User:Aritalab/Masanori Arita/Publication

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Contents

Refereed Journal Articles

  1. Ohbuchi K, Sakurai N, Kitagawa H, Sato M, Suzuki H, Kushida H, Nishi A, Yamamoto M, Hanazaki K, Arita M "Differential annotation of converted metabolites (DAC-Met): Exploration of Maoto (Ma-huang-tang)-derived metabolites in plasma using high-resolution mass spectrometry" Metabolomics 16(5), 63, 2020 (PubMed, Google Scholar )
  2. Kaminuma E, Baba Y, Mochizuki M, Matsumoto H, Ozaki H, Okayama T, Kato T, Oki S, Fujisawa T, Nakamura Y, Arita M, Ogasawara O, Kashima H, Takagi T "DDBJ Data Analysis Challenge: A Machine Learning Competition to Predict Arabidopsis Chromatin Feature Annotations From DNA Sequences" Genes & Genetic Systems 95(1), 43-50, 2020 (PubMed, Google Scholar )
  3. Tada I, Tsugawa H, Meister I, Zhang P, Shu R, Katsumi R, Wheelock CE, Arita M, Chaleckis R “Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics” Metabolites 9(11), 251, 2019 (PubMed, Google Scholar )
  4. Tsugawa H, Satoh A, Uchino H, Cajka T, Arita M, Arita M "Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics" Metabolites 9(6): E119, 2019 (PubMed, Google Scholar )
  5. Maeno S, Tanizawa Y, Kajikawa A, Kanesaki Y, Kubota E, Arita M, Dicks L, Endo A "Pseudofructophilic Leuconostoc citreum strain F192-5, isolated from satsuma mandarin peel" Applied and Environmental Microbiology, 85(20), e01077-19, 2019 (PubMed, Google Scholar )
  6. Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P “Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.” Systematic and Applied Microbiology 42(6), 126017, 2019 (PubMed, Google Scholar )
  7. Modesto M, Satti M, Watanabe K, Sciavilla P, Felis GE, Sandri C, Spiezio C, Arita M, Mattarelli P "Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada)" International Journal of Systematic and Evolutionary Microbiology, 69(10), 3041-3048, 2019 (PubMed, Google Scholar )
  8. Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Cammà C, Michelini S, Sgorbati B, Mattarelli P "Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus)" International Journal of Systematic and Evolutionary Microbiology 69(8), 2477-2485, 2019 (PubMed, Google Scholar )
  9. Tsugawa H, Nakabayashi R, Mori T, Yamada Y, Takahashi M, Rai A, Sugiyama R, Yamamoto H, Nakaya T, Yamazaki M, Kooke R, Bac-Molenaar JA, Oztolan-Erol N, Keurentjes JJB, Arita M, Saito K "A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms" Nature Methods 16(4), 295-298, 2019 (PubMed, Google Scholar )
  10. Lipidomics Standards Initiative Consortium “Lipidomics needs more standardization” Nature Metabolism 1, 745-747, 2019 (PubMed, Google Scholar )
  11. Sato M, Arita M, Kawashima T “Uncovering Ecdysozoa-specific Sphingomyelin Synthase by Phylogenetic Analysis of Metazoan Sequences” Zoological Science 36(4), 316-321, 2019 (PubMed, Google Scholar )
  12. Itoh H, Matsui M, Miyamura Y, Takeda I, Ishii J, Kumagai T, Machida M, Shibata T, Arita M "Biosynthesis of Novel Statins by Combining Heterologous Genes from Xylaria and Aspergillus" ACS Synthetic Biology, 7(12), 2783-2789, 2018 (PubMed, Google Scholar )
  13. Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR "MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines" Journal of Lipid Research, 59(10), 2001-2017, 2018 (PubMed, Google Scholar )
  14. Tanizawa Y, Tada I, Kobayashi H, Endo A, Maeno S, Toyoda A, Arita M, Nakamura Y, Sakamoto M, Ohkuma M, Tohno M "Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses" International journal of systematic and evolutionary microbiology 68: 3512-3517, 2018 (PubMed, Google Scholar )
  15. Tanaka W, Arita M "Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry" Mass Spectrometry (Tokyo), 7(1):A0066, 2018 (PubMed, Google Scholar )
