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Research Output 1987 2019

49 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
9 Citations (Scopus)

A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: Comparison with chromosome 21q

Yamada, Y., Shirakawa, T., Taylor, T. D., Okamura, K., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Muramoto, K. I., Sakaki, Y. & Ito, T., Aug 1 2006, In : DNA Sequence - Journal of DNA Sequencing and Mapping. 17, 4, p. 300-306 7 p.

Research output: Contribution to journalArticle

CpG Islands
Methylation
Human Chromosomes
Chromosomes
Tandem Repeat Sequences
134 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
2756 Citations (Scopus)

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y., Apr 10 2001, In : Proceedings of the National Academy of Sciences of the United States of America. 98, 8, p. 4569-4574 6 p.

Research output: Contribution to journalArticle

Fungal Proteins
Proteins
Spindle Pole Bodies
Genome
Protein Interaction Maps
1 Citation (Scopus)

Activation of the phagocyte NADPH oxidase

Takeshige, K., Ito, T. & Sumimoto, H., Jan 1 1996, In : Journal of Toxicological Sciences. 21, 5, p. 291-292 2 p.

Research output: Contribution to journalArticle

NADPH Oxidase
Phagocytes
Chemical activation
7 Citations (Scopus)

Affinity capture electrophoresis for sequence-specific DNA purification.

Ito, T., Smith, C. L. & Cantor, C. R., Jun 1992, In : Genetic Analysis Techniques and Applications. 9, 3, p. 96-99

Research output: Contribution to journalArticle

100 Citations (Scopus)

A functional single-nucleotide polymorphism in the human cytidine deaminase gene contributing to ara-C sensitivity

Yue, L., Saikawa, Y., Ota, K., Tanaka, M., Nishimura, R., Uehara, T., Maeba, H., Ito, T., Sasaki, T. & Koizumi, S., Jan 1 2003, In : Pharmacogenetics. 13, 1, p. 29-38 10 p.

Research output: Contribution to journalArticle

Cytidine Deaminase
Cytarabine
Single Nucleotide Polymorphism
Genes
Yeasts
171 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
158 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, p. e136

Research output: Contribution to journalArticle

Genome
Epigenomics
DNA
hydrogen sulfite
5-Methylcytosine

Analysis of chromosome 21--construction of STS map and its application for contig map construction

Sakaki, Y., Hattori, M., Tanahashi, H., Ito, T. & Tashiro, K., Jan 1 1993, In : Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 38, 3, p. 260-267 8 p.

Research output: Contribution to journalReview article

Type II Site Specific Deoxyribonucleases
Bacteriophage P1
Sequence Tagged Sites
Chromosomes, Human, Pair 21
Genetic Vectors
21 Citations (Scopus)

Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: Involvement of Pdr3 in salt tolerance

Onda, M., Ota, K., Chiba, T., Sakaki, Y. & Ito, T., May 12 2004, In : Gene. 332, 1-2, p. 51-59 9 p.

Research output: Contribution to journalArticle

Salt-Tolerance
Gene Regulatory Networks
Multiple Drug Resistance
Transcription Factors
Yeasts
9 Citations (Scopus)

An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighbors

Okamura, K., Yamada, Y., Sakaki, Y. & Ito, T., Dec 1 2004, In : DNA Research. 11, 6, p. 381-390 10 p.

Research output: Contribution to journalArticle

Genomic Imprinting
Genes
Genomic Segmental Duplications
Chromosomes, Human, Pair 18
Intergenic DNA

An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighbors.

Okamura, K., Sakaki, Y. & Ito, T., Dec 2004, In : DNA Research. 11, 6, p. 381-390

Research output: Contribution to journalArticle

85 Citations (Scopus)

A new ETV6/TEL partner gene, ARG (ABL-related gene or ABL2), identified in an AML-M3 cell line with a t(1;12)(q25;p13) translocation

Iijima, Y., Ito, T., Oikawa, T., Eguchi, M., Eguchi-Ishimae, M., Kamada, N., Kishi, K., Asano, S., Sakaki, Y. & Sato, Y., Mar 15 2000, In : Blood. 95, 6, p. 2126-2131 6 p.

Research output: Contribution to journalArticle

Acute Promyelocytic Leukemia
Protein-Tyrosine Kinases
Genes
Cells
Cell Line
7 Citations (Scopus)
66 Citations (Scopus)
Amphiphiles
src Homology Domains
Cell-Free System
NADPH Oxidase
Phagocytes
27 Citations (Scopus)
Pheromones
Proline
Yeast
Substitution reactions
Yeasts
53 Citations (Scopus)

A novel G-protein-coupled receptor gene expressed in striatum

Mizushima, K., Miyamoto, Y., Tsukahara, F., Hirai, M., Sakaki, Y. & Ito, T., Nov 1 2000, In : Genomics. 69, 3, p. 314-321 8 p.

