Research Center for Transomics Medicine

Research Output 1994 2020

2014
11 Citations (Scopus)

Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus

Fujinami, D., Matsumoto, M., Noguchi, T., Sonomoto, K. & Kohda, D., Mar 31 2014, In : Carbohydrate Research. 387, 1, p. 30-36 7 p.

Research output: Contribution to journalArticle

Pyrococcus furiosus
Asparagine
Archaea
Oligosaccharides
Polysaccharides
2 Citations (Scopus)

The finding of a group IIE phospholipase A2 gene in a specified segment of Protobothrops flavoviridis genome and its possible evolutionary relationship to group IIA phospholipase A2 genes

Yamaguchi, K., Chijiwa, T., Ikeda, N., Shibata, H., Fukumaki, Y., Oda-Ueda, N., Hattori, S. & Ohno, M., Jan 1 2014, In : Toxins. 6, 12, p. 3471-3487 17 p.

Research output: Contribution to journalArticle

Group II Phospholipases A2
Genes
Genome
Snakes
Gene encoding
10 Citations (Scopus)

The PPARγ locus makes long-range chromatin interactions with selected tissue-specific gene loci during adipocyte differentiation in a protein kinase a dependent manner

LeBlanc, S. E., Wu, Q., Barutcu, A. R., Xiao, H., Ohkawa, Y. & Imbalzano, A. N., Jan 20 2014, In : PloS one. 9, 1, e86140.

Research output: Contribution to journalArticle

PPAR gamma
adipocytes
Adipocytes
protein kinases
Protein Kinases
24 Citations (Scopus)

ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway

Adachi, S., Homoto, M., Tanaka, R., Hioki, Y., Murakami, H., Suga, H., Matsumoto, M., Nakayama, K. I., Hatta, T., Iemura, S. I. & Natsume, T., Jan 1 2014, In : Nucleic acids research. 42, 15, p. 10037-10049 13 p.

Research output: Contribution to journalArticle

LDL Receptors
RNA Stability
Phosphotransferases
Messenger RNA
Antisense Oligonucleotides
2013
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
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
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
59 Citations (Scopus)

Butyrate attenuates inflammation and lipolysis generated by the interaction of adipocytes and macrophages

Ohira, H., Fujioka, Y., Katagiri, C., Mamoto, R., Aoyama-Ishikawa, M., Amako, K., Izumi, Y., Nishiumi, S., Yoshida, M., Usami, M. & Ikeda, M., Jun 5 2013, In : Journal of atherosclerosis and thrombosis. 20, 5, p. 425-442 18 p.

Research output: Contribution to journalArticle

Butyrates
Macrophages
Lipolysis
Adipocytes
Inflammation
16 Citations (Scopus)

Contribution of structural reversibility to the heat stability of the tropomyosin shrimp allergen

Usui, M., Harada, A., Ishimaru, T., Sakumichi, E., Saratani, F., Sato-Minami, C., Azakami, H., Miyasaki, T. & Hanaoka, K., Jun 12 2013, In : Bioscience, Biotechnology and Biochemistry. 77, 5, p. 948-953 6 p.

Research output: Contribution to journalArticle

Tropomyosin
Allergens
Hot Temperature
Heating
Cooling
9 Citations (Scopus)

Development of surface-engineered yeast cells displaying phytochelatin synthase and their application to cadmium biosensors by the combined use of pyrene-excimer fluorescence

Matsuura, H., Yamamoto, Y., Muraoka, M., Akaishi, K., Hori, Y., Uemura, K., Tsuji, N., Harada, K., Hirata, K., Bamba, T., Miyasaka, H., Kuroda, K. & Ueda, M., Sep 1 2013, In : Biotechnology Progress. 29, 5, p. 1197-1202 6 p.

Research output: Contribution to journalArticle

Biosensing Techniques
Cadmium
Yeasts
Fluorescence
Heavy Metals
11 Citations (Scopus)

Diversity in the matrix structure of eggshells in the testudines (reptilia)

Kusuda, S., Yasukawa, Y., Shibata, H., Saito, T., Doi, O., Ohya, Y. & Yoshizaki, N., May 1 2013, In : Zoological science. 30, 5, p. 366-374 9 p.

