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Shuichi Kawashima - Publications

Affiliations: 
2007 Bioinformatics Boston University, Boston, MA 
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Katayama T, Kawashima S, Okamoto S, Moriya Y, Chiba H, Naito Y, Fujisawa T, Mori H, Takagi T. TogoGenome/TogoStanza: modularized Semantic Web genome database. Database : the Journal of Biological Databases and Curation. 2019. PMID 30624651 DOI: 10.1093/Database/Bay132  0.462
2018 Kawashima S, Katayama T, Hatanaka H, Kushida T, Takagi T. NBDC RDF portal: a comprehensive repository for semantic data in life sciences. Database : the Journal of Biological Databases and Curation. 2018. PMID 30576482 DOI: 10.1093/Database/Bay123  0.382
2015 Aoki-Kinoshita KF, Kinjo AR, Morita M, Igarashi Y, Chen YA, Shigemoto Y, Fujisawa T, Akune Y, Katoda T, Kokubu A, Mori T, Nakao M, Kawashima S, Okamoto S, Katayama T, et al. Implementation of linked data in the life sciences at BioHackathon 2011. Journal of Biomedical Semantics. 6: 3. PMID 25973165 DOI: 10.1186/2041-1480-6-3  0.406
2014 Kotera M, Nishimura Y, Nakagawa Z, Muto A, Moriya Y, Okamoto S, Kawashima S, Katayama T, Tokimatsu T, Kanehisa M, Goto S. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. Journal of Bioinformatics and Computational Biology. 12: 1442001. PMID 25385078 DOI: 10.1142/S0219720014420013  0.304
2014 Yamagishi J, Natori A, Tolba ME, Mongan AE, Sugimoto C, Katayama T, Kawashima S, Makalowski W, Maeda R, Eshita Y, Tuda J, Suzuki Y. Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. Genome Research. 24: 1433-44. PMID 25091627 DOI: 10.1101/Gr.158980.113  0.317
2014 Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, et al. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics. 5: 5. PMID 24495517 DOI: 10.1186/2041-1480-5-5  0.362
2013 Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, et al. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. Journal of Biomedical Semantics. 4: 6. PMID 23398680 DOI: 10.1186/2041-1480-4-6  0.384
2013 Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Research. 41: D353-7. PMID 23193276 DOI: 10.1093/Nar/Gks1239  0.473
2012 Hayashida K, Hara Y, Abe T, Yamasaki C, Toyoda A, Kosuge T, Suzuki Y, Sato Y, Kawashima S, Katayama T, Wakaguri H, Inoue N, Homma K, Tada-Umezaki M, Yagi Y, et al. Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. Mbio. 3: e00204-12. PMID 22951932 DOI: 10.1128/Mbio.00204-12  0.33
2011 Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, et al. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. Journal of Biomedical Semantics. 2: 4. PMID 21806842 DOI: 10.1186/2041-1480-2-4  0.345
2009 Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggström JZ, Goto S. Systems biology approaches and pathway tools for investigating cardiovascular disease. Molecular Biosystems. 5: 588-602. PMID 19462016 DOI: 10.1039/B902356A  0.414
2009 Wakaguri H, Suzuki Y, Katayama T, Kawashima S, Kibukawa E, Hiranuka K, Sasaki M, Sugano S, Watanabe J. Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. Nucleic Acids Research. 37: D520-5. PMID 18987005 DOI: 10.1093/Nar/Gkn856  0.318
2008 Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Research. 36: D480-4. PMID 18077471 DOI: 10.1093/Nar/Gkm882  0.43
2008 Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M. AAindex: amino acid index database, progress report 2008. Nucleic Acids Research. 36: D202-5. PMID 17998252 DOI: 10.1093/Nar/Gkm998  0.309
2007 Kawashima S, Kawashima T, Putnam NH, Rokhsar DS, Wada H, Kanehisa M. Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Informatics. International Conference On Genome Informatics. 19: 50-60. PMID 18546504 DOI: 10.11234/Gi1990.19.50  0.334
2007 Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research. 35: W625-32. PMID 17586824 DOI: 10.1093/Nar/Gkm295  0.456
2007 Masoudi-Nejad A, Goto S, Jauregui R, Ito M, Kawashima S, Moriya Y, Endo TR, Kanehisa M. EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG. Plant Physiology. 144: 857-66. PMID 17468225 DOI: 10.1104/Pp.106.095059  0.483
