Shuichi Kawashima

Shuichi Kawashima

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Shuichi Kawashima

Shuichi Kawashima

Publications by authors named "Shuichi Kawashima"

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37Publications

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NBDC RDF portal: a comprehensive repository for semantic data in life sciences.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

National Bioscience Database Center, Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/database/bay123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301334PMC
January 2018

Implementation of linked data in the life sciences at BioHackathon 2011.

J Biomed Semantics 2015 7;6. Epub 2015 Jan 7.

Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi, 980-8575 Japan.

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http://dx.doi.org/10.1186/2041-1480-6-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429360PMC
May 2015

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D353-7. Epub 2012 Nov 27.

Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8585, Japan.

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http://dx.doi.org/10.1093/nar/gks1239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531156PMC
January 2013

Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii.

Parasitol Int 2010 Jun 12;59(2):206-10. Epub 2010 Feb 12.

Department of Tropical Medicine and Parasitology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan.

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http://dx.doi.org/10.1016/j.parint.2010.01.007DOI Listing
June 2010

Domain shuffling and the evolution of vertebrates.

Genome Res 2009 Aug 14;19(8):1393-403. Epub 2009 May 14.

Okinawa Institute of Science and Technology, Uruma, Okinawa, Japan.

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http://dx.doi.org/10.1101/gr.087072.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720177PMC
August 2009

Systems biology approaches and pathway tools for investigating cardiovascular disease.

Mol Biosyst 2009 Jun 27;5(6):588-602. Epub 2009 Apr 27.

Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1039/b902356aDOI Listing
June 2009

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.

Nucleic Acids Res 2009 Jan 4;37(Database issue):D520-5. Epub 2008 Nov 4.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo. 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkn856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686583PMC
January 2009

New amino acid indices based on residue network topology.

Genome Inform 2007 ;18:152-61

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan.

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August 2008

Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

Genome Inform 2007 ;19:50-60

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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July 2008

AAindex: amino acid index database, progress report 2008.

Nucleic Acids Res 2008 Jan 12;36(Database issue):D202-5. Epub 2007 Nov 12.

Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkm998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238890PMC
January 2008

KEGG for linking genomes to life and the environment.

Nucleic Acids Res 2008 Jan 12;36(Database issue):D480-4. Epub 2007 Dec 12.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

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http://dx.doi.org/10.1093/nar/gkm882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238879PMC
January 2008

Metabolite antigens and pathway incompatibility.

Genome Inform 2006 ;17(1):184-94

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan.

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July 2007

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W625-32. Epub 2007 Jun 22.

Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkm295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933155PMC
July 2007

EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.

Plant Physiol 2007 Jun 27;144(2):857-66. Epub 2007 Apr 27.

Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1104/pp.106.095059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914165PMC
June 2007

Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis.

Proteomics 2007 Mar;7(6):900-9

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan.

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http://dx.doi.org/10.1002/pmic.200600862DOI Listing
March 2007

Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.

BMC Genomics 2007 Feb 13;8:48. Epub 2007 Feb 13.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1186/1471-2164-8-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1808063PMC
February 2007

Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic.

Traffic 2006 Aug;7(8):1104-18

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1111/j.1600-0854.2006.00451.xDOI Listing
August 2006

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W459-62

Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1093/nar/gkl066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538775PMC
July 2006

Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli.

Genome Inform 2005 ;16(1):116-24

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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January 2006

Comprehensive analysis and prediction of synthetic lethality using subcellular locations.

Genome Inform 2005 ;16(1):150-8

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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January 2006

Autoimmune diseases and peptide variations.

Genome Inform 2005 ;16(1):272-80

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan.

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January 2006

From genomics to chemical genomics: new developments in KEGG.

Nucleic Acids Res 2006 Jan;34(Database issue):D354-7

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1093/nar/gkj102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347464PMC
January 2006

ODB: a database of operons accumulating known operons across multiple genomes.

Nucleic Acids Res 2006 Jan;34(Database issue):D358-62

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkj037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347400PMC
January 2006

Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA.

Clin Cancer Res 2005 Aug;11(16):5821-6

Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan.

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http://dx.doi.org/10.1158/1078-0432.CCR-04-2055DOI Listing
August 2005

The KEGG resource for deciphering the genome.

Nucleic Acids Res 2004 Jan;32(Database issue):D277-80

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1093/nar/gkh063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308797PMC
January 2004

The KEGG databases at GenomeNet.

Nucleic Acids Res 2002 Jan;30(1):42-6

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99091PMC
http://dx.doi.org/10.1093/nar/30.1.42DOI Listing
January 2002

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.

Nucleic Acids Res 2002 Jan;30(1):119-20

Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99134PMC
http://dx.doi.org/10.1093/nar/30.1.119DOI Listing
January 2002