Research output: Contribution to journalArticle

Biogenic Amines Receptors
G-Protein-Coupled Receptors
Rodentia
Genes
Behavior Control
20 Citations (Scopus)

A novel procedure for selective cloning of Noti linking fragments from mammalian genomes

Ito, T. & Sakaki, Y., Oct 11 1988, In : Nucleic acids research. 16, 19, p. 9177-9184 8 p.

Research output: Contribution to journalArticle

Organism Cloning
Genome
Libraries
DNA
Plasmids
20 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
50 Citations (Scopus)

An SH3 domain-mediated interaction between the phagocyte NADPH oxidase factors p40phox and p47phox

Ito, T., Nakamura, R., Sumimoto, H., Takeshige, K. & Sakaki, Y., May 6 1996, In : FEBS Letters. 385, 3, p. 229-232 4 p.

Research output: Contribution to journalArticle

src Homology Domains
NADPH Oxidase
Phagocytes
Proline
Two-Hybrid System Techniques
3 Citations (Scopus)

A nuclear factor which interacts with an at-cluster in the first intron of rat α2-macroglobulin gene

Ito, T. & Sakaki, Y., Sep 15 1987, In : Biochemical and Biophysical Research Communications. 147, 2, p. 824-830 7 p.

Research output: Contribution to journalArticle

Macroglobulins
Introns
Rats
Genes
Type II DNA Topoisomerase
10 Citations (Scopus)

A parallel affinity purification method for selective isolation of polyubiquitinated proteins

Ota, K., Kito, K., Iemura, S. I., Natsume, T. & Ito, T., Aug 1 2008, In : Proteomics. 8, 15, p. 3004-3007 4 p.

Research output: Contribution to journalArticle

Ubiquitinated Proteins
Purification
Ubiquitin
Bearings (structural)
Ubiquitins
20 Citations (Scopus)

A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p

Ota, K., Kito, K., Okada, S. & Ito, T., Dec 1 2008, In : Genes to Cells. 13, 10, p. 1075-1085 11 p.

Research output: Contribution to journalArticle

F-Box Proteins
Ubiquitinated Proteins
Proteomics
Membrane Proteins
Ubiquitination
151 Citations (Scopus)

Assembly and activation of the phagocyte NADPH oxidase: Specific interaction of the N-terminal Src homology 3 domain of p47(phox) with p22(phox) is required for activation of the NADPH oxidase

Sumimoto, H., Hata, K., Mizuki, K., Ito, T., Kage, Y., Sakaki, Y., Fukumaki, Y., Nakamura, M. & Takeshige, K., Sep 25 1996, In : Journal of Biological Chemistry. 271, 36, p. 22152-22158 7 p.

Research output: Contribution to journalArticle

src Homology Domains
NADPH Oxidase
Phagocytes
Chemical activation
Proline
6 Citations (Scopus)

A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards

Kito, K., Okada, M., Ishibashi, Y., Okada, S. & Ito, T., May 1 2016, In : Proteomics. 16, 10, p. 1457-1473 17 p.

Research output: Contribution to journalArticle

Proteome
Mass spectrometry
Mass Spectrometry
Peptides
Proteins
67 Citations (Scopus)

A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes

Kito, K., Ota, K., Fujita, T. & Ito, T., Feb 1 2007, In : Journal of Proteome Research. 6, 2, p. 792-800 9 p.

Research output: Contribution to journalArticle

Multiprotein Complexes
Stoichiometry
Peptides
Proteins
Eukaryotic Initiation Factor-2B
7 Citations (Scopus)

A yeast one-hybrid system to detect methylation-dependent DNA-protein interactions

Feng, S. Y., Ota, K., Yamada, Y., Sawabu, N. & Ito, T., Jan 23 2004, In : Biochemical and Biophysical Research Communications. 313, 4, p. 922-925 4 p.

Research output: Contribution to journalArticle

Methylation
DNA Methylation
Hybrid systems
Yeast
Yeasts
8 Citations (Scopus)

A yeast one-hybrid system to screen for methylated DNA-binding proteins

Feng, S. Y., Ota, K. & Ito, T., Nov 1 2010, In : Nucleic acids research. 38, 20, p. e189

Research output: Contribution to journalArticle

DNA-Binding Proteins
Clone Cells
Yeasts
DNA Methylation
Gene Library
81 Citations (Scopus)

Barrier proteins remodel and modify chromatin to restrict silenced domains.

Oki, M., Valenzuela, L., Chiba, T., Ito, T. & Kamakaka, R. T., Mar 2004, In : Molecular and Cellular Biology. 24, 5, p. 1956-1967

Research output: Contribution to journalArticle

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
Stem cells
Epithelial Cells
37 Citations (Scopus)

Budding Yeast GCN1 Binds the GI Domain to Activate the eIF2α Kinase GCN2

Kubota, H., Ota, K., Sakaki, Y. & Ito, T., May 18 2001, In : Journal of Biological Chemistry. 276, 20, p. 17591-17596 6 p.