Research output: Contribution to journalArticle

Testudines
Reptilia
egg shell
crystals
calcite
81 Citations (Scopus)

Dynamic metabolic profiling of cyanobacterial glycogen biosynthesis under conditions of nitrate depletion

Hasunuma, T., Kikuyama, F., Matsuda, M., Aikawa, S., Izumi, Y. & Kondo, A., Jul 1 2013, In : Journal of Experimental Botany. 64, 10, p. 2943-2954 12 p.

Research output: Contribution to journalArticle

metabolomics
Glycogen
Nitrates
glycogen
nitrates
16 Citations (Scopus)
Chondrogenesis
Osteogenesis
Endoplasmic Reticulum
SKP Cullin F-Box Protein Ligases
F-Box Proteins
123 Citations (Scopus)

FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes

Hirano, A., Yumimoto, K., Tsunematsu, R., Matsumoto, M., Oyama, M., Kozuka-Hata, H., Nakagawa, T., Lanjakornsiripan, D., Nakayama, K. I. & Fukada, Y., Feb 28 2013, In : Cell. 152, 5, p. 1106-1118 13 p.

Research output: Contribution to journalArticle

Cryptochromes
Circadian Clocks
Ubiquitination
Clocks
Stabilization
6 Citations (Scopus)

Genome-wide association study of schizophrenia using microsatellite markers in the Japanese population

Shibata, H., Yamamoto, K., Sun, Z., Oka, A., Inoko, H., Arinami, T., Inada, T., Ujike, H., Itokawa, M., Tochigi, M., Watanabe, Y., Someya, T., Kunugi, H., Suzuki, T., Iwata, N., Ozaki, N. & Fukumaki, Y., Jun 2013, In : Psychiatric Genetics. 23, 3, p. 117-123 7 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Microsatellite Repeats
Single Nucleotide Polymorphism
Schizophrenia
Population
32 Citations (Scopus)

Human TREX component Thoc5 affects alternative polyadenylation site choice by recruiting mammalian cleavage factor I

Katahira, J., Okuzaki, D., Inoue, H., Yoneda, Y., Maehara, K. & Ohkawa, Y., Aug 1 2013, In : Nucleic acids research. 41, 14, p. 7060-7072 13 p.

Research output: Contribution to journalArticle

Polyadenylation
Genes
Messenger RNA
Cell Nucleus Active Transport
Chromatin Immunoprecipitation
24 Citations (Scopus)

Inflammation and Resolution Are Associated with Upregulation of Fatty Acid β-Oxidation in Zymosan-Induced Peritonitis

Fujieda, Y., Manno, A., Hayashi, Y., Rhodes, N., Guo, L., Arita, M., Bamba, T. & Fukusaki, E., Jun 11 2013, In : PloS one. 8, 6, e66270.

Research output: Contribution to journalArticle

zymosan
Zymosan
beta oxidation
peritonitis
Peritonitis
55 Citations (Scopus)
Spinal Cord Injuries
Repair
Tissue
Inflammation
Neurology
20 Citations (Scopus)

Phosphorylation of Noxo1 at threonine 341 regulates its interaction with Noxa1 and the superoxide-producing activity of Nox1

Yamamoto, A., Takeya, R., Matsumoto, M., Nakayama, K. & Sumimoto, H., Oct 1 2013, In : FEBS Journal. 280, 20, p. 5145-5159 15 p.

Research output: Contribution to journalArticle

Phosphorylation
Threonine
Superoxides
Acetates
Protein Kinase C
58 Citations (Scopus)

Simultaneous profiling of polar lipids by supercritical fluid chromatography/tandem mass spectrometry with methylation

Lee, J. W., Nishiumi, S., Yoshida, M., Fukusaki, E. & Bamba, T., Mar 1 2013, In : Journal of Chromatography A. 1279, p. 98-107 10 p.

