Research Center for Transomics Medicine

Research Output 1994 2020

6 Citations (Scopus)

A BP-Based Algorithm for Performing Bayesian Inference in Large Perceptron-Type Networks

Kabashima, Y. & Uda, S., 2004, International Conference on Algorithmic Learning Theory. p. 479-493

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Citations (Scopus)

A chromatin integration labelling method enables epigenomic profiling with lower input

Harada, A., Maehara, K., Handa, T., Arimura, Y., Nogami, J., Hayashi-Takanaka, Y., Shirahige, K., Kurumizaka, H., Kimura, H. & Ohkawa, Y., Feb 1 2019, In : Nature Cell Biology. 21, 2, p. 287-296 10 p.

Research output: Contribution to journalArticle

Epigenomics
Chromatin
Chromatin Immunoprecipitation
Histone Code
Immunoprecipitation
26 Citations (Scopus)

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation

Tomita, S., Abdalla, M. O. A., Fujiwara, S., Matsumori, H., Maehara, K., Ohkawa, Y., Iwase, H., Saitoh, N. & Nakao, M., Apr 29 2015, In : Nature communications. 6, 6966.

Research output: Contribution to journalArticle

Untranslated RNA
loci
breast
estrogens
cancer
7 Citations (Scopus)

A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples

Maehara, K., Odawara, J., Harada, A., Yoshimi, T., Nagao, K., Obuse, C., Akashi, K., Tachibana, T., Sakata, T. & Ohkawa, Y., Jan 1 2013, In : Nucleic acids research. 41, 1, p. 54-62 9 p.

Research output: Contribution to journalArticle

Encyclopedias
Chromatin Immunoprecipitation
RNA Polymerase III
RNA Polymerase II
DNA
12 Citations (Scopus)

A comparative study of the enzymologieal features of α-amylase in the Drosophila melanogaster species subgroup

Shibata, H. & Yamazaki, T., Jan 1 1994, In : Japanese Journal of Genetics. 69, 3, p. 251-258 8 p.

Research output: Contribution to journalArticle

Amylases
Drosophila melanogaster
Temperature
Phylogeny
Enzymes
21 Citations (Scopus)

Acute hyperglycemia impairs functional improvement after spinal cord injury in mice and humans

Kobayakawa, K., Kumamaru, H., Saiwai, H., Kubota, K., Ohkawa, Y., Kishimoto, J., Yokota, K., Ideta, R., Shiba, K., Tozaki-Saitoh, H., Inoue, K., Iwamoto, Y. & Okada, S., Oct 1 2014, In : Science Translational Medicine. 6, 256, 256ra137.

Research output: Contribution to journalArticle

Spinal Cord Injuries
Hyperglycemia
Obese Mice
Nervous System Trauma
Blood Glucose
1 Citation (Scopus)

Ad4BP/SF-1 regulates cholesterol synthesis to boost the production of steroids

Baba, T., Otake, H., Inoue, M., Sato, T., Ishihara, Y., Moon, J. Y., Tsuchiya, M., Miyabayashi, K., Ogawa, H., Shima, Y., Wang, L., Sato, R., Yamazaki, T., Suyama, M., Nomura, M., Choi, M. H., Ohkawa, Y. & Morohashi, K. I., Dec 1 2018, In : Communications Biology. 1, 1, 18.

Research output: Contribution to journalArticle

Open Access
steroids
Steroids
Cholesterol
cholesterol
Metabolic Networks and Pathways
15 Citations (Scopus)

Adiponectin/T-cadherin system enhances exosome biogenesis and decreases cellular ceramides by exosomal release

Obata, Y., Kita, S., Koyama, Y., Fukuda, S., Takeda, H., Takahashi, M., Fujishima, Y., Nagao, H., Masuda, S., Tanaka, Y., Nakamura, Y., Nishizawa, H., Funahashi, T., Ranscht, B., Izumi, Y., Bamba, T., Fukusaki, E., Hanayama, R., Shimada, S., Maeda, N. & 1 others, Shimomura, I., Apr 19 2018, In : JCI Insight. 3, 8

Research output: Contribution to journalArticle

Open Access
Exosomes
Ceramides
Adiponectin
Aorta
Multivesicular Bodies

A fail-safe system to prevent oncogenesis by senescence is targeted by SV40 small T antigen

Oshikawa, K., Matsumoto, M., Kodama, M., Shimizu, H. & Nakayama, K. I., Jan 1 2019, (Accepted/In press) In : Oncogene.

