Department of Biosciences and Informatics

Research Output 1987 2020

Filter
Article
2010
29 Citations (Scopus)

Metabolomic identification of the target of the filopodia protrusion inhibitor glucopiericidin A

Kitagawa, M., Ikeda, S., Tashiro, E., Soga, T. & Imoto, M., 2010 Sep 24, In : Chemistry and Biology. 17, 9, p. 989-998 10 p.

Research output: Contribution to journalArticle

Pseudopodia
Metabolomics
Glycolysis
Facilitative Glucose Transport Proteins
Respiration
65 Citations (Scopus)

Modulation of mu rhythm desynchronization during motor imagery by transcranial direct current stimulation

Matsumoto, J., Fujiwara, T., Takahashi, O., Liu, M., Kimura, A. & Ushiba, J., 2010, In : Journal of NeuroEngineering and Rehabilitation. 7, 1, 27.

Research output: Contribution to journalArticle

Imagery (Psychotherapy)
Hand
Transcranial Magnetic Stimulation
Cues
Electroencephalography
12 Citations (Scopus)

Molecular basis of chemical chaperone effects of N-octyl-β-valienamine on human β-glucosidase in low/neutral pH conditions

Jo, H., Yugi, K., Ogawa, S., Suzuki, Y. & Sakakibara, Y., 2010 Apr, In : Journal of Proteomics and Bioinformatics. 3, 4, p. 104-112 9 p.

Research output: Contribution to journalArticle

Glucosidases
Enzymes
Free energy
Hydrolases
Hydrogen bonds
11 Citations (Scopus)

mRNA display selection of a high-affinity, Bcl-XL-specific binding peptide

Matsumura, N., Tsuji, T., Sumida, T., Kokubo, M., Onimaru, M., Doi, N., Takashima, H., Miyamoto-Sato, E. & Yanagawa, H., 2010 Jul, In : FASEB Journal. 24, 7, p. 2201-2210 10 p.

Research output: Contribution to journalArticle

Display devices
Messenger RNA
Peptides
Inhibitory Concentration 50
bcl-2 Homologous Antagonist-Killer Protein
15 Citations (Scopus)

Murasaki: A fast, parallelizable algorithm to find anchors from multiple genomes

Popendorf, K., Tsuyoshi, H., Osana, Y. & Sakakibara, Y., 2010, In : PLoS One. 5, 9, e12651.

Research output: Contribution to journalArticle

Anchors
Genes
Genome
genome
Program processors
59 Citations (Scopus)
Lower Extremity
Muscles
Electromyography
Motor Neurons
Electroencephalography
7 Citations (Scopus)

Neocomplanines A and B, a complanine family isolated from the marine fireworm

Nakamura, K., Tachikawa, Y., Ohno, O., Kitamura, M., Suganuma, M. & Uemura, D., 2010 Mar 26, In : Journal of Natural Products. 73, 3, p. 303-305 3 p.

Research output: Contribution to journalArticle

Epichlorohydrin
Carbon
complanine
neocomplanine B
neocomplanine A
10 Citations (Scopus)

Network structure of projections extending from peripheral neurons in the tunic of ascidian larva

Terakubo, H. Q., Nakajima, Y., Sasakura, Y., Horie, T., Konno, A., Takahashi, H., Inaba, K., Hotta, K. & Oka, K., 2010 Aug, In : Developmental Dynamics. 239, 8, p. 2278-2287 10 p.

Research output: Contribution to journalArticle

Urochordata
Larva
Neurons
Axoneme
Ciona intestinalis
3 Citations (Scopus)

Neural substrate of sound duration discrimination during an auditory sequence in the guinea pig primary auditory cortex

Okazaki, S., Kanoh, S., Tsukada, M. & Oka, K., 2010 Jan, In : Hearing Research. 259, 1-2, p. 107-116 10 p.

Research output: Contribution to journalArticle

Auditory Cortex
Evoked Potentials
Guinea Pigs
Neurons
Brain
3 Citations (Scopus)

Neuroblastoma cells can be classified according to glycosphingolipid expression profiles identified by liquid chromatography-tandem mass spectrometry

Kaneko, T., Okita, H., Nakajima, H., Iijima, K., Ogasawara, N. A. O., Miyagawa, Y., Katagiri, Y. U., Nakagawa, A., Kiyokawa, N., Sato, T. & Fujimoto, J., 2010 Nov, In : International Journal of Oncology. 37, 5, p. 1279-1288 10 p.

Research output: Contribution to journalArticle

Glycosphingolipids
Gangliosides
Tandem Mass Spectrometry
Neuroblastoma
Liquid Chromatography
2 Citations (Scopus)

Operon structure optimization by random self-assembly

Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. & Sakakibara, Y., 2010, In : Natural Computing. 9, 1, p. 173-181 9 p.

