Research Output 1979 2020

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Article
2020
Carboxylation
Pyruvate Dehydrogenase Complex
Synechococcus
Acetyl Coenzyme A
Cloning
2019
Islands of Calleja
Neurogenesis
Dentate Gyrus
Phenotype
Lateral Ventricles
1 Citation (Scopus)

A 23 gene–based molecular prognostic score precisely predicts overall survival of breast cancer patients

Shimizu, H. & Nakayama, K., Aug 1 2019, In : EBioMedicine. 46, p. 150-159 10 p.

Research output: Contribution to journalArticle

Open Access
Genes
Breast Neoplasms
Survival
RNA Sequence Analysis
Organized Financing
8 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

Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation

Kanatsu-Shinohara, M., Yamamoto, T., Toh, H., Kazuki, Y., Kazuki, K., Imoto, J., Ikeo, K., Oshima, M., Shirahige, K., Iwama, A., Nabeshima, Y., Sasaki, H. & Shinohara, T., Aug 13 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 33, p. 16404-16409 6 p.

Research output: Contribution to journalArticle

Open Access
Glycolysis
Stem Cells
JNK Mitogen-Activated Protein Kinases
Cell Aging
Telomere Shortening

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

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

Research output: Contribution to journalArticle

Open Access
Trimeresurus
Snakes
Venoms
Alternative Splicing
Genes
1 Citation (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

Biochemical analysis of nucleosome targeting by Tn5 transposase

Sato, S., Arimura, Y., Kujirai, T., Harada, A., Maehara, K., Nogami, J., Ohkawa, Y. & Kurumizaka, H., Aug 1 2019, In : Open Biology. 9, 8, 190116.

Research output: Contribution to journalArticle

Open Access
Nucleosomes
DNA
Tn5 transposase
DNA sequences
Genomics

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

Yamanaka, S., Nishihara, H., Toh, H., Eijy Nagai, L. A., Hashimoto, K., Park, S. J., Shibuya, A., Suzuki, A. M., Tanaka, Y., Nakai, K., Carninci, P., Sasaki, H. & Siomi, H., Oct 7 2019, In : Developmental Cell. 51, 1, p. 21-34.e5

Research output: Contribution to journalArticle

DNA Methylation
Genes
Genome
Methyltransferases
Chromatin

Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme

Witwicka, H., Nogami, J., Syed, S. A., Maehara, K., Padilla-Benavides, T., Ohkawa, Y. & Imbalzano, A. N., Oct 1 2019, In : Molecular and cellular biology. 39, 19, e00063-19.

Research output: Contribution to journalArticle

Open Access
Chromatin Assembly and Disassembly
Calcineurin
Skeletal Muscle
Gene Expression
Enzymes
4 Citations (Scopus)

CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome

Unoki, M., Funabiki, H., Velasco, G., Francastel, C. & Sasaki, H., Jan 2 2019, In : Journal of Clinical Investigation. 129, 1, CI99751.

Research output: Contribution to journalArticle

Chromosome Segregation
Mutation
HEK293 Cells
Chromatin
Apoptosis
2 Citations (Scopus)

Cell-autonomous and redundant roles of Hey1 and HeyL in muscle stem cells: HeyL requires HeS1 to bind diverse DNA sites

Noguchi, Y. T., Nakamura, M., Hino, N., Nogami, J., Tsuji, S., Sato, T., Zhang, L., Tsujikawa, K., Tanaka, T., Izawa, K., Okada, Y., Doi, T., Kokubo, H., Harada, A., Uezumi, A., Gessler, M., Ohkawa, Y. & Fukada, S. I., Feb 2019, In : Development (Cambridge). 146, 4, dev163618.

Research output: Contribution to journalArticle

Open Access
Muscle Cells
Stem Cells
DNA
Myogenin
Chromatin

Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo

Akieda, Y., Ogamino, S., Furuie, H., Ishitani, S., Akiyoshi, R., Nogami, J., Masuda, T., Shimizu, N., Ohkawa, Y. & Ishitani, T., Dec 1 2019, In : Nature communications. 10, 1, 4710.

