Publications 

 

  1. Bino T, Goto Y, Maryu G, Arakawa K, Aoki K, “ Possible roles of CAHS proteins form Tardigrade in osmotic stress tolerance in mammalian cells”, Cell Struct Funct, 2024, in Press. (PubMed) 
  2. Nakamura H, Ito Y, Sato R, Chi H, Sato C, Watanabe Y, Arakawa K, “ Correlating Mechanical Properties and Sequence Motifs in Artificial Spider Silk by Targeted Motif Substitution”, ACS Biomater Sci Eng, 2024, in Press. (PubMed)

  3. Ikeda H, Oshibuchi K, Yang J, Fukuda S, Arakawa K, “ Complete genome sequence of Bulleidia sp. 10714-15 isolated from human colon cancer patients”, Microbiol Resour Announc, 2024, 0:e00937-24. (Publisher)
  4. Yamamoto PK, Fujimoto Y, Warashina T, Arakawa K, “Complete genome sequences of two Paenibacillus isolated from pegmatite in Fukushima, Japan”, Microbiol Resour Announc, 2024, 0:e00938-24. (Publisher)
  5. Ito L, Masui M, Galipon J, Arakawa K, “Complete genome sequence of polylactic acid degrading Rhodopseudomonas palustris strain R1 isolated from rice field soil”, Microbiology Resource Announcements, 2024,0:e00814-24. (Publisher)
  6. Takahashi H, Warashina T, Takahashi Y, Tanaka M, Suzuki K, Morita T, Arakawa K, “Complete genome sequence of Serratia plymuthica SWSY-3.47”, Microbiology Resource Announcements, 2024,0:e00815-24. (Publisher)
  7. Ichimura R, Tanaka K, Nakato G, Fukuda S, Arakawa K, “Complete genome sequence of Mediterraneibacter gnavus strain RI1, isolated from human feces”, Microbiology Resource Announcements, 2024,0:e00863-24. (Publisher)
  8. Ishikawa S, Tanaka S, Arakawa K, “Search for putative gene regulatory motifs in CAHS3, linked to anhydrobiosis in a tardigrade Ramazzottius varieornatus, in vivo and in silico”, Genes to Cells, 2024, inPress. (Publisher)
  9. Craig H.C, Malay A.D, Hayashi F, Mori M, Arakawa K, Numata  K, “Posttranslational modifications in spider silk influence conformation and dimerization dynamics”, MRS Bulletin, 2024, inPress. (Publisher)
  10. Sugiura K, Yoshida Y, Hayashi K, Arakawa K, Kunieda T, Matsumoto M, “Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome”, Zoological Letters, 2024,10, 11. (Publisher)
  11. Yoshida Y, Hirayama A, Arakawa K, “Transcriptome analysis of the tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin”, Proc Jpn Acad Ser B Phys Biol Sci, 2024,100(7):414-428. (PubMed) 
  12. Miyake A, Harada S, Sugiyama D, Matsumoto M, Hirata A, Miyagawa N, Toki, R, Edagawa S, Kuwabara K, OkamuraT, Sato A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Arakawa K, Takebayashi T, Iida M, “Reliability of Time-Series Plasma Metabolome Data over 6 Years in a Large-Scale Cohort Study”, Metabolites, 2024, 14(1):77. (Publisher)
  13. Kato S, Yuzawa S, Takeda T, Arakawa K, “Complete genome sequence of Kitasatospora aureofaciens Tü117”, Microbiology Resource Announcements, 2024, 13(2):e01014-23. (Publisher)
  14. Michalczyk Ł,  Gross V, Arakawa K, “Progress in research on water bears presented at the 15th International Symposium on Tardigrada (Kraków, 22nd–26th of August 2022)”, Zoological Journal of the Linnean Society, 2024, 200(1):1–11. (Publisher)
  15. Fleming J, Pisani D, Arakawa K, “The evolution of temperature and desiccation-related protein families in Tardigrada reveals the complex acquisition of extremotolerance”, Genome Biology and Evolution, 2023, 16(1):evad217.(PubMed)
  16. Naruki M, Watanabe A, Warashina T, Morita T, Arakawa K, “Complete genome sequence of Limnobacter thiooxidans CS-K2T, isolated from freshwater lake sediments in Bavaria, Germany”, Microbiology Resource Announcements, 2023,14:e00992-23. (Publisher)