Research output: Contribution to journalArticle

Self assembly
Genes
Biosynthesis
Genetic engineering
Bacilli
6 Citations (Scopus)

Regulation of notochord-specific expression of Ci-Bra downstream genes in Ciona intestinalis embryos

Takahashi, H., Hotta, K., Takagi, C., Ueno, N., Satoh, N. & Shoguchi, E., 2010 Feb, In : Zoological Science. 27, 2, p. 110-118 9 p.

Research output: Contribution to journalArticle

embryo (animal)
genes
enhancer elements
Chordata
genome
1 Citation (Scopus)

Robust and accurate prediction of noncoding RNAs from aligned sequences

Saito, Y., Sato, K. & Sakakibara, Y., 2010 Oct 15, In : BMC Bioinformatics. 11, SUPPL. 7, S3.

Research output: Contribution to journalArticle

Untranslated RNA
RNA
Base Pairing
Alignment
prediction
69 Citations (Scopus)

Sialic acid-mimic peptides as hemagglutinin inhibitors for anti-influenza therapy

Matsubara, T., Onishi, A., Saito, T., Shimada, A., Inoue, H., Taki, T., Nagata, K., Okahata, Y. & Sato, T., 2010 Jun 10, In : Journal of Medicinal Chemistry. 53, 11, p. 4441-4449 9 p.

Research output: Contribution to journalArticle

Hemagglutinins
N-Acetylneuraminic Acid
Human Influenza
Peptides
Orthomyxoviridae
5 Citations (Scopus)

Sunabedine, a novel toxic bromotyrosine-derivative alkaloid from Okinawan sponge, order Verongida

Maru, N., Koyama, T., Ohno, O., Yamada, K. & Uemura, D., 2010, In : Heterocycles. 82, 1, p. 371-375 5 p.

Research output: Contribution to journalArticle

Artemia
Experimental Melanomas
Poisons
Porifera
Cytotoxicity
37 Citations (Scopus)

Terpenoids produced by actinomycetes: Isolation, structural elucidation and biosynthesis of new diterpenes, gifhornenolones A and B from Verrucosispora gifhornensis YM28-088

Shirai, M., Okuda, M., Motohashi, K., Imoto, M., Furihata, K., Matsuo, Y., Katsuta, A., Shizuri, Y. & Seto, H., 2010 May, In : Journal of Antibiotics. 63, 5, p. 245-250 6 p.

Research output: Contribution to journalArticle

Actinobacteria
Diterpenes
Terpenes
Spectrum Analysis
Sesquiterpenes
79 Citations (Scopus)

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

Tassy, O., Dauga, D., Daian, F., Sobral, D., Robin, F., Khoueiry, P., Salgado, D., Fox, V., Caillol, D., Schiappa, R., Laporte, B., Rios, A., Luxardi, G., Kusakabe, T., Joly, J. S., Darras, S., Christiaen, L., Contensin, M., Auger, H., Lamy, C. & 9 others, Hudson, C., Rothbächer, U., Gilchrist, M. J., Makabe, K. W., Hotta, K., Fujiwara, S., Satoh, N., Satou, Y. & Lemaire, P., 2010 Oct, In : Genome Research. 20, 10, p. 1459-1468 10 p.

Research output: Contribution to journalArticle

Chordata
Urochordata
Developmental Biology
Embryonic Structures
Databases
17 Citations (Scopus)

Total synthesis of incednam, the aglycon of incednine

Ohtani, T., Tsukamoto, S., Kanda, H., Misawa, K., Urakawa, Y., Fujimaki, T., Imoto, M., Takahashi, Y., Takahashi, D. & Toshima, K., 2010 Nov 5, In : Organic Letters. 12, 21, p. 5068-5071 4 p.

Research output: Contribution to journalArticle

antibiotics
Oncogene Proteins
synthesis
Anti-Bacterial Agents
preparation
62 Citations (Scopus)

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M. & Sakakibara, Y., 2010 Apr 16, In : BMC Genomics. 11, 1, 243.

Research output: Contribution to journalArticle

Soy Foods
Bacillus subtilis
Genome
Genes
Operon
2009
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
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
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
18 Citations (Scopus)

Bicistronic DNA display for in vitro selection of Fab fragments

Sumida, T., Doi, N. & Yanagawa, H., 2009 Sep 29, In : Nucleic Acids Research. 37, 22, gkp776.