Research output: Contribution to journalArticle

Supercritical Fluid Chromatography
Methylation
Tandem Mass Spectrometry
Mass spectrometry
Lipids
3 Citations (Scopus)

The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression

Akimoto, Y., Yugi, K., Uda, S., Kudo, T., Komori, Y., Kubota, H. & Kuroda, S., Sep 9 2013, In : PloS one. 8, 9, e72780.

Research output: Contribution to journalArticle

Least-Squares Analysis
mitogen-activated protein kinase
growth factors
least squares
Intercellular Signaling Peptides and Proteins
34 Citations (Scopus)

Therapeutic activities of engrafted neural stem/precursor cells are not dormant in the chronically injured spinal cord

Kumamaru, H., Saiwai, H., Kubota, K., Kobayakawa, K., Yokota, K., Ohkawa, Y., Shiba, K., Iwamoto, Y. & Okada, S., Aug 1 2013, In : STEM CELLS. 31, 8, p. 1535-1547 13 p.

Research output: Contribution to journalArticle

Neural Stem Cells
Spinal Cord
Spinal Cord Injuries
Transplantation
Oligodendroglia
17 Citations (Scopus)

Wnt signaling regulates left-right axis formation in the node of mouse embryos

Kitajima, K., Oki, S., Ohkawa, Y., Sumi, T. & Meno, C., Aug 15 2013, In : Developmental Biology. 380, 2, p. 222-232 11 p.

Research output: Contribution to journalArticle

Embryonic Structures
Crowns
Catenins
Mesoderm
Binding Sites
29 Citations (Scopus)

β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation

Villacorte, M., Suzuki, K., Hirasawa, A., Ohkawa, Y., Suyama, M., Maruyama, T., Aoki, D., Ogino, Y., Miyagawa, S., Terabayashi, T., Tomooka, Y., Nakagata, N. & Yamada, G., Jul 18 2013, In : Oncogene. 32, 29, p. 3477-3482 6 p.

Research output: Contribution to journalArticle

Endometrial Hyperplasia
Catenins
Epithelium
Adenocarcinoma
Organogenesis
2012
26 Citations (Scopus)
Spinal Cord Injuries
Cytokines
Spinal Cord
Chemokines
Infiltration
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
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
67 Citations (Scopus)

A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples

Narumi, R., Murakami, T., Kuga, T., Adachi, J., Shiromizu, T., Muraoka, S., Kume, H., Kodera, Y., Matsumoto, M., Nakayama, K., Miyamoto, Y., Ishitobi, M., Inaji, H., Kato, K. & Tomonaga, T., Nov 2 2012, In : Journal of Proteome Research. 11, 11, p. 5311-5322 12 p.

Research output: Contribution to journalArticle

Phosphopeptides
Biomarkers
Phosphorylation
Tissue
Breast Neoplasms
12 Citations (Scopus)

Characterization of bisphenol a metabolites produced by Portulaca oleracea cv. by liquid chromatography coupled with tandem mass spectrometry

Watanabe, I., Harada, K., Matsui, T., Miyasaka, H., Okuhata, H., Tanaka, S., Nakayama, H., Kato, K., Bamba, T. & Hirata, K., May 29 2012, In : Bioscience, Biotechnology and Biochemistry. 76, 5, p. 1015-1017 3 p.

Research output: Contribution to journalArticle

Portulaca
Liquid chromatography
Metabolites
Tandem Mass Spectrometry
Liquid Chromatography
67 Citations (Scopus)

Chd2 interacts with H3.3 to determine myogenic cell fate

Harada, A., Okada, S., Konno, D., Odawara, J., Yoshimi, T., Yoshimura, S., Kumamaru, H., Saiwai, H., Tsubota, T., Kurumizaka, H., Akashi, K., Tachibana, T., Imbalzano, A. N. & Ohkawa, Y., Jul 4 2012, In : EMBO Journal. 31, 13, p. 2994-3007 14 p.

Research output: Contribution to journalArticle

DNA Helicases
Genes
Cell Differentiation
Chromatin Assembly and Disassembly
Essential Genes
25 Citations (Scopus)

Comprehensive identification of substrates for f-box proteins by differential proteomics analysis

Yumimoto, K., Matsumoto, M., Oyamada, K., Moroishi, T. & Nakayama, K. I., Jun 1 2012, In : Journal of Proteome Research. 11, 6, p. 3175-3185 11 p.