  17. Oshibuchi K, Yang J, Obana N, Fukuda S, Arakawa K, “Complete genome sequence of Solobacterium moorei JCM 10645T isolated from a human stool sample”, Microbiology Resource Announcements, 2023,14:e00965-23. (Publisher)
  18. Kawashima T, Watanabe Y, Arakawa K, “Complete genome sequence of Actinoplanes sichuanensis strain 03-723T”, Microbiology Resource Announcements, 2023, 14:e00662-23. (Publisher)
  19. Tanaka S, Arakawa K, “Reply to Tanaka and Kunieda: Control protein GFP also shows a mesh-like structure in desiccating tardigrade cells”, PNAS, 2023, 120(48):e2316451120. (PubMed)
  20. Suzuki Y, Fukazawa A, Sugawara K, Galipon J, Arakawa K, “Complete genome sequence of PETase type IIa-harboring Marinobacter nanhaiticus D15-8W, isolated from a South China Sea sediment”, Microbiology Resource Announcements, 2023, e00868-23. (Publisher)
  21. Sato A, Arakawa K, Kakui K, “Two new species in Leptocheliidae (Crustacea: Peracarida: Tanaidacea) from Japan, with notes on their phylogenetic position and aspects of morphology”, Zoologischer Anzeiger, 2023, 306:51-68. (Publisher)
  22. Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomar Y, Yoda T, Nakagawa S, “Nondomain biopolymers: Flexible molecular strategies to acquire biological functions”, Genes to Cells, 2023, 28(8):539-552. (Publisher)
  23. Nakamura H, Kono N, Mori M, Masunaga H, Numata K, Arakawa K, “Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk”, Biomacromolecules, 2023, 24(5):2042-2051. (PubMed)
  24. Watanabe Y, Arakawa K, “Molecular mechanisms of the high performance of spider silks revealed through multi-omics analysis”, Biophysics and Physicobiology, 2023, e200014. (Publisher)
  25. Arakawa K, “A Nanopore Sequencing Course for Graduate School Curriculum”, Methods Mol. Biol, 2023, 2632:113-127. (PubMed)
  26. Takasuka K, Arakawa K, “The Method of Eliminating the Wolbachia EndosymbiontGenomes from Insect Samples Prior to a Long-Read Sequencing”, Methods Mol. Biol, 2023, 2632:101-112. (PubMed)
  27. Arakawa K, “Ultralow-Input Genome Library Preparation for Nanopore Sequencing with Droplet MDA”, Methods Mol. Biol, 2023, 2632:91-100. (PubMed)
  28. Tanaka S, Aoki K, Arakawa K, “In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada”, PNAS, 2023, 120(5): e2216739120. (Publisher)
  29. Arakawa K, Kono N, Malay A.D, Tateishi A, Ifuku N, Masunaga H, Sato R, Tsuchiya K, Ohtoshi R, Pedrazzoli D, Shinohara A, Ito Y, Nakamura H, Tanikawa  A, Suzuki Y, Ichikawa T, Fujita S, Fujiwara M, Tomita M, Blamires S.J, Chuah J-A, Craig H, Foong C.P, Greco G, Guan J, Holland C, Kaplan D.L, Sudesh K, Mandal B.B, Norma-Rashid.Y, Oktaviani N.A, Preda R.C, Pugno N.M, Rajkhowa R, Wang X, Yazawa K, Zheng Z, Numata K, “1000 spider silkomes: Linking sequences to silk physical properties”, Science Advances, 2022, 8(41):eabo604. (Publisher)
  30. Huang M, Miura MC, Inoue R, Sato A, Kamezaki K, Tomita M, Mori M, Arakawa K, Kanai A, “Dataset for proteomic analysis of Escherichia coli before and after severe heat shock stress”, Journal of Proteome Data and Methods, 2022, 4:1. (Publisher)
  31. Iwai H, Mori M, Tomita M, Kono N, Arakawa K, “Molecular Evidence of Chemical Disguise by the Socially Parasitic Spiny Ant Polyrhachis lamellidens (Hymenoptera: Formicidae) When Invading a Host Colony”, Frontiers in Ecology and Evolution, 2022, 10:915517. (Publisher)