2007 Okamoto S, Yamanishi Y, Ehira S, Kawashima S, Tonomura K, Kanehisa M. Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis. Proteomics. 7: 900-9. PMID 17370268 DOI: 10.1002/Pmic.200600862  0.501
2007 Okuda S, Kawashima S, Kobayashi K, Ogasawara N, Kanehisa M, Goto S. Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. Bmc Genomics. 8: 48. PMID 17298663 DOI: 10.1186/1471-2164-8-48  0.428
2006 Yoshizawa AC, Kawashima S, Okuda S, Fujita M, Itoh M, Moriya Y, Hattori M, Kanehisa M. Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic (Copenhagen, Denmark). 7: 1104-18. PMID 16882042 DOI: 10.1111/J.1600-0854.2006.00451.X  0.331
2006 Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S. EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Research. 34: W459-62. PMID 16845049 DOI: 10.1093/Nar/Gkl066  0.423
2006 Okuda S, Katayama T, Kawashima S, Goto S, Kanehisa M. ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Research. 34: D358-62. PMID 16381886 DOI: 10.1093/Nar/Gkj037  0.461
2006 Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research. 34: D354-7. PMID 16381885 DOI: 10.1093/Nar/Gkj102  0.412
2005 Yamada T, Kawashima S, Mamitsuka H, Goto S, Kanehisa M. Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Informatics. International Conference On Genome Informatics. 16: 150-8. PMID 16362917 DOI: 10.11234/Gi1990.16.150  0.612
2005 Okuda S, Kawashima S, Goto S, Kanehisa M. Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. Genome Informatics. International Conference On Genome Informatics. 16: 116-24. PMID 16362913 DOI: 10.11234/Gi1990.16.116  0.459
2005 Tamori A, Yamanishi Y, Kawashima S, Kanehisa M, Enomoto M, Tanaka H, Kubo S, Shiomi S, Nishiguchi S. Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 11: 5821-6. PMID 16115921 DOI: 10.1158/1078-0432.Ccr-04-2055  0.336
2004 Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome Nucleic Acids Research. 32: D277-D280. PMID 14681412 DOI: 10.1093/Nar/Gkh063  0.48
2002 Kawashima T, Kawashima S, Kohara Y, Kanehisa M, Makabe KW. Update of MAGEST: Maboya gene expression patterns and Sequence Tags Nucleic Acids Research. 30: 119-120. PMID 11752271 DOI: 10.1093/Nar/30.1.119  0.476
2002 Kanehisa M, Goto S, Kawashima S, Nakaya A. Thed KEGG databases at GenomeNet Nucleic Acids Research. 30: 42-46. PMID 11752249 DOI: 10.1093/Nar/30.1.42  0.531
2001 Ohmori M, Ikeuchi M, Sato N, Wolk P, Kaneko T, Ogawa T, Kanehisa M, Goto S, Kawashima S, Okamoto S, Yoshimura H, Katoh H, Fujisawa T, Ehira S, Kamei A, et al. Characterization of genes encoding multi-domain proteins in the genome of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 Dna Research. 8: 271-284. PMID 11858227 DOI: 10.1093/Dnares/8.6.271  0.422
2001 Sato Y, Nakaya A, Shiraishi K, Kawashima S, Goto S, Kanehisa M. SSDB: Sequence Similarity Database in KEGG Genome Informatics. 12: 230-231. DOI: 10.11234/Gi1990.12.230  0.326
2000 Kawashima T, Kawashima S, Kanehisa M, Nishida H, Makabe KW. MAGEST: MAboya gene expression patterns and sequence tags. Nucleic Acids Research. 28: 133-5. PMID 10592202 DOI: 10.1093/Nar/28.1.133  0.389
2000 Kawashima S, Nakaya A, Okuji Y, Goto S, Kanehisa M. Extraction of Correlated Gene Clusters from Multiple Graph Structures: Application Genome Informatics. 11: 272-273. DOI: 10.11234/Gi1990.11.272  0.331
2000 Goto S, Kamiya T, Kawashima S, Miyazaki S, Okuji Y, Numata Y, Kanehisa M. KEGG/EXPRESSION: A Database for Browsing and Analysing Microarray Expression Data Genome Informatics. 11: 222-223. DOI: 10.11234/Gi1990.11.222  0.389
1999 Nakao M, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M. Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG. Genome Informatics. 10: 94-103. DOI: 10.11234/Gi1990.10.94  0.515
1997 Kawashima S, Katayama T, Kanehisa M. Construction of Molecular Interaction Database and Searching for Similar Pathways Genome Informatics. 8: 298-299. DOI: 10.11234/Gi1990.8.298  0.332
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