  16. Itoh H, Miura A, Matsui M, Arazoe T, Nishida K, Kumagai T, Arita M, Tamano K, Machida M, Shibata T "Knockout of the SREBP system increases production of the polyketide FR901512 in filamentous fungal sp. No. 14919 and lovastatin in Aspergillus terreus ATCC20542" Applied Microbiology and Biotechnology, 102(3):1393-1405, 2018 (PubMed, Google Scholar )
  17. Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O "Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics" Nature Methods 15:53-56, 2018 (PubMed, Google Scholar )
  18. Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M, Arita M, Ohkuma M, Kobayashi H "Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage" International Journal of Systematic and Evolutionary Microbiology 67(9):3639-3644, 2017 (PubMed, Google Scholar )
  19. Tanizawa Y, Kobayashi H, Kaminuma E, Sakamoto M, Ohkuma M, Nakamura Y, Arita M, Tohno M "Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri" Bioscience of microbiota food and health 36(3):129-134, 2017 (PubMed, Google Scholar )
  20. Tada I, Tanizawa Y, Endo A, Tohno M, Arita M "Revealing the genomic differences between two subgroups in Lactobacillus gasseri" Bioscience of microbiota food and health 36(4):155-159, 2017 (PubMed, Google Scholar )
  21. Tsugawa H, Ikeda K, Tanaka W, Senoo Y, Arita M, Arita M "Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library" Journal of Cheminformatics 9:19, 2017 doi: 10.1186/s13321-017-0205-3 (PubMed, Google Scholar )
  22. Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O "SPLASH, a hashed identifier for mass spectra" Nature Biotechnol 34(11):1099-1101, 2016 (PubMed, Google Scholar )
  23. Padermshoke A, Ogawa T, Nishio K, Nakazawa M, Nakamoto M, Okazawa A, Kanaya S, Arita M, Ohta D "Critical Involvement of Environmental Carbon Dioxide Fixation to Drive Wax Ester Fermentation in Euglena" PLoS ONE 11(9):e0162827, 2016 (PubMed, Google Scholar )
  24. Maeno S, Tanizawa Y, Kanesaki Y, Kubota E, Kumar H, Dicks L, Salminen S, Nakagawa J, Arita M, Endo A "Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation" Syst Appl Microbiol 39(8):516-526, 2016 (PubMed, Google Scholar )
  25. Yamada O, Machida M, Hosoyama A, Goto M, Takahashi T, Futagami T, Yamagata Y, Takeuchi M, Kobayashi T, Koike H, Abe K, Asai K, Arita M, Fujita N, Fukuda K, Higa KI, Horikawa H, Ishikawa T, Jinno K, Kato Y, Kirimura K, Mizutani O, Nakasone K, Sano M, Shiraishi Y, Tsukahara M, Gomi K "Genome sequence of Aspergillus luchuensis NBRC 4314" DNA Research 23(6):507-515, 2016 (PubMed, Google Scholar )
  26. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M "DFAST and DAGA: web-based integrated genome annotation tools and resources" Biosci Microbiota Food Health. 35(4):173-184, 2016 (PubMed, Google Scholar )
  27. Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M. "Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software" Analytical Chemistry 88(16):7946-7958, 2016 (PubMed, Google Scholar )
  28. Sriyudthsak K, Mejia RF, Arita M, Hirai MY. "PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems" Nucleic Acids Research, 44(W1):W205-211, 2016 (PubMed, Google Scholar )
  29. Mukaida S, Ogawa T, Ohishi K, Tanizawa Y, Ohta D, Arita M. "The effect of rapamycin on biodiesel-producing protist Euglena gracilis" Biosci Biotechnol Biochem, 80:1223-1229, 2016 (PubMed, Google Scholar )
  30. Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S "Data standards can boost metabolomics research, and if there is a will, there is a way" Metabolomics 12(1):14, 2016 (PubMed, Google Scholar )
  31. Endo A, Tanizawa Y, Tanaka N, Maeno S, Kumar H, Shiwa Y, Okada S, Yoshikawa H, Dicks L, Nakagawa J, Arita M "Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp." BMC Genomics 16(1):1117, 2015 (PubMed, Google Scholar )