  32. Yoshida Y, Tanaka S, “Deciphering the Biological Enigma—Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki”, Insects,  2022, 13(6):557. (Publisher)
  33. Ishikawa S, Huang M, Tomita A, Kurihara Y, Watanab R, Iwai H, Arakawa K, “Complete Genome Sequences of Four Bacteria Isolated from the Gut of a Spiny Ant (Polyrhachis lamellidens)”, Microbiology Resource Announcements, 2022, e00333-22. (Publisher)
  34. Takeda T, Fukumitsu N, Yuzawa S, Arakawa K, “Complete Genome Sequence of Streptomyces albus Strain G153”, Microbiology Resource Announcements, 2022, e00332-22. (Publisher)
  35. Yoshida Y, Satoh T, Ota C, Tanaka S, Horikawa D.D, Tomita M, Kato Koichi, Arakawa K, “Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades”, BMC Genomics, 2022, 23, 405. (Publisher)
  36. Kurihara Y, Iwai H, Kono N, Tomita M, Arakawa K, “Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment”, Biol Open, 2022, 11(3): bio058956. (Publisher)
  37. Miyazawa K, Itoh S.G, Yoshida Y, Arakawa K, Okumura H, “Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence”, J. Phys. Chem. B, 2022, 126 (12): 2361-2368. (Publisher)
  38. Arakawa K, “Examples of Extreme Survival: Tardigrade Genomics and Molecular Anhydrobiology”, Annual Review of Animal Biosciences, 2022, 10: 17-33. (Publisher)
  39. Kono N, Ohtoshi R, Malay A.D, Mori M, Masunaga H, Yoshida Y, Nakamura H,Numata K,  Arakawa K “Darwin’s bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression”, Open Biol, 2021, 11(12): 210242. (Publisher)
  40. Kakui K, Fleming J.F, Mori M, Fujiwara Y, Arakawa K “Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk”, Genome Biology and Evolution, 2021, 13(12):e281. (Publisher)
  41. Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K, Arakawa K “ Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada”, BMC Genomics, 2021, 22, 813. (Publisher)
  42. Yagi-Utsumi M, Aoki K, Watanabe H, Song C, Nishimura S, Satoh T, Yanaka S,  Ganser C, Tanaka S, Schnapka V, Goh E.W, Furutani Y, Murata K, Uchihashi T, Arakawa K, Kato K “Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade”, Sci Rep, 2021, 11:21328. (Publisher)
  43. Kono N, Nakamura H, Ohtoshi R, Arakawa K, “Transcriptomic data during development of a two-spotted cricket Gryllus bimaculatus”, Data in Brief, 2021, 38:107388. (Publisher)
  44. Iwai H, Kurihara Y, Kono N, Tomita M, Arakawa K, “The evidence of temporary social parasitism by Polyrhachis lamellidens (Hymenoptera, Formicidae) in a Camponotus obscuripes colony (Hymenoptera, Formicidae)”, Insectes Sociaux, 2021, 68:375-382 . (Publisher)
  45. Miyazawa K, Itoh S.G, Watanabe H, Uchihashi T, Yanaka S, Yagi-Utsumi M, Kato K, Arakawa K, Okumura H, “Tardigrade Secretory-Abundant Heat-Soluble Protein Has a Flexible β-Barrel Structure in Solution and Keeps This Structure in Dehydration”, J. Phys. Chem. B, 2021, 125 (32): 9145-9154. (Publisher)
  46. Kono N, Nakamura H, Mori M, Yoshida Y, Ohtoshi R, Malay A.D, Pedrazzoli Moran DA, Tomita M, Numata K,  Arakawa K, “Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk”, PNAS, 2021, 118(31): e2107065118. (Publisher)
  47. Watanabe Y, Takeuchi N, Yang J, Obana N, Morinaga K, Kusada H, Tamaki H, Fukuda S, Arakawa K, “Complete Genome Sequence of Atopobiaceae Bacterium Strain P1, Isolated from Mouse Feces”, Microbiology Resource Announcements, 2021, 10(28):e00627-21. (Publisher)
  48. Watanabe Y, Arakawa K, “Complete Genome Sequences of Two Lysobacter Strains, Isolated from Seawater (Lysobacter caseinilyticus) and Soil (Lysobacter helvus) in South Korea”, Microbiology Resource Announcements, 2021, 10(28):e00337-21. (Publisher)