Research output: Contribution to journalArticle

Simian virus 40
Viral Tumor Antigens
Carcinogenesis
Oncogenes
Heterochromatin
12 Citations (Scopus)

A genome-wide analysis identifies a Notch-RBP-Jk-IL-7Ra axis that controls IL-17-Producing γδ T cell homeostasis in mice

Nakamura, M., Shibata, K., Hatano, S., Sato, T., Ohkawa, Y., Yamada, H., Ikuta, K. & Yoshikai, Y., Jan 1 2015, In : Journal of Immunology. 194, 1, p. 243-251 9 p.

Research output: Contribution to journalArticle

Interleukin-17
Homeostasis
Genome
T-Lymphocytes
Interleukin-7
26 Citations (Scopus)
Spinal Cord Injuries
Cytokines
Spinal Cord
Chemokines
Infiltration
7 Citations (Scopus)

Agplus: A rapid and flexible tool for aggregation plots

Maehara, K. & Ohkawa, Y., Jul 31 2015, In : Bioinformatics. 31, 18, p. 3046-3047 2 p.

Research output: Contribution to journalArticle

Nucleic Acid Regulatory Sequences
Transcription Initiation Site
Aggregation
Agglomeration
Transcription

A highly sensitive determination method for acrylamide in beverages, grains, and confectioneries by supercritical fluid chromatography tandem mass spectrometry

Yoshioka, T., Izumi, Y., Nagatomi, Y., Miyamoto, Y., Suzuki, K. & Bamba, T., Oct 1 2019, In : Food Chemistry. 294, p. 486-492 7 p.

Research output: Contribution to journalArticle

supercritical fluid chromatography
Supercritical Fluid Chromatography
Beverages
Acrylamide
acrylamides
8 Citations (Scopus)

A high phosphorus diet affects lipid metabolism in rat liver: A DNA microarray analysis

Chun, S., Bamba, T., Suyama, T., Ishijima, T., Fukusaki, E., Abe, K. & Nakai, Y., May 2016, In : PloS one. 11, 5, e0155386.

Research output: Contribution to journalArticle

Microarray Analysis
Microarrays
Nutrition
Oligonucleotide Array Sequence Analysis
Lipid Metabolism
11 Citations (Scopus)

Akt1-mediated Gata3 phosphorylation controls the repression of IFNÎ 3 in memory-type Th2 cells

Hosokawa, H., Tanaka, T., Endo, Y., Kato, M., Shinoda, K., Suzuki, A., Motohashi, S., Matsumoto, M., Nakayama, K. I. & Nakayama, T., Apr 7 2016, In : Nature communications. 7, 11289.

Research output: Contribution to journalArticle

Th2 Cells
phosphorylation
Phosphorylation
Cytokines
Data storage equipment
27 Citations (Scopus)

A large-scale targeted proteomics assay resource based on an in vitro human proteome

Matsumoto, M., Matsuzaki, F., Oshikawa, K., Goshima, N., Mori, M., Kawamura, Y., Ogawa, K., Fukuda, E., Nakatsumi, H., Natsume, T., Fukui, K., Horimoto, K., Nagashima, T., Funayama, R., Nakayama, K. & Nakayama, K. I., Feb 28 2017, In : Nature Methods. 14, 3, p. 251-258 8 p.

Research output: Contribution to journalArticle

Proteome
Proteomics
Assays
Proteins
Monitoring
77 Citations (Scopus)

Alteration of intra-pancreatic target-organ specificity by abrogation of Aire in NOD mice

Niki, S., Oshikawa, K., Mouri, Y., Hirota, F., Matsushima, A., Yano, M., Han, H., Bando, Y., Izumi, K., Matsumoto, M., Nakayama, K. I., Kuroda, N. & Matsumoto, M., May 1 2006, In : Journal of Clinical Investigation. 116, 5, p. 1292-1301 10 p.