Research output: Contribution to journalArticle

Ubiquitination
Ligases
Ubiquitin
Proteomics
Substrates
1 Citation (Scopus)

Comprehensive study of protein ubiquitylation sites by conjugation of engineered lysine-less ubiquitin

Oshikawa, K., Matsumoto, M. & Nakayama, K. I., Dec 1 2012, In : Seikagaku. 84, 6, p. 479-487 9 p.

Research output: Contribution to journalReview article

Ubiquitination
Ubiquitin
Lysine
Proteins
12 Citations (Scopus)

Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation

Nakagome, S., Mano, S., Kozlowski, L., Bujnicki, J. M., Shibata, H., Fukumaki, Y., Kidd, J. R., Kidd, K. K., Kawamura, S. & Oota, H., Jun 1 2012, In : Molecular Biology and Evolution. 29, 6, p. 1569-1585 17 p.

Research output: Contribution to journalArticle

Crohn disease
Genetic Selection
natural selection
Crohn Disease
Haplotypes
32 Citations (Scopus)

Crystal structure of the c-terminal globular domain of oligosaccharyltransferase from archaeoglobus fulgidus at 1.75 Åresolution

Matsumoto, S., Igura, M., Nyirenda, J., Matsumoto, M., Yuzawa, S., Noda, N., Inagaki, F. & Kohda, D., May 22 2012, In : Biochemistry. 51, 20, p. 4157-4166 10 p.

Research output: Contribution to journalArticle

Archaeoglobus
Archaeoglobus fulgidus
Archaea
Crystal structure
Glycosylation
41 Citations (Scopus)

Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells

Kumamaru, H., Ohkawa, Y., Saiwai, H., Yamada, H., Kubota, K., Kobayakawa, K., Akashi, K., Okano, H., Iwamoto, Y. & Okada, S., Nov 26 2012, In : Nature communications. 3, 1140.

Research output: Contribution to journalArticle

spinal cord injuries
transplantation
sequencing
Neural Stem Cells
stem cells
39 Citations (Scopus)

Direct isopropanol production from cellobiose by engineered Escherichia coli using a synthetic pathway and a cell surface display system

Soma, Y., Inokuma, K., Tanaka, T., Ogino, C., Kondo, A., Okamoto, M. & Hanai, T., Jul 1 2012, In : Journal of Bioscience and Bioengineering. 114, 1, p. 80-85 6 p.

Research output: Contribution to journalArticle

Cellobiose
2-Propanol
Escherichia coli
Display devices
beta-Glucosidase
37 Citations (Scopus)

Genetic reevaluation of the Role of F-Box proteins in cyclin D1 degradation

Kanie, T., Onoyama, I., Matsumoto, A., Yamada, M., Nakatsumi, H., Tateishi, Y., Yamamura, S., Tsunematsu, R., Matsumoto, M. & Nakayama, K. I., Feb 1 2012, In : Molecular and cellular biology. 32, 3, p. 590-605 16 p.

Research output: Contribution to journalArticle

F-Box Proteins
Cyclin D1
Fibroblasts
Half-Life
Ubiquitination
13 Citations (Scopus)

Identification of biomarkers of stent restenosis with serum metabolomic profiling using gas chromatography/mass spectrometry

Hasokawa, M., Shinohara, M., Tsugawa, H., Bamba, T., Fukusaki, E., Nishiumi, S., Nishimura, K., Yoshida, M., Ishida, T. & Hirata, K. I., Aug 2 2012, In : Circulation Journal. 76, 8, p. 1864-1873 10 p.

Research output: Contribution to journalArticle

Metabolomics
Gas Chromatography-Mass Spectrometry
Stents
Biomarkers
Serum
9 Citations (Scopus)

Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays

Ohkawa, Y., Mallappa, C., Vallaster, C. S. D. & Imbalzano, A. N., Jan 2 2012, Myogenesis: Methods and Protocols. DiMario, J. (ed.). p. 517-530 14 p. (Methods in Molecular Biology; vol. 798).