  49. Fleming J.F, Pisani D, Arakawa K, “New Tardigrade Opsins and Differential Expression Analyses shows ontogenic variation in light perception”, Genome Biology and Evolution, 2021, 13(8):evab164.(PubMed)
  50. Takahashi H, Yang J, Yamamoto H, Fukuda S, Arakawa K, “Complete Genome Sequence of Adlercreutzia equolifaciens subsp. celatus DSM 18785”, Microbiology Resource Announcements, 2021, 10(19): e00354-21. (Publisher)
  51. Yoshida Y, Horikawa DD, Sakashita T, Yokota Y, Kobayashi Y, Tomita M, Arakawa K, “RNA sequencing data for gamma radiation response in the extremotolerant tardigrade Ramazzottius varieornatus”, Data in Brief, 2021, 36:107111. (Publisher)
  52. Fujiwara M, Kono N, Hirayama A, Malay A.D, Nakamura H, Ohtoshi R, Numata K, Tomita M, Arakawa K, “Xanthurenic Acid Is the Main Pigment of Trichonephila clavata Gold Dragline Silk”, Biomolecules, 2021, 11(4):563. (Publisher)
  53. Warashina T, Yamamura S, Suzuki H, Amachi S, Arakawa K, “Complete Genome Sequence of Geobacter sp. Strain SVR, an Antimonate-Reducing Bacterium Isolated from Antimony-Rich Mine Soil”, Microbiology Resource Announcements, 2021, 10(14):e00142-21. (Publisher)
  54. Berger C.A, Brewer M.S, Kono N, Nakamura H, Arakawa K, Kennedy S.R, Wood H.M, Adams S.A, Gillespie R.G, “Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders”, BMC Ecology and Evolution, 2021, 21(1):48. (PubMed)
  55. Arakawa K, Mori M, Kono N, Suzuki T, Gotoh T, Shimano S, “Proteomic evidence for the silk fibroin genes of spider mites (order Trombidiformes: Family Tetranychidae)”, Journal of Proteomics, 2021, 239:104195. (Publisher)
  56. Nishimura K, Ikarashi M, Yasuda Y, Sato M, Guerrero MC, Galipon J, Arakawa K, “Complete Genome Sequence of Sphingomonas paucimobilis Strain Kira, Isolated from Human Neuroblastoma SH-SY5Y Cell Cultures Supplemented with Retinoic Acid”, Microbiology Resource Announcements, 2021, 10(6):e01156-20. (PubMed)
  57. Arakawa K, Numata K, “Reconsidering the “glass transition” hypothesis of intrinsically unstructured CAHS proteins in desiccation tolerance of tardigrades”, Molecular Cell, 2021, 81(3):409-410. (Publisher)
  58. Fleming J.F, Arakawa K, “Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019)”, Zoologica Scripta, 2021, 50(3): 376-382. (Publisher)
  59. Stec D, Krzywański Ł, Arakawa K, Michalczyk Ł, “A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada)”, Zoological Lett, 2020, 6:2. (PubMed)
  60. Malay A.D, Suzuki T, Katashima T, Kono N, Arakawa K, Numata K, “Spider silk self-assembly via modular liquid-liquid phase separation and nanofibrillation”, Science Advances, 2020, 6(45):eabb6030. (Publisher)
  61. Kono N, Nakamura H, Mori M, Tomita M, Arakawa K, “Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies”, Scientific Reports, 15721(2020). (Publisher)
  62. Kondo K, Mori M, Tomita M, Arakawa K, “Pre‐treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris”, FEBS Open Bio, 2020,10(9):1774-1781. (Publisher)
  63. Sakata R. C, Ishiguro S, Mori H, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H, Yachie N, “Base editors for simultaneous introduction of C-to-T and A-to-G mutations”, Nature Biotechnology, 2020, 38(7):865-869. (Publisher)
  64. Inoue H, Shibata S, Ii K, Inoue J, Fukuda S, Arakawa K, “Complete Genome Sequence of Bifidobacterium longum Strain Jih1, Isolated from Human Feces”, Microbiology Resource Announcements, 2020, 9(22):e00319-20. (Publisher)
