Publications

 

  1. Tanaka Y, Ogawa T, Maruta T, Yoshida Y, Arakawa K, Ishikawa T, “Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis”, FEBS Lett, 2017, 591(10): 1360-1370.(PubMed)
  2. Iwai HHorikawa DD*, Arakawa K, Tomita M, Komatsu T, Maruyama M, “Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae)”, Biodiversity Data Journal, 2016, 4: e10185.(PubMed)
  3. Hashimoto T,  Horikawa DD*, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A,  Aizu M, Enomoto A, Kondo K, Tanaka S, Hara Y, Koshikawa S, Sagara H, Miura T, Yokobori S, Miyagawa K, Suzuki Y, Kubo T, Oyama M, Kohara Y, Fujiyama A, Arakawa K , Katayama T, Toyoda A, Kunieda T, “Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein”, Nature Communications, 2016, 7:12808. (PubMed)
  4. Arakawa K*, Yoshida Y, Tomita M, “Genome sequencing of a single tardigrade Hypsibius dujardini individual”, Scientific Data, 2016, 3:160063. (PubMed)
  5. Arakawa K*, “No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade”, PNAS, 2016, 113(22):E3057. (PubMed)
  6. Yoshida Y, Tomiyama T, Maruta T, Tomita M, Ishikawa T, Arakawa K*, “De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions”, BMC Genomics, 2016, 17(1):182.(PubMed)
  7. Kono N, Nakamura H, Ito Y, Tomita M, Arakawa K*, “Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly”, Molecular Ecology Resources, 2016, 16(3):662-672. (PubMed)
  8. Horikawa DD, Arakawa K, “Tardigrades – Ultimate animals surviving extreme environments”, SFC Journal, 2015, 15(1), 246-260. (Publisher)
  9. Oshita K, Tomita M, Arakawa K*, “G-Links: a gene-centric link acquisition service”, F1000 Research, 2015, 3:285. (PubMed)
  10. Tanaka S, Tanaka J, Miwa Y, Horikawa DD, Katayama T, Arakawa K, Toyoda A, Kubo T, Kunieda T, “Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells”, PLoS One, 2015, 10:e0118272. (PubMed)
  11. Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, Iida T, Yasunaga T, Horii T, Arakawa K, Kasahara M, Nakamura S, “Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes”, BMC Genomics, 2014, 15:699. (PubMed)
  12. Kono NArakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M, “Undesigned selection for replication termination of bacterial chromosomes”, J. Mol. Biol. 2014, 426(16):2918-2927. (PubMed)
  13. Arakawa K*, Tomita M, “Genome Analysis Workshop: a Personal Genomics class at Keio SFC”, Keio SFC Journal, 2014, 14(1):158-177. (Publisher)
  14. Nakada T, Tsuchida Y, Arakawa K, Ito T and Tomita M, “Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae)”, Phycological Research, 2014, 62(3):232-236. (Publisher)
  15. BioHackathon 2011/2012, “BioHackathon series in 2011 and 2012: penetration of ontology and Linked Data in life science domains”, Journal of Biomedical Semantics, 2014, 5:5. (Publisher)
  16. Arakawa K, “Comparative metabolomics of anhydrobiosis in tardigrade Ramazzottius varieornatus”, Journal of Japanese Society for Extremophiles, 2013, 11(2), 75-82. (Publisher)
  17. Arakawa K, Tomita M, “Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation”, Methods Mol. Biol. 2013, 985:459-470. (PubMed)
  18. Itaya H, Oshita K, Arakawa K, Tomita M, “GEMBASSY: an EMBOSS Associated Software Package for Comprehensive Genome Analyses”, Source Code for Biology and Medicine, 2013, 8(1):17. (PubMed)
  19. Horikawa DD, Cumbers J, Sakakibara I, Rogoff D, Leuko S, Harnoto R, Arakawa K, Katayama T, Kunieda T, Toyoda A, Fujiyama A, Rothschild LJ, “Analysis of DNA Repair and Protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after Exposure to UVC Radiation”, PLoS One, 2013, 8(6):e6479. (PubMed)
  20. Hisano Y, Ota S, Arakawa K, Muraki M, Kono N, Oshita K, Sakuma T, Tomita M, Yamamoto T, Okada Y, Kawahara A, “Quantitative assay for TALEN activity at endogenous genomic loci”, Biology Open, 2013, 2(4):363-367. (Publisher)
  21. BioHackathon 2010, “The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies”, Journal of Biomedical Semantics, 2013, 4:6. (Publisher)
  22. 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, “Two families of novel abundant heat-soluble proteins in an anhydrobiotic tardigrade”, PLoS One, 2012, 7(8):e44209. (PubMed)
  23. Kono NArakawa K*, Tomita M, “Validation of bacterial replication termination models using simulation of genomic mutations”, PLoS One, 2012, 7(4): e34526. (PubMed)
