Papers - Arakawa, Kazuharu
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The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Toshiaki Katayama*, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A Vos, David Withers, Chisato Yamasaki, Christ
Journal of Biomedical Semantics 4 6 2013
Research paper (scientific journal), Joint Work, Accepted
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Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
ARAKAWA Kazuharu, TOMITA Masaru
Current Genomics 13 ( 1 ) 4-15 2012
Research paper (scientific journal), Joint Work, Accepted
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Validation of bacterial replication termination models using simulation of genomic mutations
KONO Nobuaki, ARAKAWA Kazuharu, TOMITA Masaru
PLoS One 7 ( 4 ) e34526 2012
Research paper (scientific journal), Joint Work, Accepted
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Two families of novel abundant heat-soluble proteins in an anhydrobiotic tardigrade
Yamaguchi A, Tanaka S, Yamaguchi S, Kuwahara H, Takamura C, Ohmi S, Horikawa DD, Toyoda A, Katayama T, Arakawa K, Fujiyama A, Kubo T, Kunieda T
PLoS One 7 ( 8 ) e44209 2012
Research paper (scientific journal), Joint Work, Accepted
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Metabolic flux analysis and visualization
TOYA Yoshihiro, KONO Nobuaki, ARAKAWA Kazuharu, TOMITA Masaru
Journal of Proteome Research 10 ( 8 ) 3313-3323 2011.08
Research paper (scientific journal), Joint Work, Accepted
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The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
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, Fernandez JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.
Journal of Biomedical Semantics 2 ( 1 ) 4 2011.08
Research paper (scientific journal), Joint Work
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Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index
ARAKAWA Kazuharu, Suzuki H, Tomita M
BMC Genomics 10 640 2009.12
Research paper (scientific journal), Joint Work, Accepted
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Pathway Projector: Web-based Zoomable Pathway Browser using KEGG Atlas and Google Maps API
Kono N, ARAKAWA Kazuharu, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M
PLoS One 4 ( 11 ) e7710 2009.11
Research paper (scientific journal), Joint Work, Accepted
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A web server for interactive and zoomable Chaos Game Representation images
ARAKAWA Kazuharu,Oshita K, Tomita M
Source Code for Biology and Medicin 4 6 2009.09
Research paper (scientific journal), Joint Work, Accepted
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Genome Projector: zoomable genome map with multiple views
ARAKAWA Kazuharu, TAMAKI, Satoshi, KONO, Nobuaki, KIDO, Nobuhiro, IKEGAMI Keita, OGAWA Ryu, TOMITA Masaru
BMC Bioinformatics 10 31 2009.01
Research paper (scientific journal), Joint Work
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Visualizing Complex Omics Information - Scientific Visualization for Genomics and Systems Biology
ARAKAWA Kazuharu
BIOforum Europe 6 27-29 2008
Research paper (scientific journal), Joint Work
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Comparative study of circadian oscillatory network models of Drosophila
ARAKAWA Kazuharu
Artificial Life 14 ( 1 ) 29-48 2008
Research paper (scientific journal), Joint Work, Accepted
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Computational Genome Analysis Using The G-language System
ARAKAWA Kazuharu
Genes, Genomes and Genomics 2 ( 1 ) 1-13 2008
Research paper (scientific journal), Joint Work
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Noise-reduction filtering for accurate detection of replication termini in bacterial genomes
ARAKAWA Kazuharu
Febs Letters 581 ( 2 ) 253-258 2007
Research paper (scientific journal), Joint Work, Accepted
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Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes
ARAKAWA Kazuharu
Evolutionary Bioinformatics 3 279-286 2007
Research paper (scientific journal), Joint Work, Accepted
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The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection
ARAKAWA Kazuharu
Evolutionary Bioinformatics 3 145-154 2007
Research paper (scientific journal), Joint Work, Accepted
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Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics
ARAKAWA Kazuharu
Genomics Proteomics Bioinformatics 5 ( 1 ) 53-58 2007
Research paper (scientific journal), Joint Work, Accepted
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Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
ARAKAWA Kazuharu
Science 316 ( 5824 ) 593-597 2007
Research paper (scientific journal), Joint Work, Accepted
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In Silico Screening of Archaeal tRNA-encoding Genes Having Multiple Introns with Bulge-Helix-Bulge Splicing Motifs
ARAKAWA Kazuharu
RNA 13 ( 5 ) 671-681 2007
Research paper (scientific journal), Joint Work, Accepted
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Significance of the genomic properties of Chi sites validated from the distribution of all octamers in Escherichia coli
ARAKAWA Kazuharu
Gene 392 ( 1-2 ) 239-246 2007
Research paper (scientific journal), Joint Work, Accepted