Takeshi Itoh

Last updated: Sep 13, 2018 at 10:14

Name	Takeshi Itoh
URL	http://www.naro.affrc.go.jp/english/naac/index.html
Affiliation	National Agriculture and Food Research Organization
Section	Bioinformatics Team, Advanced Analysis Center
Job title	Leader
Degree	Ph.D.(Nara Institute of Science and Technology)
ORCID ID	0000-0002-6291-4233

Research Interests

Database(176) , Molecular Evolution(71) , Bioinformatics(276)

Research Areas

Biological Science / Molecular biology / Molecular Biology
Basic biology / Evolutionary biology / Evolutionary Biology
Genome science / Genome biology / Genomics

Awards & Honors

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2008

The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology, The Young Scientists’ Prize, Ministry of Education, Culture, Sports, Science and Technology

2007

Young Scientist Initiative Award, Society of Evolutionary Studies, Japan

Published Papers

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The Nipponbare genome and the next-generation of rice genomics research in Japan.

Rice (New York, N.Y.) Dec 2016 [Refereed]

Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection.

Breeding science Sep 2016 [Refereed]

Improvement of barley genome annotations by deciphering the Haruna Nijo genome.

DNA research : an international journal for rapid publication of reports on genes and genomes Feb 2016 [Refereed]

The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

Plant & cell physiology Jan 2016 [Refereed]

TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice.

Plant & cell physiology Jan 2016 [Refereed]

The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.

Scientific Reports Nov 2015 [Refereed]

Whole-genome analysis of herbicide-tolerant mutant rice generated by Agrobacterium-mediated gene targeting.

Plant & cell physiology Jan 2015 [Refereed]

Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)

Molecular breeding : new strategies in plant improvement Jan 2015 [Refereed]

A novel rice cytochrome P450 gene, CYP72A31, confers tolerance to acetolactate synthase-inhibiting herbicides in rice and Arabidopsis.

Plant physiology Nov 2014 [Refereed]

Transcriptome analysis of barley identifies heat shock and HD-Zip I transcription factors up-regulated in response to multiple abiotic stresses

Molecular breeding : new strategies in plant improvement Aug 2014 [Refereed]

Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice.

DNA research : an international journal for rapid publication of reports on genes and genomes Aug 2014 [Refereed]

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.

Science (New York, N.Y.) Jul 2014 [Refereed]

MEGANTE: a web-based system for integrated plant genome annotation.

Plant & cell physiology Jan 2014 [Refereed]

Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.

DNA research : an international journal for rapid publication of reports on genes and genomes 2014 [Refereed]

Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.

PloS one 2014 [Refereed]

bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes.

Breeding science Dec 2013 [Refereed]

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.

Plant molecular biology Dec 2013 [Refereed]

A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy.

DNA research : an international journal for rapid publication of reports on genes and genomes Dec 2013 [Refereed]

TASUKE: a web-based visualization program for large-scale resequencing data.

Bioinformatics (Oxford, England) Jul 2013 [Refereed]

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

Plant & cell physiology Feb 2013 [Refereed]

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

Rice (New York, N.Y.) Feb 2013 [Refereed]

Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat.

BMC genomics 2013 [Refereed]

Independent domestication of Asian rice followed by gene flow from japonica to indica.

Molecular biology and evolution May 2012 [Refereed]

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

Frontiers in plant science 2012 [Refereed]

Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.

PloS one 2012 [Refereed]

Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interaction.

BMC plant biology 2012 [Refereed]

Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.

The Plant journal : for cell and molecular biology Jun 2011 [Refereed]

Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison.

Gene May 2011 [Refereed]

Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries.

Plant physiology May 2011 [Refereed]

Unlocking the barley genome by chromosomal and comparative genomics.

The Plant cell Apr 2011 [Refereed]

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Genome biology and evolution 2011 [Refereed]

Asymmetric distribution of gene expression in the centromeric region of rice chromosome 5.

Frontiers in plant science 2011 [Refereed]

Efficient plant gene identification based on interspecies mapping of full-length cDNAs.

DNA research : an international journal for rapid publication of reports on genes and genomes Oct 2010 [Refereed]

SALAD database: a motif-based database of protein annotations for plant comparative genomics.

Nucleic acids research Jan 2010 [Refereed]

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

BMC genomics 2010 [Refereed]

Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis.

BMC genomics 2010 [Refereed]

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

Bioinformatics (Oxford, England) Dec 2009 [Refereed]

Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis.

Plant physiology Mar 2009 [Refereed]

Genome-wide validation of Magnaporthe grisea gene structures based on transcription evidence.

FEBS letters Feb 2009 [Refereed]

In silico identification of short nucleotide sequences associated with gene expression of pollen development in rice.

Plant & cell physiology Oct 2008 [Refereed]

The Rice Annotation Project Database (RAP-DB): 2008 update.

Nucleic acids research Jan 2008 [Refereed]

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Nucleic acids research Jan 2008 [Refereed]

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Nucleic acids research Jan 2008 [Refereed]

Birth and death of genes promoted by transposable elements in Oryza sativa.

Gene May 2007 [Refereed]

Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes.

Gene Mar 2007 [Refereed]

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Genome research Feb 2007 [Refereed]

Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana.

Molecular biology and evolution Jan 2007 [Refereed]

Alternative splicing in human transcriptome: functional and structural influence on proteins.

Gene Oct 2006 [Refereed]

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.

Nucleic acids research Jul 2006 [Refereed]

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information.

Nucleic acids research Jan 2006 [Refereed]

Misc

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Genomic overview of the complete gene set of Oryza sativa L. ssp. japonica

ITOH Takeshi, TANAKA Tsuyoshi

農林水産技術研究ジャーナル = Research Journal of Food and Agriculture 31(3) 30-33 Mar 2008

Books etc

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Genetics and Genomics of Rice (Plant Genetics and Genomics: Crops and Models)

Springer Aug 2016 ISBN:1493941321

Rice Functional Genomics: Challenges, Progress and Prospects

Springer Oct 2010 ISBN:1441923756

Association Memberships

Society for Molecular Biology and Evolution(18) , SOCIETY OF EVOLUTIONARY STUDIES, JAPAN(236) , THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS(519) , THE GENETICS SOCIETY OF JAPAN(204)