  24. Arakawa K*, Tomita M, “Measures of Compositional Strand Bias Related to Replication Machinery and its Applications”, Current Genomics, 2012, 13(1):4-15. (PubMed)
  25. BioHackathon 2009, “The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications”, Journal of Biomedical Semantics, 2011, 2:4. (PubMed)
  26. Toya Y, Kono NArakawa K*, Tomita M, “Metabolic flux analysis and visualization”, Journal of Proteome Research, 2011, 10(8):3313-3323. (PubMed)
  27. Oshita K, Arakawa K*. Tomita M, “KBWS: an EMBOSS associated package for accessing bioinformatics web services”, Source Code for Biology and Medicine, 2011, 6(1):8. (PubMed)
  28. Kono NArakawa K*, Tomita M, “Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes”, BMC Genomics, 2011, 12(1):19. (PubMed)
  29. BioHackathon2008, “The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows”, Journal of Biomedical Semantics, 2010, 1:8. (PubMed)
  30. Arakawa K*, Kido N, Oshita K, Tomita M, “G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces”, Nucleic Acids Research, 2010, 48:W700-W705. (PubMed)
  31. Arakawa K*, Suzuki H, Tomita M, “Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index”, BMC Genomics, 2009, 10:640. (PubMed)
  32. Kono NArakawa K*, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M, “Pathway Projector: Web-based Zoomable Pathway Browser using KEGG Atlas and Google Maps API”, PLoS One, 2009, 4(11):e7710. (PubMed)
  33. Arakawa K*, Oshita K, Tomita M, “A web server for interactive and zoomable Chaos Game Representation images”, Source Code for Biology and Medicine, 2009, 4:6. (PubMed)
  34. 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, 10:31.(PubMed)
  35. Arakawa K, Yachie N, Tomita M, “Visualizing Complex Omics Information – Scientific Visualization for Genomics and Systems Biology”, BIOforum Europe 2008, 6:27-29 (PDF).
  36. Arakawa K*, Suzuki H, Tomita M, “Computational Genome Analysis Using The G-language System”, Genes, Genomes and Genomics, 2008, 2(1): 1-13.(PDF)
  37. 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):29-48.(PubMed)
  38. Arakawa K, Tomita M, “Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes”, Evolutionary Bioinformatics, 2007, 3:279-286. (PubMed)
  39. Arakawa K, Tomita M, “The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection”, Evolutionary Bioinformatics, 2007, 3:145-154. (PubMed)
  40. Tamaki S, Arakawa K*, Kono N, Tomita M, “Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics”, Genomics Proteomics Bioinformatics, 2007, 5(1): 53-58. (PubMed)
  41. 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 A, Harada A, 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, 2007, 316(5824): 593-597. (PubMed)
  42. 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, 2007, 13(5): 671-681. (PubMed)
  43. 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):239-246. (PubMed)
  44. Arakawa K, Saito R, Tomita M, “Noise-reduction filtering for accurate detection of replication termini in bacterial genomes”, FEBS Letters, 2007, 581(2):253-258. (PubMed).
  45. Arakawa K, Tomita M, “Large-scale Modeling for Systems Biology”, BIOforum Europe, 2006, 10:54-55 (PDF).
  46. 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(PDF)
  47. Kono NArakawa K*, Tomita M, “MEGU: Pathway mapping web-service based on KEGG and SVG”, In Silico Biology, 2006, 6(6):621-655. (PubMed).
  48. 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):6909-6914.(PubMed).
  49. 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, 7:168 (PubMed)
  50. Arakawa K, Nakayama Y, Tomita M, “GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness”, In Silico Biology, 2006, 6:0006 (PubMed)
  51. Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M, “Comprehensive software suite for bioinformatics analysis of cDNAs”, Genomics Proteomics Bioinformatics, 2005, 3(3):179-188 (PubMed)
  52. Arakawa K, Kono N, Yamada Y, Mori H, and Tomita M, “KEGG-based pathway visualization tool for complex omics data”, In Silico Biology, 2005, 5:0039 (PubMed)
  53. 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, 2003, 19(2):305-306 (PubMed)
  54. 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):207-215 (PubMed)