Research output: Contribution to journalArticle

Open Access
embryos
Zebrafish
Embryonic Structures
beta Catenin
gradients

CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors

Miki, M., ono, T., Fujimori, N., Takaoka, T., Kawabe, K., Miyasaka, Y., Takao, O., Saito, D., Nakamura, M., Ohkawa, Y., Oda, Y., Suyama, M., Ito, T. & Ogawa, Y., Jul 1 2019, In : Cancer Medicine. 8, 8, p. 3748-3760 13 p.

Research output: Contribution to journalArticle

Open Access
Matrix Metalloproteinase 7
Neuroendocrine Tumors
Recurrence
Genes
Neoplasms
Heavy Ion Radiotherapy
Sarcoma
Spine
Spinal Cord Compression
Compression Fractures
Open Access
Supercritical Fluid Chromatography
supercritical fluids
liquid chromatography
High performance liquid chromatography
chromatography

Comparison of sequential derivatization with concurrent methods for GC/MS-based metabolomics

Miyagawa, H. & Bamba, T., Feb 1 2019, In : Journal of Bioscience and Bioengineering. 127, 2, p. 160-168 9 p.

Research output: Contribution to journalArticle

Metabolomics
Metabolites
Gas chromatography
Gas Chromatography-Mass Spectrometry
Mass spectrometry
2 Citations (Scopus)

Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes

Srivastava, A., Tama, F., Kohda, D. & Miyashita, O., Jan 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 1, p. 81-90 10 p.

Research output: Contribution to journalArticle

Disulfides
Molecular Dynamics Simulation
Membranes
Peptides
Molecular dynamics

Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations

Srivastava, A., Bala, S., Motomura, H., Kohda, D., Tama, F. & Miyashita, O., Jan 1 2019, (Accepted/In press) In : Biochimica et Biophysica Acta - General Subjects. 129417.

Research output: Contribution to journalArticle

Mitochondrial Proteins
Molecular Dynamics Simulation
Molecular dynamics
Crystals
Computer simulation

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

Bala, S., Shinya, S., Srivastava, A., Ishikawa, M., Shimada, A., Kobayashi, N., Kojima, C., Tama, F., Miyashita, O. & Kohda, D., Jan 1 2019, (Accepted/In press) In : Biochimica et Biophysica Acta - General Subjects. 129418.

Research output: Contribution to journalArticle

Conformations
Crystals
Proteins
Yeasts
Yeast
3 Citations (Scopus)

Development of a practical online supercritical fluid extraction–supercritical fluid chromatography/mass spectrometry system with an integrated split-flow method

Sakai, M., Hayakawa, Y., Funada, Y., Ando, T., Fukusaki, E. & Bamba, T., May 10 2019, In : Journal of Chromatography A. 1592, p. 161-172 12 p.

Research output: Contribution to journalArticle

Supercritical Fluid Chromatography
Supercritical fluids
Chromatography
Mass spectrometry
Mass Spectrometry
1 Citation (Scopus)

Disruption of FBXL5-mediated cellular iron homeostasis promotes liver carcinogenesis

Muto, Y., Moroishi, T., Ichihara, K., Nishiyama, M., Shimizu, H., Eguchi, H., Moriya, K., Koike, K., Mimori, K., Mori, M., Katayama, Y. & Nakayama, K., Apr 1 2019, In : Journal of Experimental Medicine. 216, 4, p. 950-965 16 p.

Research output: Contribution to journalArticle

Open Access
Carcinogenesis
Homeostasis
Iron
Iron Overload
Liver

Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes

Konno, D., Kishida, C., Maehara, K., Ohkawa, Y., Kiyonari, H., Okada, S. & Matsuzaki, F., Aug 1 2019, In : Development (Cambridge). 146, 15, dev174243.

Research output: Contribution to journalArticle

Open Access
Telencephalon
Homeobox Genes
Gene Dosage
Olfactory Bulb
Neurogenesis
3 Citations (Scopus)

Elucidating functions of DP1 and DP2 subunits from the Thermococcus kodakarensis family D DNA polymerase

Takashima, N., Ishino, S., Oki, K., Takafuji, M., Yamagami, T., Matsuo, R., Mayanagi, K. & Ishino, Y., Jan 22 2019, In : Extremophiles. 23, 1, p. 161-172 12 p.