Research output: Contribution to journalArticle

Organ Specificity
Inbred NOD Mouse
Acinar Cells
Islets of Langerhans
Thymus Gland
3 Citations (Scopus)

Alterations in Docosahexaenoic Acid-Related Lipid Cascades in Inflammatory Bowel Disease Model Mice

Nishiumi, S., Izumi, Y. & Yoshida, M., Jun 1 2018, In : Digestive Diseases and Sciences. 63, 6, p. 1485-1496 12 p.

Research output: Contribution to journalArticle

Docosahexaenoic Acids
Inflammatory Bowel Diseases
Knockout Mice
Interleukin-10
Lipids
11 Citations (Scopus)

Alterations in Fetal Leydig Cell Gene Expression during Fetal and Adult Development

Miyabayashi, K., Shima, Y., Inoue, M., Sato, T., Baba, T., Ohkawa, Y., Suyama, M. & Morohashi, K. I., May 1 2017, In : Sexual Development. 11, 2, p. 53-63 11 p.

Research output: Contribution to journalArticle

Leydig Cells
Fetal Development
Gene Expression
Testis
Mitochondrial Genes

Alternative mRNA splicing in three venom families underlying a possible production of divergent venom proteins of the habu snake, protobothrops flavoviridis

Ogawa, T., Oda-Ueda, N., Hisata, K., Nakamura, H., Chijiwa, T., Hattori, S., Isomoto, A., Yugeta, H., Yamasaki, S., Fukumaki, Y., Ohno, M., Satoh, N. & Shibata, H., Oct 9 2019, In : Toxins. 11, 10, 581.

Research output: Contribution to journalArticle

Open Access
Trimeresurus
Snakes
Venoms
Alternative Splicing
Genes
3 Citations (Scopus)

Ameliorating effects of D-47, a newly developed compound, on lipid metabolism in an animal model of familial hypercholesterolemia (WHHLMI rabbits)

Tamura, S., Koike, Y., Takeda, H., Koike, T., Izumi, Y., Nagasaka, R., Tsunoda, T., Tori, M., Ogawa, K., Bamba, T. & Shiomi, M., Mar 5 2018, In : European Journal of Pharmacology. 822, p. 147-153 7 p.

Research output: Contribution to journalArticle

Hyperlipoproteinemia Type II
Lipid Metabolism
Animal Models
Rabbits
Fats

A metabolite of dietary glucosylceramide from pineapples improves the skin barrier function in hairless mice

Kuwata, T., Hashimoto, T., Ohto, N., Kuwahara, H., Lee, J. W., Bamba, T. & Mizuno, M., Mar 1 2017, In : Journal of Functional Foods. 30, p. 228-236 9 p.

Research output: Contribution to journalArticle

Ananas
Glucosylceramides
Hairless Mouse
pineapples
interleukins
112 Citations (Scopus)

A metabolomic approach to lung cancer

Hori, S., Nishiumi, S., Kobayashi, K., Shinohara, M., Hatakeyama, Y., Kotani, Y., Hatano, N., Maniwa, Y., Nishio, W., Bamba, T., Fukusaki, E., Azuma, T., Takenawa, T., Nishimura, Y. & Yoshida, M., Nov 1 2011, In : Lung Cancer. 74, 2, p. 284-292 9 p.

Research output: Contribution to journalArticle

Metabolomics
Lung Neoplasms
Serum
Healthy Volunteers
Biomarkers

An albino mutant of the Japanese rat snake (Elaphe climacophora) carries a nonsense mutation in the tyrosinase gene

Iwanishi, S., Zaitsu, S., Shibata, H. & Nitasaka, E., Jan 1 2018, In : Genes and Genetic Systems. 93, 4, p. 163-167 5 p.

