayashi, K., Hoshi, M. & Matsumoto, M., 2011 Feb, In : Biological Bulletin. 220, 1, p. 47-56 10 p.

Research output: Contribution to journalArticle

Planarians
bisphenol A
estradiol
gonads
Estradiol
129 Citations (Scopus)

Effects of neurofeedback training with an electroencephalogram-based brain-computer interface for hand paralysis in patients with chronic stroke: A preliminary case series study

Shindo, K., Kawashima, K., Ushiba, J., Ota, N., Ito, M., Ota, T., Kimura, A. & Liu, M., 2011 Oct, In : Journal of Rehabilitation Medicine. 43, 10, p. 951-957 7 p.

Research output: Contribution to journalArticle

Neurofeedback
Brain-Computer Interfaces
Paralysis
Electroencephalography
Hand
21 Citations (Scopus)

Engineering the promiscuous racemase activity of an arylmalonate decarboxylase

Kourist, R., Miyauchi, Y., Uemura, D. & Miyamoto, K., 2011 Jan 10, In : Chemistry - A European Journal. 17, 2, p. 557-563 7 p.

Research output: Contribution to journalArticle

Racemases and Epimerases
Substrates
Carboxylic Acids
Carboxylic acids
Bearings (structural)