Research output: Contribution to journalArticle

Thermococcus
Transcription Factor DP1
Archaea
DNA-Directed DNA Polymerase
DNA

Frequent Detection of Pituitary-Derived PrPres in Human Prion Diseases

Honda, H., Matsumoto, M., Shijo, M., Hamasaki, H., Sadashima, S., Suzuki, S. O., Aishima, S., Kai, K., Nakayama, K. I., Sasagasako, N. & Iwaki, T., Oct 1 2019, In : Journal of neuropathology and experimental neurology. 78, 10, p. 922-929 8 p.

Research output: Contribution to journalArticle

Prion Diseases
Pituitary Gland
Growth Hormone
Human Growth Hormone
Gerstmann-Straussler-Scheinker Disease

Gas chromatography-mass spectrometry metabolomics-based prediction of potato tuber sprouting during long-term storage

Fukuda, T., Takamatsu, K., Bamba, T. & Fukusaki, E., Aug 1 2019, In : Journal of Bioscience and Bioengineering. 128, 2, p. 249-254 6 p.

Research output: Contribution to journalArticle

Metabolomics
Biomarkers
Solanum tuberosum
Gas chromatography
Gas Chromatography-Mass Spectrometry

Generation of Nanog reporter mice that distinguish pluripotent stem cells from unipotent primordial germ cells

Terada, M., Kawamata, M., Kimura, R., Sekiya, S., Nagamatsu, G., Hayashi, K., Horisawa, K. & Suzuki, A., Jan 1 2019, (Accepted/In press) In : Genesis. e23334.

Research output: Contribution to journalArticle

Pluripotent Stem Cells
Germ Cells
Transgenic Mice
Transcription Factors
Gene Expression

Germline mutation: De novo mutation in reproductive lineage cells

Sakumi, K., Jan 1 2019, In : Genes and Genetic Systems. 94, 1, p. 3-12 10 p.

Research output: Contribution to journalArticle

Open Access
Germ-Line Mutation
Mutation Rate
Genome
Mutation
Cell Division
1 Citation (Scopus)

Histone H3K9 Methyltransferase G9a in Oocytes Is Essential for Preimplantation Development but Dispensable for CG Methylation Protection

Au Yeung, W. K., Brind'Amour, J., Hatano, Y., Yamagata, K., Feil, R., Lorincz, M. C., Tachibana, M., Shinkai, Y. & Sasaki, H., Apr 2 2019, In : Cell Reports. 27, 1, p. 282-293.e4

Research output: Contribution to journalArticle

Open Access
Methylation
Oocytes
Chromatin
Chromosome Segregation
Chromosomes

Identification of genomic alterations acquired during treatment with EGFR-TKIs in non-small cell lung cancer

Kubo, N., Harada, T., Shiraishi, Y., Nosaki, K., Nakagaki, N., Takeshita, M., Ouchi, H., Iwama, E., Tanaka, K., Okamoto, I., Sasaki, H. & Nakanishi, Y., Feb 1 2019, In : Anticancer research. 39, 2, p. 671-677 7 p.

Research output: Contribution to journalArticle

Epidermal Growth Factor Receptor
Non-Small Cell Lung Carcinoma
Protein-Tyrosine Kinases
Therapeutics
Exome
1 Citation (Scopus)

Identification of metabolites associated with onset of CAD in diabetic patients using ce-ms analysis: A pilot study

Omori, K., Katakami, N., Yamamoto, Y., Ninomiya, H., Takahara, M., Matsuoka, T. A., Bamba, T., Fukusaki, E. & Shimomura, I., Jan 1 2019, In : Journal of atherosclerosis and thrombosis. 26, 3, p. 233-245 13 p.

Research output: Contribution to journalArticle

Open Access
Metabolites
Coronary Artery Disease
Medical problems
Arteries
Galactosamine

Identification of novel serum markers for the progression of coronary atherosclerosis in WHHLMI rabbits, an animal model of familial hypercholesterolemia

Shiomi, M., Takeda, H., Irino, Y., Kimura, N., Yamada, S., Kuniyoshi, N., Kikumori, A., Koike, Y., Koike, T., Yoshida, M., Izumi, Y., Shinohara, M., Bamba, T. & Ishida, T., May 1 2019, In : Atherosclerosis. 284, p. 18-23 6 p.