Research output: Chapter in Book/Report/Conference proceedingChapter

Skeletal Muscle Satellite Cells
Chromatin Immunoprecipitation
Skeletal Muscle
Cultured Cells
Histone Code
18 Citations (Scopus)

Latent process genes for cell differentiation are common decoders of neurite extension length

Watanabe, K., Akimoto, Y., Yugi, K., Uda, S., Chung, J., Nakamuta, S., Kaibuchi, K. & Kuroda, S., May 1 2012, In : Journal of cell science. 125, 9, p. 2198-2211 14 p.

Research output: Contribution to journalArticle

Neurites
Cell Differentiation
Genes
Nerve Growth Factors
Nerve Growth Factor
75 Citations (Scopus)

Metabolic profiling of lipids by supercritical fluid chromatography/mass spectrometry

Bamba, T., Lee, J. W., Matsubara, A. & Fukusaki, E., Aug 10 2012, In : Journal of Chromatography A. 1250, p. 212-219 8 p.

Research output: Contribution to journalArticle

Supercritical Fluid Chromatography
Mass spectrometry
Mass Spectrometry
Lipids
Throughput
11 Citations (Scopus)

Metabolite profiles correlate closely with neurobehavioral function in experimental spinal cord injury in rats

Fujieda, Y., Ueno, S., Ogino, R., Kuroda, M., Jönsson, T. J., Guo, L., Bamba, T. & Fukusaki, E., Aug 13 2012, In : PloS one. 7, 8, e43152.

Research output: Contribution to journalArticle

Metabolites
Spinal Cord Injuries
spinal cord
Rats
Metabolomics
32 Citations (Scopus)

Myeloperoxidase exacerbates secondary injury by generating highly reactive oxygen species and mediating neutrophil recruitment in experimental spinal cord injury

Kubota, K., Saiwai, H., Kumamaru, H., Maeda, T., Ohkawa, Y., Aratani, Y., Nagano, T., Iwamoto, Y. & Okada, S., Jul 15 2012, In : Spine. 37, 16, p. 1363-1369 7 p.

Research output: Contribution to journalArticle

Neutrophil Infiltration
Spinal Cord Injuries
Peroxidase
Reactive Oxygen Species
Wounds and Injuries

New horizons in biological research developed by nextgeneration proteomics: Say good-bye to western blotting

Nakatsumi, H., Matsumoto, M. & Nakayama, K., Dec 1 2012, In : Seikagaku. 84, 1, p. 53-57 5 p.

Research output: Contribution to journalArticle

Mass spectrometry
Peptides
Proteomics
27 Citations (Scopus)

Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin

Oshikawa, K., Matsumoto, M., Oyamada, K. & Nakayama, K. I., Feb 3 2012, In : Journal of Proteome Research. 11, 2, p. 796-807 12 p.

Research output: Contribution to journalArticle

Ubiquitination
Proteome
Ubiquitin
Lysine
Proteins
19 Citations (Scopus)

Surf4 modulates STIM1-dependent calcium entry

Fujii, Y., Shiota, M., Ohkawa, Y., Baba, A., Wanibuchi, H., Kinashi, T., Kurosaki, T. & Baba, Y., Jun 15 2012, In : Biochemical and Biophysical Research Communications. 422, 4, p. 615-620 6 p.

Research output: Contribution to journalArticle

Endoplasmic Reticulum
Cluster Analysis
Carrier Proteins
B-Lymphocytes
Cell Membrane
2011
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
7 Citations (Scopus)

CDase is a pan-ceramidase in Drosophila

Yuan, C., Rao, R. P., Jesmin, N., Bamba, T., Nagashima, K., Pascual, A., Preat, T., Fukusaki, E., Acharya, U. & Acharya, J. K., Jan 1 2011, In : Molecular biology of the cell. 22, 1, p. 33-43 11 p.

Research output: Contribution to journalArticle

Ceramidases
Alkaline Ceramidase
Drosophila
Ceramides
Persuasive Communication