  65. Kurihara Y, Kawai S, Ayano Sakai, Galipon J, Arakawa K, “Complete Genome Sequence of Halomonas meridiana Strain Eplume2, Isolated from a Hydrothermal Plume in the Northeast Pacific Ocean”, Microbiology Resource Announcements, 2020, 9(20):e00330-20. (Publisher)
  66. Seo K, Tanaka K, Fukuda S, Arakawa K, “Complete Genome Sequences of Two Cutibacterium acnes Strains Isolated from an Orthopedic Surgical Site”, Microbiology Resource Announcements, 2020, 9(17):e00290-20. (Publisher)
  67. Sugiura K, Arakawa K, Matsumoto M, “Distribution of Macrobiotus shonaicus Stec, Arakawa & Michalczyk, 2018 (Tardigrada: Eutardigrada: Macrobiotidae) in Japan”ZooTaxa, 2020, 4767(1):56-70. (Publisher)
  68. Takahashi Y, Takahashi H, Galipon J, Arakawa K, “Complete Genome Sequence of Halomonas meridiana Strain Slthf1, Isolated from a Deep-Sea Thermal Vent”, Microbiology Resource Announcements, 2020, 9(16):e00292-20. (Publisher)
  69. Murai Y, Masuda T,Onuma Y,Yamamoto D.E,Takeuchi N,Mori H,Masuyama N,Ishiguro S, Yachie N, Arakawa K, “Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment”, Microbiology Resource Announcements, 2020, 9(16):e00291-20. (Publisher)
  70. Takeyama N,Huang M,Sato K, Galipon J, Arakawa K, “Complete Genome Sequence of Halomonas hydrothermalis Strain Slthf2, a Halophilic Bacterium Isolated from a Deep-Sea Hydrothermal-Vent Environment“, Microbiology Resource Announcements, 2020, 9 (15):e00294-20. (Publisher) 

  71. Arakawa K,“Simultaneous Metabarcoding of Eukaryotes and Prokaryotes to Elucidate the Community Structures within Tardigrade Microhabitats”, Diversity, 2020, 12(3):110. (Publisher)

  72. Mapalo MA, Arakawa K, Baker CM, Persson DK, Mirano-Bascos D, Giribet G, “The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across Ecdysozoa”, G3(Bethesda), 2020 Jan 22, 10(3):1137-1148. (PubMed)

  73. Yoshida Y, Sugiura K, Tomita M, Matsumoto M, Arakawa K, “Comparison of the transcriptomes of two tardigrades with different hatching coordination”, BMC Development Biology,  2019, 19(1):24. (Publisher) 

  74. Kondo K, Mori M, Tomita M, Arakawa K, “AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential upregulator is PP2A”, Genes to Cells, 2019, 24(12):768-780. (Publisher)

  75. Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RB, “Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii”, Molecular Ecology, 2019, 28(17):3977-3993. (Publisher)

  76. Yoshida Y, Novel RW, Arakawa K, Baxter M, “Horizontal Gene Transfer in Metazoa: Examples and Methods”, Horizontal Gene Transfer, 2019, 203-226.(Publisher)

  77. Masuda T, Kono N, Tomita M, Arakawa K, “Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coligenomes”, Bio-protocol, 2019, 9(15): e3329. (Publisher)

  78. Kono N, Nakamura H, Ohtoshi R, Pedrazzoli Moran DA, Shinohara A, Yoshida Y, Fujiwara M, Mori M, Tomita M, Arakawa K, “Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue”, Scientific Reports 9, 8380(2019). (Publisher)

  79. Nagata S, Ii KM, Tsukimi T, Miura MC, Galipon J, Arakawa K, “Complete genome sequence of Halomonas olivaria, a moderately halophilic bacterium isolated from olive processing effluents, obtained by nanopore sequencing”, Microbiol Resour Announc, 2019, 8:e00144-19. (Publisher)

  80. Saito M, Nishigata A, Galipon J, Arakawa K, “Complete Genome Sequence of Halomonas sulfidaeris Strain Esulfide1 Isolated from a Metal Sulfide Rock at a Depth of 2,200 Meters, Obtained Using Nanopore Sequencing”, Microbiol Resour Announc, 2019, 8(23):e00327-19. (Publisher)