Research output: Contribution to journalArticle

Hyperlipoproteinemia Type II
Coronary Artery Disease
Animal Models
Biomarkers
Rabbits

Improved quantitation of lipid classes using supercritical fluid chromatography with a charged aerosol detector

Takeda, H., Takahashi, M., Hara, T., Izumi, Y. & Bamba, T., Jan 1 2019, In : Journal of Lipid Research. 60, 8, p. 1465-1474 10 p.

Research output: Contribution to journalArticle

Open Access
Supercritical Fluid Chromatography
Aerosols
Detectors
Lipids
Molecules
1 Citation (Scopus)

Intragenic antagonistic roles of protein and circRNA in tumorigenesis

Guarnerio, J., Zhang, Y., Cheloni, G., Panella, R., Mae Katon, J., Simpson, M., Matsumoto, A., Papa, A., Loretelli, C., Petri, A., Kauppinen, S., Garbutt, C., Petur Nielsen, G., Deshpande, V., Castillo-Martin, M., Cordon-Cardo, C., Dimitrios, S., Clohessy, J. G., Batish, M. & Pandolfi, P. P., Aug 1 2019, In : Cell Research. 29, 8, p. 628-640 13 p.

Research output: Contribution to journalArticle

Carcinogenesis
Neoplasms
Proteins
Angiogenesis Inducing Agents
Transcription Factors

Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection

Kobayakawa, K., DePetro, K. A., Zhong, H., Pham, B., Hara, M., Harada, A., Nogami, J., Ohkawa, Y. & Edgerton, V. R., Jan 1 2019, In : Neurorehabilitation and Neural Repair.

Research output: Contribution to journalArticle

Spinal Cord
Synapses
RNA
Synaptophysin
Gene Ontology

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans

Fujii, M., Murakami, Y., Karasawa, Y., Sumitomo, Y., Fujita, S., Koyama, M., Uda, S., Kubota, H., Inoue, H., Konishi, K., Oba, S., Ishii, S. & Kuroda, S., Dec 1 2019, In : npj Systems Biology and Applications. 5, 1, 31.

Research output: Contribution to journalArticle

Open Access
Glucose
Blood
Blood Glucose
Eating
Insulin

Long-term maintenance of functional primary human hepatocytes using small molecules

Katsuda, T., Kawamata, M., Inoue, A., Yamaguchi, T., Abe, M. & Ochiya, T., Jan 1 2019, (Accepted/In press) In : FEBS Letters.

Research output: Contribution to journalArticle

Cytochrome P-450 CYP3A
Hepatocytes
Drug Discovery
Molecules
Cytochrome P-450 CYP1A2

Macrophage centripetal migration drives spontaneous healing process after spinal cord injury

Kobayakawa, K., Ohkawa, Y., Yoshizaki, S., Tamaru, T., Saito, T., Kijima, K., Yokota, K., Hara, M., Kubota, K., Matsumoto, Y., Harimaya, K., Ozato, K., Masuda, T., Makoto, T., Tamura, T., Inoue, K., Reggie Edgerton, V., Iwamoto, Y., Nakashima, Y. & Okada, S., May 15 2019, In : Science Advances. 5, 5, eaav5086.

Research output: Contribution to journalArticle

Open Access
spinal cord injuries
macrophages
healing
interferon
lesions

miR-124 dosage regulates prefrontal cortex function by dopaminergic modulation

Kozuka, T., Omori, Y., Watanabe, S., Tarusawa, E., Yamamoto, H., Chaya, T., Furuhashi, M., Morita, M., Sato, T., Hirose, S., Ohkawa, Y., Yoshimura, Y., Hikida, T. & Furukawa, T., Dec 1 2019, In : Scientific reports. 9, 1, 3445.

Research output: Contribution to journalArticle

Prefrontal Cortex
MicroRNAs
Central Nervous System
Methamphetamine
Pyramidal Cells

Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones

Katoh-Fukui, Y., Baba, T., Sato, T., Otake, H., Nagakui-Noguchi, Y., Shindo, M., Suyama, M., Ohkawa, Y., Tsumura, H., Morohashi, K-I. & Fukami, M., Mar 1 2019, In : Bone. 120, p. 219-231 13 p.