  32. Tanaka K, Arita M, Sakurai H, Ono N, Tezuka Y "Analysis of Chemical Properties of Edible and Medicinal Ginger by Metabolomics Approach" Biomed Research International 2015:671058, 2015 (PubMed, Google Scholar )
  33. Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis" Nature Methods 12(6), 523-526, 2015 (PubMed, Google Scholar )
  34. Li D, Ono N, Sato T, Sugiura T, Altaf-Ul-Amin M, Ohta D, Suzuki H, Arita M, Tanaka K, Ma Z, Kanaya S "Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species" Plant Cell Physiology, 56(5), 843-851, 2015 (PubMed, Google Scholar )
  35. Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N "Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses" Frontiers in Bioengineering and Biotechnology, 3:38, 2015 (PubMed, Google Scholar )
  36. Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M "Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage" BMC Genomics, 16:240, 2015 (PubMed, Google Scholar )
  37. Tanaka K, Arita M, Li D, Ono N, Tezuka Y, Kanaya S "Metabolomic Characterization of a Low Phytic Acid and High Anti-oxidative Cultivar of Turmeric" Natural Product Communications, 10(2), 329-334, 2015 (PubMed, Google Scholar )
  38. Tsugawa H, Ohta E, Izumi Y, Ogiwara A, Yukihira D, Bamba T, Fukusaki E, Arita M "MRM-DIFF: Data Processing Strategy for Differential Analysis in Large Scale MRM-based Lipidomics Studies" Frontiers in Genetics, 5:471, 2015 (PubMed, Google Scholar )
  39. Hasegawa Y, Arita M "Optimal implementations for reliable circadian clocks" Physical Review Letters, 113(10), 108101, 2014 (PubMed, Google Scholar )
  40. Tsugawa H, Kanazawa M, Ogiwara A, Arita M "MRMPROBS suite for metabolomics using large-scale MRM assays" Bioinformatics, 30(16), 2379-2380, 2014 (PubMed, Google Scholar )
  41. Furuhashi T, Ogawa T, Nakai R, Nakazawa M, Okazawa A, Padermschoke A, Nishio K, Hirai MY, Arita M, Ohta D "Wax ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry: toward understanding of wax ester fermentation under hypoxia" Metabolomics, 11(1), 175-183, 2015 (PubMed, Google Scholar )
  42. Ogawa T, Furuhashi T, Okazawa A, Nakai R, Nakazawa M, Kind T, Fiehn O, Kanaya S, Arita M, Ohta D "Exploration of Polar Lipid Accumulation Profiles in Euglena gracilis Using LipidBlast, a MS/MS Spectral Library Constructed in Silico" Bioscience Biotechnology and Biochemistry 78(1), 14-18, 2014 (PubMed, Google Scholar )
  43. Hasegawa Y, Arita M "Circadian clocks optimally adapt to sunlight for reliable synchronization" Journal of the Royal Society Interface 11(92):20131018, 2014 (PubMed, Google Scholar )
  44. Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E "MRMPROBS: Data Assessment and Metabolite Identification Tool for Large-scale MRM-based Widely Targeted Metabolomics" Analytical Chemistry, 85(10), 5191–5199, 2013 (PubMed, Google Scholar )
  45. Hasegawa Y, Arita M "Enhanced entrainability of genetic oscillators by period mismatch" Journal of the Royal Society Interface 10(81) 20121020, 2013 (PubMed, Google Scholar )
  46. Hasegawa Y, Arita M "Fluctuating noise drives Brownian transport" Journal of the Royal Society Interface 9(77), 3554-3363, 2012 (PubMed, Google Scholar )
  47. Peng CH, Lin SH, Peng SC, Lyu PC, Arita M, Tang CY "Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast" Comparative and Functional Genomics 2012(653174), 2012 (PubMed, Google Scholar )
  48. Lin SH, Yoshimoto M, Lyu PC, Tang CY, Arita M "Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species" Journal of Evolutionary Bioinformatics, 7:1-14, 2012 (PubMed, Google Scholar )
  49. Hasegawa Y, Arita M "Escape Process and Stochastic Resonance Under Noise Intensity Fluctuation" Physics Letters A, 375, 3450-3458, 2011 (PubMed, Google Scholar )