Research output: Contribution to journalArticle

Immunoglobulin Fab Fragments
DNA
Emulsions
Ribosomes
Bacteriophages
2 Citations (Scopus)

Cell-based in vivo dual imaging probes using genetically expressed tags and chemical contrast agents

Hasegawa, Y., Honda, A., Umezawa, K., Niino, Y., Oka, K., Chiba, T., Aiso, S., Tanimoto, A., Citterio, D. & Suzuki, K., 2009, In : Chemical Communications. 27, p. 4040-4042 3 p.

Research output: Contribution to journalArticle

Contrast Media
Imaging techniques
Magnetic resonance
Fluorescent Dyes
Labeling
84 Citations (Scopus)
GM1 Gangliosidosis
Galactosidases
Enzymes
Gaucher Disease
Glucosidases
58 Citations (Scopus)

Dextran Coated Gadolinium Phosphate Nanoparticles for Magnetic Resonance Tumor Imaging

Hifumi, H., Yamaoka, S., Tanimoto, A., Akatsu, T., Shindo, Y., Honda, A., Citterio, D., Oka, K., Kuribayashi, S. & Suzuki, K., 2009, In : Journal of Materials Chemistry. 19, 35, p. 6393-6399 7 p.

Research output: Contribution to journalArticle

Dextran
Gadolinium
Magnetic resonance
Dextrans
Tumors
15 Citations (Scopus)

Duck-billed platypus venom peptides induce Ca2+ influx in neuroblastoma cells

Kita, M., Black, D. S., Ohno, O., Yamada, K., Kigoshi, H. & Uemura, D., 2009 Dec 23, In : Journal of the American Chemical Society. 131, 50, p. 18038-18039 2 p.

Research output: Contribution to journalArticle

Platypus
Mammals
Ducks
Venoms
Neuroblastoma
5 Citations (Scopus)

FMRFamide elicits chromatophore expansion and retraction depending on its type and development in the squid, Sepioteuthis lessoniana

Suzuki, M., Kimura, T., Ogawa, H., Hotta, K. & Oka, K., 2009 Dec, In : Invertebrate Neuroscience. 9, 3-4, p. 185-193 9 p.

Research output: Contribution to journalArticle

FMRFamide
Chromatophores
Decapodiformes
Pharmacology
Muscles
6 Citations (Scopus)
Small Nucleolar RNA
Untranslated RNA
Caenorhabditis elegans
Base Pairing
Genome
46 Citations (Scopus)

Inhibition of influenza virus infections by sialylgalactose-binding peptides selected from a phage library

Matsubara, T., Sumi, M., Kubota, H., Taki, T., Okahata, Y. & Sato, T., 2009 Jul 23, In : Journal of Medicinal Chemistry. 52, 14, p. 4247-4256 10 p.

Research output: Contribution to journalArticle

Virus Diseases
Orthomyxoviridae
Bacteriophages
Peptides
Carbohydrates
38 Citations (Scopus)

Integrating statistical predictions and experimental verifications for enhancing protein-chemical interaction predictions in virtual screening

Nagamine, N., Shirakawa, T., Minato, Y., Torii, K., Kobayashi, H., Imoto, M. & Sakakibara, Y., 2009 Jun, In : PLoS Computational Biology. 5, 6, e1000397.

Research output: Contribution to journalArticle

Virtual Screening
chemical interactions
Screening
screening
Proteins
9 Citations (Scopus)

Interaction of notochord-derived fibrinogen-like protein with Notch regulates the patterning of the central nervous system of Ciona intestinalis embryos

Yamada, S., Hotta, K., Yamamoto, T. S., Ueno, N., Satoh, N. & Takahashi, H., 2009 Apr 1, In : Developmental Biology. 328, 1, p. 1-12 12 p.

Research output: Contribution to journalArticle

Ciona intestinalis
Notch Receptors
Notochord
Fibrinogen
Embryonic Structures
7 Citations (Scopus)

In vitro selection of GTP-binding proteins by block shuffling of estrogen-receptor fragments

Tsuji, T., Onimaru, M., Doi, N., Miyamoto-Sato, E., Takashima, H. & Yanagawa, H., 2009 Dec 18, In : Biochemical and Biophysical Research Communications. 390, 3, p. 689-693 5 p.

Research output: Contribution to journalArticle

GTP-Binding Proteins
Estrogen Receptors
Alternative Splicing
Affinity chromatography
Proteins
3 Citations (Scopus)

Microbial kinetic resolution of 2-substituted-1-propanol

Miyamoto, K., Fujimori, K., Hirano, J. I. & Ohta, H., 2009, In : Biocatalysis and Biotransformation. 27, 1, p. 66-70 5 p.

Research output: Contribution to journalArticle

Phenylethyl Alcohol
1-Propanol
Propionates
Propanol
Soil
5 Citations (Scopus)

Network features and pathway analyses of a signal transduction cascade

Yanashima, R., Kitagawa, N., Matsubara, Y., Weatheritt, R., Oka, K., Kikuchi, S., Tomita, M. & Ishizaki, S., 2009 May 29, In : Frontiers in Neuroinformatics. 3, MAY, 13.