Research output: Contribution to journalArticle

Monophenol Monooxygenase
Snakes
Nonsense Codon
Pets
Genes
42 Citations (Scopus)

Analysis of CDMA systems that are characterized by eigenvalue spectrum

Takeda, K., Uda, S. & Kabashima, Y., 2006, In : Europhysics Letters. 76, p. 1193-1199

Research output: Contribution to journalArticle

12 Citations (Scopus)

Analysis of cellular signal transduction from an information theoretic approach

Uda, S. & Kuroda, S., Mar 1 2016, In : Seminars in Cell and Developmental Biology. 51, p. 24-31 8 p.

Research output: Contribution to journalReview article

Signal Transduction
Information Theory
Cell Differentiation
Cell Death
Cell Proliferation
23 Citations (Scopus)

Analysis of long-chain polyprenols using supercritical fluid chromatography and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Bamba, T., Fukusaki, E., Nakazawa, Y., Sato, H., Ute, K., Kitayama, T. & Kobayashi, A., May 2 2003, In : Journal of Chromatography A. 995, 1-2, p. 203-207 5 p.

Research output: Contribution to journalArticle

Supercritical Fluid Chromatography
Ionization
Mass spectrometry
Desorption
Mass Spectrometry
6 Citations (Scopus)

An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites

Oishi, T., Tanaka, K. I., Hashimoto, T., Shinbo, Y., Jumtee, K., Bamba, T., Fukusaki, E., Suzuki, H., Shibata, D., Takahashi, H., Asahi, H., Kurokawa, K., Nakamura, Y., Hirai, A., Nakamura, K., Altaf-Ul-Amin, M. & Kanaya, S., 2009, In : Plant Biotechnology. 26, 1, p. 167-174 8 p.

Research output: Contribution to journalArticle

Metabolomics
Databases
metabolites
metabolomics
prediction

A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

Koganebuchi, K., Gakuhari, T., Takeshima, H., Sato, K., Fujii, K., Kumabe, T., Kasagi, S., Sato, T., Tajima, A., Shibata, H., Ogawa, M. & Oota, H., Jul 2018, In : PloS one. 13, 7, e0200170.

Research output: Contribution to journalArticle

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Chromosomes
baits
Genes
445 Citations (Scopus)

An F-box protein, FWD1, mediates ubiquitin-dependent proteolysis of β-catenin

Kitagawa, M., Hatakeyama, S., Shirane, M., Matsumoto, M., Ishida, N., Hattori, K., Nakamichi, I., Kikuchi, A., Nakayama, K. I. & Nakayama, K., May 4 1999, In : EMBO Journal. 18, 9, p. 2401-2410 10 p.

Research output: Contribution to journalArticle

F-Box Proteins
Proteolysis
Catenins
Ubiquitin
Ubiquitination
6 Citations (Scopus)

An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure in samples of limited cell number

Ohkawa, Y., Mallappa, C., Vallaster, C. S. D. & Imbalzano, A. N., Jan 2 2012, Myogenesis: Methods and Protocols. DiMario, J. (ed.). p. 531-542 12 p. (Methods in Molecular Biology; vol. 798).

Research output: Chapter in Book/Report/Conference proceedingChapter

Enzyme Assays
Chromatin
Cell Count
Biomedical Technology Assessment
Cues
18 Citations (Scopus)
Flavonoids
Methylation
Liquid chromatography
Liquid Chromatography
Isotopes
26 Citations (Scopus)

An optogenetic system for interrogating the temporal dynamics of Akt

Katsura, Y., Kubota, H., Kunida, K., Kanno, A., Kuroda, S. & Ozawa, T., Oct 1 2015, In : Scientific reports. 5, 14589.

Research output: Contribution to journalArticle

Optogenetics
Light
Muscular Atrophy
Protein-Serine-Threonine Kinases
Lighting
2 Citations (Scopus)

A novel frameshift mutation of DDHD1 in a Japanese patient with autosomal recessive spastic paraplegia

Miura, S., Morikawa, T., Fujioka, R., Kosaka, K., Yamada, K., Hattori, G., Motomura, M., Taniwaki, T. & Shibata, H., Aug 1 2016, In : European Journal of Medical Genetics. 59, 8, p. 413-416 4 p.