  81. Kono N, Arakawa K, “Nanopore sequencing: Review of potential applications in functional genomics”, Develop Growth Differ, 2019; 00: 1– 11. (Publisher)
  82. Kono N, Nakamura H, Ohtoshi R, Tomita M, Numata K, Arakawa K, “The bagworm genome reveals a unique fibroin gene that provides high tensile strength”,Communications Biology 2, Article number: 148 (2019). (Publisher)
  83. Evans-Yamamoto D, Takeuchi N, Masuda T, Murai Y, Onuma Y, Mori H, Masuyama N, Ishiguro S, Yachie N, Arakawa K, ” Complete genome sequence of Psychrobacter sp. strain KH172YL61, isolated from deep-sea sediments in the Nankai Trough, Japan”,  Microbiol Resour Announc, 2019, 8:e00326-19. (Publisher)
  84.  Sugiura K, Minato H, Suzuki AC,  Arakawa K, Kunieda T, Matsumoto M, “Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada)”, Zoological Science 36(2), (12 April 2019). (Publisher)
  85. Ohshima Y, Kono N, Yokota Y, Watanabe S, Sasaki I, Ishioka NS, Sakashita T, Arakawa K, “Anti-tumor effects and potential therapeutic response biomarkers in a-emitting meta–211At-astato-benzylguanidine therapy for malignant pheochromocytoma explored by RNA-sequencing.” Theranostics 2019; 9(6):1538-1549. (Publisher)
  86.  Ii KM, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K, “Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert”, J Genomics 2019; 7:18-25. (Publisher)
  87.  Fleming J, Kristensen R, Sørensen Martin, Park T, Arakawa K, Blaxter M, Rebecchi L, Guidetti R, Williams T, Roberts N, Vinther J, Pisani D, “Molecular palaeontology illuminates evolution of ecdysozoan vision”, Proceedings of the Royal Society B, 2018, 285(1892):2180.(Publisher)
  88. Kono N, Tomita M, Arakawa K, “Accelerated laboratory evolution reveals the influence of replication on the GC skew in Escherichia coli”, Genome Biology and Evolution, 2018, evy237. (Publisher)
  89. Arakawa K*, Kono N, Ohtoshi R, Hiroyuki N, Tomita M, “The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae)”, Mitochondrial DNA B Resour, 2018, 3(2):812-813. (Publisher)
  90. Arakawa K* “The complete mitochondrial genome of Echiniscus testudo (Heterotardigrada: Echiniscidae)”, Mitochondrial DNA B Resour, 2018, 3(2):810-811. (Publisher)
  91. Yoshida Y, Konno S, Nishino R, Murai Y, Tomita M, Arakawa K*, “Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen”, J. Vis. Exp., 2018, 137:e57615. (Publisher)
  92. Stec D, Arakawa K*, Michalczyk Ł, “An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group”, PLoS ONE, 2018, 13(2): e0192210. (Publisher)
  93. Ohta T, Kawashima T,  Shinozaki NO, Dobashi A, Hiraoka S, Hoshino T, Kanno K, Kataoka T, Kawashima S, Matsui M, Nemoto W,  Nishijima S, Suganuma N, Suzuki H, Taguchi Y-h, Takenaka Y, Tanigawa Y, Tsuneyoshi M, Yoshitake K, Sato Y, Yamashita R, Arakawa K, Iwasaki W, “Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago”, J. Plant Res., 2018, 131(4):709-717. (Publisher)
  94. Kono N, Tomita M, Arakawa K, “eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria” BMC Genomics, 2017 18:784. (Publisher)
  95. Malay AD,  Arakawa K, Numata K, “Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins” PloS One, 2017,12(8):e0183397. (PubMed)
  96. Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, Ishino K, Komine S, Kunieda T, Tomita M, Blaxter M, Arakawa K, “Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus”, PLoS Biol, 2017, 15(7):e2002266. (PubMed)
  97. 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)