Research output: Contribution to journalArticle

Eukaryotic Initiation Factor-2
Saccharomycetales
Yeast
Phosphotransferases
Bearings (structural)
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
26 Citations (Scopus)

Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor

Okada, S., Ota, K. & Ito, T., Dec 1 2009, In : Protein Science. 18, 12, p. 2518-2527 10 p.

Research output: Contribution to journalArticle

Periplasmic Binding Proteins
Nanosensors
Fluorescence Resonance Energy Transfer
Ligands
Proteins

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
55 Citations (Scopus)

Comparative genome analysis of the mouse imprinted gene Impact and its nonimprinted human homolog IMPACT: Toward the structural basis for species-specific imprinting

Okamura, K., Hagiwara-Takeuchi, Y., Li, T., Vu, T. H., Hirai, M., Hattori, M., Sakaki, Y., Hoffman, A. R. & Ito, T., Dec 1 2000, In : Genome Research. 10, 12, p. 1878-1889 12 p.

Research output: Contribution to journalArticle

Islands
Genome
CpG Islands
Introns
Genes
15 Citations (Scopus)

Comparative genomics approach toward critical determinants for the imprinting of an evolutionarily conserved gene Impact

Okamura, K., Sakaki, Y. & Ito, T., Apr 15 2005, In : Biochemical and Biophysical Research Communications. 329, 3, p. 824-830 7 p.

Research output: Contribution to journalArticle

Tandem Repeat Sequences
Genomics
Mammals
Rodentia
Genes
3 Citations (Scopus)

Detecting protein – DNA interactions using a modified yeast one-hybrid system

Ota, K., Feng, S. Y. & Ito, T., Jan 1 2014, In : Methods in Molecular Biology. 1164, p. 39-50 12 p.

Research output: Contribution to journalArticle

Reporter Genes
Yeasts
DNA
DNA-Binding Proteins
DNA Methylation
39 Citations (Scopus)

Developmentally-regulated expression of mNapor encoding an apoptosis-induced ELAV-type RNA binding protein

Choi, D. K., Ito, T., Tsukahara, F., Hirai, M. & Sakaki, Y., Sep 3 1999, In : Gene. 237, 1, p. 135-142 8 p.

Research output: Contribution to journalArticle

RNA-Binding Proteins
Neuroblastoma
Apoptosis
Chromosomes, Human, Pair 2
3' Untranslated Regions
24 Citations (Scopus)

Differential display analysis of gene expression in developing embryos of Xenopus laevis

Adati, N., Ito, T., Koga, C., Kito, K., Sakaki, Y. & Shiokawa, K., May 17 1995, In : BBA - Gene Structure and Expression. 1262, 1, p. 43-51 9 p.

Research output: Contribution to journalArticle

Xenopus laevis
Dermatoglyphics
Gene expression
Embryonic Structures
Genes
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
14 Citations (Scopus)

Differentially expressed MHC class II-associated invariant chain in rat stomach pyloric mucosa with N-methyl-N'-nitro-N-nitrosoguanidine exposure

Furihata, C., Oka, M., Yamamoto, M., Ito, T., Ichinose, M., Miki, K., Tatematsu, M., Sakaki, Y. & Reske, K., May 6 1997, In : Cancer Research. 57, 8, p. 1416-1418 3 p.

Research output: Contribution to journalArticle

Methylnitronitrosoguanidine
Stomach
Mucous Membrane
Northern Blotting
Reverse Transcription
21 Citations (Scopus)

Discovery of a novel compound: Insight into mechanisms for acrylamide-induced axonopathy and colchicine-induced apoptotic neuronal cell death

Nakagawa-Yagi, Y., Choi, D. K., Ogane, N., Shimada, S. I., Seya, M., Momoi, T., Ito, T. & Sakaki, Y., Aug 3 2001, In : Brain Research. 909, 1-2, p. 8-19 12 p.

Research output: Contribution to journalArticle

Focal Adhesion Kinase 2
Focal Adhesion Protein-Tyrosine Kinases
Acrylamide
Colchicine
Cell Death
13 Citations (Scopus)

Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics

Kito, K., Kawaguchi, N., Okada, S. & Ito, T., Jun 1 2008, In : Proteomics. 8, 12, p. 2366-2370 5 p.

Research output: Contribution to journalArticle

Proteomics
Cyclins
Fungal Proteins
Isotopes
Purification
20 Citations (Scopus)

Diverse DNA methylation statuses at alternative promoters of human genes in various tissues

Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S. & Suzuki, Y., Nov 16 2006, In : DNA Research. 13, 4, p. 155-167 13 p.

Research output: Contribution to journalArticle

DNA Methylation
CpG Islands
Genes
Methylation
Alleles

DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Umeyama, T. & Ito, T., Jul 1 2018, In : Current Protocols in Molecular Biology. 123, 1, e60.

Research output: Contribution to journalArticle

Nucleosomes
Chromosome Mapping
DNA
Genome
Proteins
4 Citations (Scopus)

DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Umeyama, T. & Ito, T., Oct 3 2017, In : Cell Reports. 21, 1, p. 289-300 12 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromosome Mapping
Genes
DNA
Proteins
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
6 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
11 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