Research output: Contribution to journalArticle

Frameshift Mutation
Mutation
Paraplegia
Genes
Lower Extremity
3 Citations (Scopus)

A novel missense mutation of RYR1 in familial idiopathic hyper CK-emia

Sano, K., Miura, S., Fujiwara, T., Fujioka, R., Yorita, A., Noda, K., Kida, H., Azuma, K., Kaieda, S., Yamamoto, K., Taniwaki, T., Fukumaki, Y. & Shibata, H., Sep 15 2015, In : Journal of the Neurological Sciences. 356, 1-2, p. 142-147 6 p., 13864.

Research output: Contribution to journalArticle

Missense Mutation
Creatine Kinase
Pedigree
Nucleotides
Genes
3 Citations (Scopus)

A novel missense variant (Gln220Arg) of GNB4 encoding guanine nucleotide-binding protein, subunit beta-4 in a Japanese family with autosomal dominant motor and sensory neuropathy

Miura, S., Morikawa, T., Fujioka, R., Noda, K., Kosaka, K., Taniwaki, T. & Shibata, H., Sep 2017, In : European Journal of Medical Genetics. 60, 9, p. 474-478 5 p.

Research output: Contribution to journalArticle

Guanine Nucleotides
Protein Subunits
Carrier Proteins
Exome
Lower Extremity
100 Citations (Scopus)

Anovel serum metabolomics-based diagnostic approach to pancreatic cancer

Kobayashi, T., Nishiumi, S., Ikeda, A., Yoshie, T., Sakai, A., Matsubara, A., Izumi, Y., Tsumura, H., Tsuda, M., Nishisaki, H., Hayashi, N., Kawano, S., Fujiwara, Y., Minami, H., Takenawa, T., Azuma, T. & Yoshida, M., Apr 1 2013, In : Cancer Epidemiology Biomarkers and Prevention. 22, 4, p. 571-579 9 p.

Research output: Contribution to journalArticle

Metabolomics
Pancreatic Neoplasms
Chronic Pancreatitis
Serum
Healthy Volunteers
2 Citations (Scopus)

Anti-tumour effects of antimicrobial peptides, components of the innate immune system, against haematopoietic tumours in Drosophila mxc mutants

Araki, M., Kurihara, M., Kinoshita, S., Awane, R., Sato, T., Ohkawa, Y. & Inoue, Y. H., Jan 1 2019, In : DMM Disease Models and Mechanisms. 12, 6, dmm037721.

Research output: Contribution to journalArticle

Open Access
Immune system
Drosophila
Tumors
Immune System
Peptides
8 Citations (Scopus)

A one-step immunostaining method to visualize rodent muscle fiber type within a single specimen

Sawano, S., Komiya, Y., Ichitsubo, R., Ohkawa, Y., Nakamura, M., Tatsumi, R., Ikeuchi, Y. & Mizunoya, W., Nov 2016, In : PloS one. 11, 11, 0166080.

Research output: Contribution to journalArticle

muscle fibers
Muscle
Rodentia
rodents
Muscles
1 Citation (Scopus)

A panel of specific monoclonal antibodies directed against various phosphorylated histones H3

Yoshimi, T., Ohkawa, Y., Azuma, M. & Tachibana, T., Apr 1 2013, In : Monoclonal Antibodies in Immunodiagnosis and Immunotherapy. 32, 2, p. 119-124 6 p.

Research output: Contribution to journalArticle

Histones
Monoclonal Antibodies
Epigenomics
Histone Code
Phosphorylation

Application of metabolomics for discrimination and sensory predictive modeling of food products

Putri, S. P., Bamba, T. & Fukusaki, E., Dec 1 2013, Hot Topics in Metabolomics: Food and Nutrition. Future Medicine Ltd., p. 54-64 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolomics
14 Citations (Scopus)

Application of supercritical fluid carbon dioxide to the extraction and analysis of lipids

Lee, J. W., Fukusaki, E. & Bamba, T., Oct 1 2012, In : Bioanalysis. 4, 19, p. 2413-2422 10 p.

