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Research Output 2001 2019

  • 1083 Citations
  • 12 h-Index
  • 30 Article
  • 1 Chapter
  • 1 Review article
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Article
2019

Base-Resolution Methylome of Retinal Pigment Epithelial Cells Used in the First Trial of Human Induced Pluripotent Stem Cell-Based Autologous Transplantation

Araki, H., Miura, F., Watanabe, A., Morinaga, C., Kitaoka, F., Kitano, Y., Sakai, N., Shibata, Y., Terada, M., Goto, S., Yamanaka, S., Takahashi, M. & Ito, T., Oct 8 2019, In : Stem Cell Reports. 13, 4, p. 761-774 14 p.

Research output: Contribution to journalArticle

Open Access
Induced Pluripotent Stem Cells
Retinal Pigments
Autologous Transplantation
Macular Degeneration
DNA Methylation
Open Access
Single-Stranded DNA
Ligation
Genome
Libraries
DNA Nucleotidylexotransferase
8 Citations (Scopus)

Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion

Matsuda, T., Irie, T., Katsurabayashi, S., Hayashi, Y., Nagai, T., Hamazaki, N., Adefuin, A. M. D., Miura, F., Ito, T., Kimura, H., Shirahige, K., Takeda, T., Iwasaki, K., Imamura, T. & Nakashima, K., Feb 6 2019, In : Neuron. 101, 3, p. 472-485.e7

Research output: Contribution to journalArticle

Microglia
Epigenomics
Neurons
Transcription Factors
Genes
2018
7 Citations (Scopus)

Epigenetic landscape influences the liver cancer genome architecture

Hama, N., Totoki, Y., Miura, F., Tatsuno, K., Saito-Adachi, M., Nakamura, H., Arai, Y., Hosoda, F., Urushidate, T., Ohashi, S., Mukai, W., Hiraoka, N., Aburatani, H., Ito, T. & Shibata, T., Dec 1 2018, In : Nature communications. 9, 1, 1643.

Research output: Contribution to journalArticle

genome
Liver Neoplasms
liver
Epigenomics
Liver

Epigenome mapping of human normal purified hepatocytes: Personal epigenome variation and genome-epigenome correlation

Arai, E., Miura, F., Totoki, Y., Yamashita, S., Tian, Y., Gotoh, M., Ojima, H., Nakagawa, H., Takahashi, Y., Nakamura, H., Hama, N., Kato, M., Kimura, H., Suzuki, Y., Ito, T., Shibata, T. & Kanai, Y., Jul 2018, In : Epigenomics. 10, 7, p. 955-979 25 p.

Research output: Contribution to journalArticle

Methylation
Hepatocytes
Histone Code
Genome
RNA Sequence Analysis
8 Citations (Scopus)

Mapping of histone-binding sites in histone replacement-completed spermatozoa

Yoshida, K., Muratani, M., Araki, H., Miura, F., Suzuki, T., Dohmae, N., Katou, Y., Shirahige, K., Ito, T. & Ishii, S., Dec 1 2018, In : Nature communications. 9, 1, 3885.

Research output: Contribution to journalArticle

spermatozoa
nuclease
genes
Histones
Spermatozoa

Maternal protein restriction alters the renal ptger1 DNA methylation state in SHRSP offspring

Miyoshi, M., Sato, M., Saito, K., Otani, L., Shirahige, K., Miura, F., Ito, T., Jia, H. & Kato, H., Oct 5 2018, In : Nutrients. 10, 10, 1436.

Research output: Contribution to journalArticle

Receptors, Prostaglandin E, EP1 Subtype
DNA methylation
DNA Methylation
prostaglandins
kidneys
1 Citation (Scopus)

Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA

Miura, F., Fujino, T., Kogashi, K., Shibata, Y., Miura, M., Isobe, H. & Ito, T., Sep 19 2018, In : Nucleic acids research. 46, 16, p. e95

Research output: Contribution to journalArticle

Open Access
Triazoles
Azides
Single-Stranded DNA
Ligation
Alkynes
2017
10 Citations (Scopus)

DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells

Sanosaka, T., Imamura, T., Hamazaki, N., Chai, M. C., Igarashi, K., Ideta-Otsuka, M., Miura, F., Ito, T., Fujii, N., Ikeo, K. & Nakashima, K., Sep 19 2017, In : Cell Reports. 20, 12, p. 2992-3003 12 p.