  98. Iwai H, Horikawa 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)
  99. 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)
  100. Arakawa K*, Yoshida Y, Tomita M, “Genome sequencing of a single tardigrade Hypsibius dujardini individual”, Scientific Data, 2016, 3:160063. (PubMed)
  101. Arakawa K*, “No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade”, PNAS, 2016, 113(22):E3057. (PubMed)
  102. 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)
  103. 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)
  104. Horikawa DD, Arakawa K, “Tardigrades – Ultimate animals surviving extreme environments”, SFC Journal, 2015, 15(1), 246-260. (Publisher)
  105. Oshita K, Tomita M, Arakawa K*, “G-Links: a gene-centric link acquisition service”, F1000 Research, 2015, 3:285. (PubMed)
  106. 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)
  107. 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)
  108. Kono N, Arakawa 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)
  109. Arakawa K*, Tomita M, “Genome Analysis Workshop: a Personal Genomics class at Keio SFC”, Keio SFC Journal, 2014, 14(1):158-177. (Publisher)
  110. 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)
  111. 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)
  112. Arakawa K, “Comparative metabolomics of anhydrobiosis in tardigrade Ramazzottius varieornatus”, Journal of Japanese Society for Extremophiles, 2013, 11(2), 75-82. (Publisher)
  113. Arakawa K, Tomita M, “Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation”, Methods Mol. Biol. 2013, 985:459-470. (PubMed)
  114. 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)
  115. 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)
  116. 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)
  117. BioHackathon 2010, “The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies”, Journal of Biomedical Semantics, 2013, 4:6. (Publisher)
  118. 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)
  119. Kono N, Arakawa K*, Tomita M, “Validation of bacterial replication termination models using simulation of genomic mutations”, PLoS One, 2012, 7(4): e34526. (PubMed)
  120. Arakawa K*, Tomita M, “Measures of Compositional Strand Bias Related to Replication Machinery and its Applications”, Current Genomics, 2012, 13(1):4-15. (PubMed)
  121. BioHackathon 2009, “The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications”, Journal of Biomedical Semantics, 2011, 2:4. (PubMed)
  122. Toya Y, Kono N, Arakawa K*, Tomita M, “Metabolic flux analysis and visualization”, Journal of Proteome Research, 2011, 10(8):3313-3323. (PubMed)
  123. 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)
  124. Kono N, Arakawa K*, Tomita M, “Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes”, BMC Genomics, 2011, 12(1):19. (PubMed)
  125. BioHackathon2008, “The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows”, Journal of Biomedical Semantics, 2010, 1:8. (PubMed)
  126. 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)
  127. 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)
  128. Kono N, Arakawa 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)
  129. 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)
  130. 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)
  131. Arakawa K, Yachie N, Tomita M, “Visualizing Complex Omics Information – Scientific Visualization for Genomics and Systems Biology”, BIOforum Europe 2008, 6:27-29 (PDF).