Research output: Contribution to journalReview article

Supercritical Fluid Chromatography
Supercritical fluids
Carbon Dioxide
Lipids
Environmental Pollution
60 Citations (Scopus)

Application of supercritical fluid chromatography/mass spectrometry to lipid profiling of soybean

Lee, J. W., Uchikata, T., Matsubara, A., Nakamura, T., Fukusaki, E. & Bamba, T., Feb 1 2012, In : Journal of Bioscience and Bioengineering. 113, 2, p. 262-268 7 p.

Research output: Contribution to journalArticle

Supercritical Fluid Chromatography
Soybeans
Lipids
Mass spectrometry
Mass Spectrometry
23 Citations (Scopus)

A quantitative image cytometry technique for time series or population analyses of signaling networks

Ozaki, Y. I., Uda, S., Saito, T. H., Chung, J., Kubota, H. & Kuroda, S., Sep 10 2010, In : PloS one. 5, 4, e9955.

Research output: Contribution to journalArticle

Image Cytometry
Cell signaling
Time series
time series analysis
Systems Biology
6 Citations (Scopus)

A rat monoclonal antibody against the chromatin remodeling factor CHD5

Yoshimura, S., Yoshimi, T., Ohkawa, Y., Azuma, M. & Tachibana, T., Feb 1 2010, In : Hybridoma. 29, 1, p. 63-66 4 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
DNA-Binding Proteins
Monoclonal Antibodies
Immunoblotting
Antibodies
71 Citations (Scopus)

Association analysis of polymorphisms in the upstream region of the human dopamine D4 receptor gene (DRD4) with schizophrenia and personality traits

Mitsuyasu, H., Hirata, N., Sakai, Y., Shibata, H., Takeda, Y., Ninomiya, H., Kawasaki, H., Tashiro, N. & Fukumaki, Y., Mar 10 2001, In : Journal of Human Genetics. 46, 1, p. 26-31 6 p.

Research output: Contribution to journalArticle

Dopamine D4 Receptors
Personality
Schizophrenia
Exons
Genes
8 Citations (Scopus)

Association analysis of the glutamic acid decarboxylase 2 and the glutamine synthetase genes (GAD2, GLUL) with schizophrenia

Arai, S., Shibata, H., Sakai, M., Ninomiya, H., Lwata, N., Ozaki, N. & Fukumaki, Y., Feb 1 2009, In : Psychiatric Genetics. 19, 1, p. 6-13 8 p.

Research output: Contribution to journalArticle

Glutamate Decarboxylase
Schizophrenia
Genes
Single Nucleotide Polymorphism
Haplotypes
38 Citations (Scopus)

Association study of polymorphisms in synaptic vesicle-associated genes, SYN2 and CPLX2, with schizophrenia

Lee, H. J., Song, J. Y., Kim, J. W., Jin, S. Y., Hong, M. S., Park, J. K., Chung, J. H., Shibata, H. & Fukumaki, Y., Aug 31 2005, In : Behavioral and Brain Functions. 1, 15.

Research output: Contribution to journalArticle

Synapsins
Synaptic Vesicles
Schizophrenia
Genes
Haplotypes
39 Citations (Scopus)

Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia

Deng, X., Shibata, H., Ninomiya, H., Tashiro, N., Iwata, N., Ozaki, N. & Fukumaki, Y., Aug 6 2004, In : BMC Psychiatry. 4, 21.

Research output: Contribution to journalArticle

Excitatory Amino Acid Transporter 2
Schizophrenia
Haplotypes
Genes
Single Nucleotide Polymorphism
30 Citations (Scopus)

Association study of polymorphisms in the GluR5 kainate receptor gene (GRIK1) with schizophrenia

Shibata, H., Joo, A., Fujii, Y., Tani, A., Makino, C., Hirata, N., Kikuta, R., Ninomiya, H., Tashiro, N. & Fukumaki, Y., Oct 30 2001, In : Psychiatric Genetics. 11, 3, p. 139-144 6 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Schizophrenia
Genes
Haplotypes
Polymerase Chain Reaction