User Profile


Kazuharu Arakawa
Fujisawa, Japan
Research Interests:
Bioinformatics, Systems Biology
Institute for Advanced Biosciences, Keio University
About gaou:
Assistant Professor at Institute for Advanced Biosciences, Keio University
Publications in PubMed
  1. Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M. Genome Projector: zoomable genome map with multiple views. BMC bioinformatics 2009 10. DOI:10.1186/1471-2105-10-31.
  2. Ogawa Y, Arakawa K, Kaizu K, Miyoshi F, Nakayama Y, Tomita M. Comparative study of circadian oscillatory network models of Drosophila. Artificial life 2008 14(1). DOI:10.1162/artl.2008.14.1.29.
  3. Tamaki S, Arakawa K, Kono N, Tomita M. Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics, proteomicsbioinformatics / Beijing Genomics Institute 2007 5(1). DOI:10.1016/S1672-0229(07)60014-X.
  4. Kono N, Arakawa K, Tomita M. MEGU: pathway mapping web-service based on KEGG and SVG. In silico biology 2006 6(6). DOI:10.1016/S1672-0229(07)60014-X.
  5. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (New York, N.Y.) 2007 316(5824). DOI:10.1126/science.1132067.
  6. Sugahara J, Yachie N, Arakawa K, Tomita M. In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (New York, N.Y.) 2007 13(5). DOI:10.1261/rna.309507.
  7. Arakawa K, Uno R, Nakayama Y, Tomita M. Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene 2007 392(1-2). DOI:10.1016/j.gene.2006.12.022.
  8. Arakawa K, Saito R, Tomita M. Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. FEBS letters 2007 581(2). DOI:10.1016/j.febslet.2006.12.021.
  9. Yachie N, Arakawa K, Tomita M. On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli. FEBS letters 2006 580(30). DOI:10.1016/j.febslet.2006.11.053.
  10. Arakawa K, Nakayama Y, Tomita M. GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness. In silico biology 2006 6(1-2). DOI:10.1016/j.febslet.2006.11.053.
  11. Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M. GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC bioinformatics 2006 7. DOI:10.1186/1471-2105-7-168.
  12. Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M. A comprehensive software suite for the analysis of cDNAs. Genomics, proteomicsbioinformatics / Beijing Genomics Institute 2005 3(3). DOI:10.1186/1471-2105-7-168.
  13. Arakawa K, Kono N, Yamada Y, Mori H, Tomita M. KEGG-based pathway visualization tool for complex omics data. In silico biology 2005 5(4). DOI:10.1186/1471-2105-7-168.
  14. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics (Oxford, England) 2003 19(2). DOI:10.1186/1471-2105-7-168.
  15. Uno R, Nakayama Y, Arakawa K, Tomita M. The orientation bias of Chi sequences is a general tendency of G-rich oligomers. Gene 2000 259(1-2). DOI:10.1186/1471-2105-7-168.
Arakawa K, Yachie N, Tomita M, "Visualizing Complex Omics Information - Scientific Visualization for Genomics and Systems Biology", BIOforum Europe 2008, 6:27-29.
Arakawa K, Tomita M, "Large-scale Modeling for Systems Biology", BIOforum Europe, 2006, 10:54-55.
Arakawa K, Tomita M, "G-language System as a platform for large-scale analysis of high-throughput omics data", Journal of Pesticide Science, 2006, 31(3):282-288.
History of Education and Employment
2006-2009, Post-doc, Institute for Advanced Biosciences, Keio University