Research output: Contribution to journalArticle

Neural Stem Cells
Stem cells
Epigenomics
Mental Competency
Neurons
7 Citations (Scopus)

Software updates in the illumina hiseq platform affect whole-genome bisulfite sequencing

Toh, H., Shirane, K., Miura, F., Kubo, N., Ichiyanagi, K., Hayashi, K., Saitou, M., Suyama, M., Ito, T. & Sasaki, H., Jan 5 2017, In : BMC Genomics. 18, 1, 31.

Research output: Contribution to journalArticle

Software
Genome
Methylation
Libraries
DNA
10 Citations (Scopus)

The AP-1 transcription factor JunB is required for Th17 cell differentiation

Yamazaki, S., Tanaka, Y., Araki, H., Kohda, A., Sanematsu, F., Arasaki, T., Duan, X., Miura, F., Katagiri, T., Shindo, R., Nakano, H., Ito, T., Fukui, Y., Endo, S. & Sumimoto, H., Dec 1 2017, In : Scientific reports. 7, 1, 17402.

Research output: Contribution to journalArticle

Th17 Cells
Transcription Factor AP-1
Cell Differentiation
Helper-Inducer T-Lymphocytes
Autoimmune Experimental Encephalomyelitis
2016
5 Citations (Scopus)

DNA methylation errors in cloned mouse sperm by germ line barrier evasion

Koike, T., Wakai, T., Jincho, Y., Sakashita, A., Kobayashi, H., Mizutani, E., Wakayama, S., Miura, F., Ito, T. & Kono, T., Jun 1 2016, In : Biology of Reproduction. 94, 6, 128.

Research output: Contribution to journalArticle

DNA Methylation
Germ Cells
Spermatozoa
Genome
Epigenomics
2015
3 Citations (Scopus)

Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape

Yokoyama, T., Miura, F., Araki, H., Okamura, K. & Ito, T., Aug 12 2015, In : BMC Genomics. 16, 1, 594.

Research output: Contribution to journalArticle

Methylation
Genome
Cell Lineage
Neoplasms
hydrogen sulfite
12 Citations (Scopus)

DNA methylation and gene expression in Mimulus guttatus

Colicchio, J. M., Miura, F., Kelly, J. K., Ito, T. & Hileman, L. C., Jul 7 2015, In : BMC Genomics. 16, 1, 507.

Research output: Contribution to journalArticle

Mimulus
DNA Methylation
Methylation
Gene Expression
Cytosine Nucleotides
22 Citations (Scopus)

Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging

Miura, F. & Ito, T., Jan 1 2015, In : DNA Research. 22, 1, p. 13-18 6 p.

Research output: Contribution to journalArticle

DNA
Genome
Costs and Cost Analysis
Firearms
hydrogen sulfite
2013
150 Citations (Scopus)

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

Kobayashi, H., Sakurai, T., Miura, F., Imai, M., Mochiduki, K., Yanagisawa, E., Sakashita, A., Wakai, T., Suzuki, Y., Ito, T., Matsui, Y. & Kono, T., Apr 1 2013, In : Genome Research. 23, 4, p. 616-627 12 p.

Research output: Contribution to journalArticle

Germ Cells
Methylation
DNA
Epigenomics
Genome
144 Citations (Scopus)

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

Shirane, K., Toh, H., Kobayashi, H., Miura, F., Chiba, H., Ito, T., Kono, T. & Sasaki, H., Apr 1 2013, In : PLoS Genetics. 9, 4, e1003439.

Research output: Contribution to journalArticle

methyltransferases
Methyltransferases
methylation
DNA Methylation
Methylation
2012
154 Citations (Scopus)

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

Miura, F., Enomoto, Y., Dairiki, R. & Ito, T., Sep 1 2012, In : Nucleic Acids Research. 40, 17

Research output: Contribution to journalArticle

Genome
Epigenomics
DNA
hydrogen sulfite
5-Methylcytosine
14 Citations (Scopus)

Long-lived dichotomous lineages of the proteasome subunit beta type 8 (PSMB8) gene surviving more than 500 million years as alleles or paralogs

Tsukamoto, K., Miura, F., Fujito, N. T., Yoshizaki, G. & Nonaka, M., Oct 1 2012, In : Molecular Biology and Evolution. 29, 10, p. 3071-3079 9 p.

Research output: Contribution to journalArticle

proteasome endopeptidase complex
Proteasome Endopeptidase Complex
allele
Alleles
alleles
2011
19 Citations (Scopus)

Translation initiation: A regulatory role for poly(A) tracts in front of the AUG codon in saccharomyces cerevisiae

Xia, X., Mackay, V., Yao, X., Wu, J., Miura, F., Ito, T. & Morris, D. R., Oct 1 2011, In : Genetics. 189, 2, p. 469-478 10 p.

