Yasukazu Nakamura
National Institute of Genetics, Japan · Genome Informatics Laboratory
Molecular Biology, Biotechnology, Bioinformatics
307Impact points
85Publications
4Followers
Contact Details
Publications
The Integral Membrane Protein SEN1 is Required for Symbiotic Nitrogen Fixation in Lotus japonicus Nodules.
Plant & cell physiology.
Legume plants establish symbiotic association with bacteria called rhizobia, resulting in the formation of nitrogen-fixing root nodules. A Lotus japonicus symbiotic mutant, sen1, forms nodules that
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.
Nucleic acids research.
The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of
The International Nucleotide Sequence Database Collaboration.
Nucleic acids research.
The members of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) set out to capture, preserve and present globally comprehensive public domain nucleotide
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
Journal of biomedical semantics. 2(1):4.
ABSTRACT: BACKGROUND: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure
The International Nucleotide Sequence Database Collaboration.
Nucleic acids research. 39(Database issue):D15-8.
Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The
SNP Discovery and Linkage Map Construction in Cultivated Tomato.
DNA research : an international journal for rapid publication of reports on genes and genomes.
Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single
DDBJ progress report.
Nucleic acids research.
The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.
The EMBO journal.
In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
Journal of biomedical semantics. 1(1):8.
ABSTRACT: Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands
An interspecific linkage map of SSR and intronic polymorphism markers in tomato.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
Despite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using public
Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510.
DNA research : an international journal for rapid publication of reports on genes and genomes.
We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa
Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies.
Advances in experimental medicine and biology. 680:125-135.
The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration with NCBI and EBI. As one of the three major public databases,
Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Standards in genomic sciences. 2(3):357-60.
This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a
Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation.
Nature. 462(7272):514-7.
Homocitrate is a component of the iron-molybdenum cofactor in nitrogenase, where nitrogen fixation occurs. NifV, which encodes homocitrate synthase (HCS), has been identified from various diazotrophs
DDBJ launches a new archive database with analytical tools for next-generation sequence data.
Nucleic acids research.
The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has collected and released 1 701 110 entries/1 116 138 614 bases between July 2008 and June 2009. A few highlighted data releases from
CyanoBase: the cyanobacteria genome database update 2010.
Nucleic acids research.
CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information,
Development of a Bacterial Cell Enrichment Method and its Application to the Community Analysis in Soybean Stems.
Microbial ecology.
A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem
Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics.
DNA research : an international journal for rapid publication of reports on genes and genomes. 15(5):297-308.
Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide
Genome Structure of the Legume, Lotus japonicus.
DNA research : an international journal for rapid publication of reports on genes and genomes.
The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural
Following
Soichi Ogishima
Tokyo Medical and Dental University
Martin Senger
King Abdullah University of...
Daisuke Shibata
Kazusa DNA Research Instiute
Takatomo Fujisawa
National Institute of Genetics
Yukiko Yamazaki
National Institute of Genetics

Academic Degrees
Dr
Research Keywords
Database, Bacteria, Plant Biology, Gene Mapping, Genomics
Past Advisors
Kikuo Sen, Kanji Ohyama, Toshimichi Ikemura, Satoshi Tabata
Current Location
Mishima, Japan