  132. Arakawa K*, Suzuki H, Tomita M, “Computational Genome Analysis Using The G-language System”, Genes, Genomes and Genomics, 2008, 2(1): 1-13.(PDF)
  133. 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)
  134. 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)
  135. 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)
  136. 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)
  137. 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)
  138. 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)
  139. 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)
  140. 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).
  141. Arakawa K, Tomita M, “Large-scale Modeling for Systems Biology”, BIOforum Europe, 2006, 10:54-55 (PDF).
  142. 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)
  143. Kono N, Arakawa K*, Tomita M, “MEGU: Pathway mapping web-service based on KEGG and SVG”, In Silico Biology, 2006, 6(6):621-655. (PubMed).
  144. 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).
  145. 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)
  146. 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)
  147. 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)
  148. 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)
  149. 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)
  150. 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. 田中冴, 荒川和晴, “最強生物クマムシの乾眠メカニズムの解席“, Keio SFC Journal, 2023, 22(2), 178-190. (Publisher)
  2. 荒川和晴, “クモ1,000種の解析からクモ糸高機能発現メカニズムを解明する“, 実験医学, 2023, 41(4), 580-584. (Publisher)
  3. 荒川和晴, “生物材料・生体機能発現と液‒液相分離: クマムシ乾眠とクモの糸”, 生化学, 2022, 94(4), 537-547. (Web).
  4. 荒川和晴, “クモ糸高機能発現メカニズムの解明：人工クモ糸の強度を倍化するSpiCEの発見”, 生物物理, 2022, 62(3), 181-183. (Web).
  5. 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)
  6. 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)
  7. 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)
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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
  13. 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. “都市とアートとイノベーション―創造性とライフスタイルが描く都市未来“, 共著, 幻冬舎, 2024, ISBN:9784344041981 (紀伊國屋書店)
  2. “SFCバイオの軌跡“, 荒川和晴(編), KEIO SFC JOURNAL, 2023, 22(2). (Publisher)
  3. “新種発見！ 見つけて、調べて、名付ける方法“, 共著, 山と渓谷社, 2022, ISBN-13: 978-4635063203 (Amazon)
  4. “実験医学別冊　最強のステップUPシリーズ ロングリードWET&DRY解析ガイド　シークエンスをもっと自由に！“, 編集, 羊土社, 2021, ISBN-13: 978-4-7581-2253-5 (Publisher)
  5. “Nanopore Sequencing Methods and Protocols”, 荒川和晴, Springer Nature, 2023(SpringerLink)
  6. “ロングリードWET&DRY解析ガイド　シークエンスをもっと自由に！”, 荒川和晴 宮本真理編 ,羊土社, 2021(実験医学online)
  7. “次世代シークエンサーDRY解析教本 単行本”, 清水厚志 坊農秀雅  (著, 編集), 学研メディカル秀潤社, 2019(Amazon)
  8. “どこでも　誰でも　より長く　ナノポアシークエンサーが研究の常識を変える！”, 荒川和晴 企画, 2018(実験医学online)
  9. “人工知能学大辞典”, 人工知能学会 編, 共立出版, 2017 (Amazon)
  10. “水の生き物（学研の図鑑LIVE）”, 武田正倫 監修, 学研, 2016(Amazon)
  11. “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)
  12. “Metabolomics – The Frontier of Systems Biology”, 共著, Springer-Verlag, 2005:211-220 (Amazon)
  13. “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)