Research output: Contribution to journalArticle

Poly A
Codon
Saccharomyces cerevisiae
Untranslated Regions
Yeasts
2010
11 Citations (Scopus)

Transspecies dimorphic allelic lineages of the proteasome subunit β-type 8 gene (PSMB8) in the teleost genus Oryzias

Miura, F., Tsukamoto, K., Mehta, R. B., Naruse, K., Magtoon, W. & Nonaka, M., Dec 14 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 50, p. 21599-21604 6 p.

Research output: Contribution to journalArticle

Oryzias
Proteasome Endopeptidase Complex
Genes
Peptides
Introns
2008
48 Citations (Scopus)

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs

Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y. & Ito, T., Nov 29 2008, In : BMC Genomics. 9, 574.

Research output: Contribution to journalArticle

Saccharomycetales
Transcriptome
Complementary DNA
Polymerase Chain Reaction
Messenger RNA
54 Citations (Scopus)

Sphingosine 1-phosphate regulates the egress of IgA plasmablasts from Peyer's patches for intestinal IgA responses

Gohda, M., Kunisawa, J., Miura, F., Kagiyama, Y., Kurashima, Y., Higuchi, M., Ishikawa, I., Ogahara, I. & Kiyono, H., Apr 15 2008, In : Journal of Immunology. 180, 8, p. 5335-5343 9 p.

Research output: Contribution to journalArticle

Peyer's Patches
Immunoglobulin A
Emigration and Immigration
B-Lymphocytes
Lysosphingolipid Receptors
2007
57 Citations (Scopus)

Sphingosine 1-phosphate regulates peritoneal B-cell trafficking for subsequent intestinal IgA production

Kunisawa, J., Kurashima, Y., Gohda, M., Higuchi, M., Ishikawa, I., Miura, F., Ogahara, I. & Kiyono, H., May 1 2007, In : Blood. 109, 9, p. 3749-3756 8 p.

Research output: Contribution to journalArticle

Immunoglobulin A
B-Lymphocytes
Cells
Lysosphingolipid Receptors
Immunization
2006
169 Citations (Scopus)

A large-scale full-length cDNA analysis to explore the budding yeast transcriptome

Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S. & Ito, T., Nov 21 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 47, p. 17846-17851 6 p.

Research output: Contribution to journalArticle

Saccharomycetales
Transcription Initiation Site
Transcriptome
Open Reading Frames
Complementary DNA
2005
19 Citations (Scopus)

A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3′-end subsequences

Miura, F., Uematsu, C., Sakaki, Y. & Ito, T., Dec 1 2005, In : Bioinformatics. 21, 24, p. 4363-4370 8 p.

Research output: Contribution to journalArticle

Subsequence
Specificity
Uniqueness
Polymerase Chain Reaction
CDNA
2004
133 Citations (Scopus)

A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q

Yamada, Y., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Sakaki, Y. & Ito, T., Feb 1 2004, In : Genome Research. 14, 2, p. 247-266 20 p.

Research output: Contribution to journalArticle

CpG Islands
Human Chromosomes
Methylation
Alleles
X Chromosome
2001

Comparative analysis for expressed genes by polymerase chain reaction using module-shuffling primers.

Uematsu, C., Nishida, J., Okano, K., Kambara, H., Miura, F., Ito, T. & Sakaki, Y., Jan 1 2001, In : Nucleic acids research. Supplement (2001). 1, p. 91-92 2 p.

Research output: Contribution to journalArticle

Polymerase Chain Reaction
Genes
Electrophoresis
Complementary DNA
Yeasts
8 Citations (Scopus)

Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast

Miura, F., Yada, T., Nakai, K., Sakaki, Y. & Ito, T., Sep 7 2001, In : FEBS Letters. 505, 1, p. 103-108 6 p.

Research output: Contribution to journalArticle

Saccharomycetales
Multiple Drug Resistance
Bearings (structural)
Yeast
Transcription Factors
5 Citations (Scopus)

Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells

Uematsu, C., Nishida, J., Okano, K., Miura, F., Ito, T., Sakaki, Y. & Kambara, H., Aug 15 2001, In : Nucleic acids research. 29, 16, 1 p.

Research output: Contribution to journalArticle

Multiplex Polymerase Chain Reaction
Color
Gene Expression
Electrophoresis
Gels