Research output: Contribution to journalArticle

Boidae
Signal transduction
Cytoskeletal Proteins
Signal Transduction
Transcription factors
12 Citations (Scopus)

Observations of the distribution of GM3 in membrane microdomains by atomic force microscopy

Iijima, K., Soga, N., Matsubara, T. & Sato, T., 2009 Sep 15, In : Journal of Colloid and Interface Science. 337, 2, p. 369-374 6 p.

Research output: Contribution to journalArticle

Lipid bilayers
Sphingomyelins
Cholesterol
Atomic force microscopy
Glycosphingolipids
1 Citation (Scopus)

Oligomycin induced the proteasomal degradation of cyclin D1 protein

Kanai, M., Iba, S., Okada, R., Tashiro, E. & Imoto, M., 2009 Aug, In : Journal of Antibiotics. 62, 8, p. 425-429 5 p.

Research output: Contribution to journalArticle

Oligomycins
Cyclin D1
Proteins
Retinoblastoma Protein
Biological Products
3 Citations (Scopus)

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Amano, H., Funahashi, A., Hiroi, N. & Oguri, K., 2009, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5453, p. 368-373 6 p.

Research output: Contribution to journalArticle

Field Programmable Gate Array
Field programmable gate arrays (FPGA)
Simulator
Pipelines
Simulators
26 Citations (Scopus)

Rapid antibody selection by mRNA display on a microfluidic chip

Tabata, N., Sakuma, Y., Honda, Y., Doi, N., Takashima, H., Miyamoto-Sato, E. & Yanagawa, H., 2009, In : Nucleic Acids Research. 37, 8, e64.

Research output: Contribution to journalArticle

Microfluidics
Messenger RNA
Antibodies
Proteins
Single-Chain Antibodies

Sequence and structural analyses for functional non-coding RNAs

Sakakibara, Y. & Sato, K., 2009, In : Natural Computing Series. 9783540888680, p. 63-79 17 p.

Research output: Contribution to journalArticle

RNA
Kernel Function
Context-free Grammar
Secondary Structure
Discrimination
73 Citations (Scopus)

Simultaneous live cell imaging using dual FRET sensors with a single excitation light

Niino, Y., Hotta, K. & Oka, K., 2009 Jun 24, In : PLoS One. 4, 6, e6036.

Research output: Contribution to journalArticle

Fluorescence Resonance Energy Transfer
energy transfer
image analysis
fluorescence
Imaging techniques
5 Citations (Scopus)

Structural analysis of glycosphingolipid analogues obtained by the saccharide primer method using CE-ESI-MS

Zhu, X., Hatanaka, K., Yamagata, T. & Sato, T., 2009, In : Electrophoresis. 30, 20, p. 3519-3526 8 p.

Research output: Contribution to journalArticle

Glycosphingolipids
Structural analysis
Madin Darby Canine Kidney Cells
Cells
Column chromatography
16 Citations (Scopus)
Glycosylation
Support vector machines
Proteins
Polysaccharides
Cellular radio systems
495 Citations (Scopus)

The Systems Biology Graphical Notation

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., 2009 Aug, In : Nature Biotechnology. 27, 8, p. 735-741 7 p.

Research output: Contribution to journalArticle

Systems Biology
Visual languages
Language
Cell signaling
Unified Modeling Language
11 Citations (Scopus)

Transcriptional regulation of human fibroblast growth factor receptor 1 by E2F-1

Kanai, M., Tashiro, E., Maruki, H., Minato, Y. & Imoto, M., 2009 Jun 1, In : Gene. 438, 1-2, p. 49-56 8 p.

Research output: Contribution to journalArticle

Receptor, Fibroblast Growth Factor, Type 1
Fibroblast Growth Factor Receptors
Neoplasms
Chromatin Immunoprecipitation
Electrophoretic Mobility Shift Assay
50 Citations (Scopus)

Whole-genome tiling array analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions

Akama, T., Suzuki, K., Tanigawa, K., Kawashima, A., Wu, H., Nakata, N., Osana, Y., Sakakibara, Y. & Ishii, N., 2009 May, In : Journal of Bacteriology. 191, 10, p. 3321-3327 7 p.

Research output: Contribution to journalArticle

Mycobacterium leprae
Pseudogenes
Genome
RNA
Nude Rats
2008
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
82 Citations (Scopus)
G(M1) Ganglioside
Amyloidogenic Proteins
Presynaptic Terminals
Cluster Analysis
Alzheimer Disease
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
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