Research output: Contribution to journalArticle

Mesenchymal Stromal Cells
Bone and Bones
Cell Lineage
Genes
Polycomb-Group Proteins
1 Citation (Scopus)

Novel components of germline sex determination acting downstream of foxl3 in medaka

Kikuchi, M., Nishimura, T., Saito, D., Shigenobu, S., Takada, R., Gutierrez-Triana, J. A., Cerdán, J. L. M., Takada, S., Wittbrodt, J., Suyama, M. & Tanaka, M., Jan 1 2019, In : Developmental Biology. 445, 1, p. 80-89 10 p.

Research output: Contribution to journalArticle

Oryzias
Germ Cells
Sex Differentiation
Chromatids
Ubiquitin-Protein Ligases

Oxidative stress induces different tissue dependent effects on Mutyh-deficient mice

Chen, J., Huang, Z., Wu, X., Kang, J., Ren, Y., Gao, W., Lu, X., Wang, J., Ding, W., Nakabeppu, Y., Fan, Y. & Wang, Y., Nov 1 2019, In : Free Radical Biology and Medicine. 143, p. 482-493 12 p.

Research output: Contribution to journalArticle

Oxidative stress
Galactose
Oxidative Stress
Tissue
Liver
1 Citation (Scopus)

Pathological changes of distal motor neurons after complete spinal cord injury

Yokota, K., Kubota, K., Kobayakawa, K., Saito, T., Hara, M., Kijima, K., Maeda, T., Katoh, H., Ohkawa, Y., Nakashima, Y. & Okada, S., Jan 9 2019, In : Molecular Brain. 12, 1, 4.

Research output: Contribution to journalArticle

Motor Neurons
Spinal Cord Injuries
Spinal Cord
Microdissection
Thoracic Injuries

Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7

Hanawa-Suetsugu, K., Itoh, Y., Ab Fatah, M., Nishimura, T., Takemura, K., Takeshita, K., Kubota, S., Miyazaki, N., Wan Mohamad Noor, W. N. I., Inaba, T., Nguyen, N. T. H., Hamada-Nakahara, S., Oono-Yakura, K., Tachikawa, M., Iwasaki, K., Kohda, D., Yamamoto, M., Kitao, A., Shimada, A. & Suetsugu, S., Dec 1 2019, In : Nature communications. 10, 1, 4763.

Research output: Contribution to journalArticle

Open Access
Phagocytosis
assemblies
Bins
proteins
membranes

Pillars Article: Restoration of T Cell Development in RAG-2-Deficient Mice by Functional TCR Transgenes. Science. 1993. 259: 822-825

Shinkai, Y., Koyasu, S., Nakayama, K., Murphy, K. M., Loh, D. Y., Reinherz, E. L. & Alt, F. W., Mar 1 2019, In : Journal of immunology (Baltimore, Md. : 1950). 202, 5, p. 1317-1320 4 p.

Research output: Contribution to journalArticle

Transgenes
T-Lymphocytes

Poorly controlled diabetes during pregnancy and lactation activates the Foxo1 pathway and causes glucose intolerance in adult offspring

Inoguchi, Y., Ichiyanagi, K., Ohishi, H., Maeda, Y., Sonoda, N., Ogawa, Y., Inoguchi, T. & Sasaki, H., Dec 1 2019, In : Scientific reports. 9, 1, 10181.

Research output: Contribution to journalArticle

Open Access
Glucose Intolerance
Streptozocin
Lactation
Pregnancy
Gluconeogenesis
Heavy Ion Radiotherapy
Spontaneous Fractures
Single-Photon Emission-Computed Tomography
Bone and Bones
Bone Remodeling
4 Citations (Scopus)

Prevention of cancer dormancy by Fbxw7 ablation eradicates disseminated tumor cells

Shimizu, H., Takeishi, S., Nakatsumi, H. & Nakayama, K., Feb 21 2019, In : JCI insight. 4, 4

Research output: Contribution to journalArticle

Neoplasms
Breast Neoplasms
Drug Therapy
Paclitaxel
Heterografts
Arm Injuries
Ossification of Posterior Longitudinal Ligament
Pectoralis Muscles
Prone Position
Brachial Plexus