  Review Papers (Japanese)

 

  1. 荒川和晴, “最強生物クマムシの御家騒動とオープンサイエンス”, バイオサイエンスとインダストリー, 2017, 75(2), 150. (Web)
  2. 荒川和晴, “G-language Systemによる生物情報データベース活用法”, 計測と制御, 2014, 53(5), 419-425. (Publisher)
  3. 荒川和晴, “変わりゆく研究者コミュニティと学会の群雄割拠”, 実験医学, 2013, 31(6), 952. (Publisher)
  4. 堀川大樹,阿部 渉.荒川和晴,会津智幸,片山俊明,國枝武和,鈴木 忠,豊田 敦, “研コミュ白書 第4回クマムシ研究者コミュニティー:市民との対話ツールとしてのクマムシ”, 細胞工学, 2012, 31(11). (Web).
  5. 荒川和晴, “生命活動とは何か – 生命情報科学が向うべき道”, 日本バイオインフォマティクス学会ニュースレター, 2012, 25:2-3. (PDF).
  6. 荒川和晴, 入江直樹, 谷上賢瑞, 中村昇太, “研コミュ白書 第3回NGS現場の会:次世代シークエンサーの現場にいる人たちの交流の場”, 細胞工学, 2012, 31(9). (Web).
  7. 荒川和晴, “G-language Project: バイオインフォマティクス研究のためのワークベンチ”, 日本バイオインフォマティクス学会ニュースレター, 2012, 24:4-5 (PDF).
  8. 八谷剛史、入江直樹、荒川和晴, “Close Up 実験法:次世代シークエンサー活用術”, 実験医学, 2011, 7月号
  9. 荒川和晴, “次世代バイオインフォマティクスツールを目指して -G-language Project-“, 日本バイオインフォマティクス学会ニュースレター, 2006, 12:3-4 (PDF).

 

  Books

 

  1. “水の生き物(学研の図鑑LIVE)”, 武田正倫 監修, 学研, 2016(Amazon)
  2. “オープンソースで学ぶバイオインフォマティクス”, オープバイオ研究会編, 東京電機大学出版, 2008(Amazon)
  3. “Metabolomics – The Frontier of Systems Biology”, 共著, Springer-Verlag, 2005:211-220 (Amazon)
  4. “メタボローム研究の最前線”, 共著, シュプリンガー・フェアラーク, 2003:191-197 (Amazon)

 

 

  Books (Translations)

 

  1. “RとBioconductorを用いたバイオインフォマティクス”, 共著, シュプリンガー・フェアラーク, 2007, ISBN 978-4-431-73464-2 (Amazon)

 

  Educational Tools

  1. “ミクロモンスターLED内臓ズーム顕微鏡&調査キット”, 学研教育出版, 2015 (Amazon)