  50. Redestig H, Kusano M, Ebana K, Kobayashi M, Oikawa A, Okazaki Y, Matsuda F, Arita M, Fujita N, Saito K "Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics" BMC Systems Biology 5(1):176, 2011 (PubMed, Google Scholar )
  51. Tsugawa H, Tsujimoto Y, Arita M, Bamba T, Fukusaki E "GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA)" BMC Bioinformatics 12:131, 2011 (PubMed, Google Scholar )
  52. Scalbert A, Andres-Lacueva C, Arita M, Kroon P, Manach C, Urpi-Sarda M, Wishart D "Databases on Food Phytochemicals and Their Health-Promoting Effects" Journal of Agricultural and Food Chemistry 59(9), 4331-4348, 2011 (PubMed, Google Scholar )
  53. Hasegawa Y, Arita M "Noise-intensity fluctuation in Langevin model and its higher-order Fokker–Planck equation" Physica A 390(6) 1051-1063, 2011 (PubMed, Google Scholar )
  54. Tanaka K, Hayashi K, Fahad A, Arita M "Multi-stage mass spectrometric analysis of saponins in glycyrrhiza radix" Natural Product Communications 6(1):7-10, 2011 (PubMed, Google Scholar )
  55. Kusano M, Redestig H, Hirai T, Oikawa A, Matsuda F, Fukushima A, Arita M, Watanabe S, Yano M, Hiwasa-Tanase K, Ezura H, Saito K "Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment" PLoS One 6(2):e16989, 2011 (PubMed, Google Scholar )
  56. Fukushima A, Kusano M, Redestig H, Arita M, Saito K "Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach" BMC Systems Biology 5:1, 2011 (PubMed, Google Scholar )
  57. Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T "MassBank: a public repository for sharing mass spectral data for life sciences" Journal of Mass Spectrometry 45(7), 703-714, 2010 (PubMed, Google Scholar )
  58. Redestig H, Kusano M, Fukushima A, Matsuda F, Saito K, Arita M "Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis" BMC Bioinformatics 11:214, 2010 (PubMed, Google Scholar )
  59. Hasegawa Y, Arita M "Bistable stochastic processes in the q-exponential family" Physica A 389(21):4450-4461, 2010 (PubMed, Google Scholar )
  60. Takemoto K, Arita M "Nested structure acquired through simple evolutionary process" Journal of Theoretical Biology 264(3), 782-786, 2010 (PubMed, Google Scholar )
  61. Morioka R, Arita M, Sakamoto K, Kawaguchi S, Tei H, Horimoto K "Period–phase map: two-dimensional selection of circadian rhythm-related genes" IET System Biology 3(6), 487-495, 2009 (PubMed, Google Scholar )
  62. Fukushima A, Kanaya S, Arita M "Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach" Plant Biotechnology 26, 485-493, 2009 (PubMed, Google Scholar )
  63. Redestig H, Fukushima A, Stenlund H, Moritz T, Arita M, Saito K, Kusano M "Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data" Analytical Chemistry 81(19), 7974-7980, 2009 (PubMed, Google Scholar )
  64. Hasegawa Y, Arita M "Properties of the maximum q-likelihood estimator for independent random variables" Physica A 388, 3399-3412, 2009 (PubMed, Google Scholar )
  65. Takemoto K, Arita M "Heterogeneous distribution of metabolites across plant species" Physica A 388(13), 2771-2780, 2009 (PubMed, Google Scholar )
  66. Arita M "A pitfall of wiki solution for biological databases" Briefings Bioinformatics 10(3), 295-296, 2009
    Interview article by a web magazine "Bioinform" in Jan 2009 (PubMed, Google Scholar )
  67. Fukushima A, Wada M, Kanaya S, Arita M "SVD-based anatomy of gene-expression for correlation analysis in Arabidopsis thaliana" DNA research 15(6), 367-374, 2008 　 (PubMed, Google Scholar )
  68. Arita M, Suwa K "Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database" BMC BioData Mining 1:7, 2008 　 (PubMed, Google Scholar )
  69. Sato S, Arita M, Soga T, Nishioka T, Tomita M "Time-resolved metabolomics reveals metabolic modulation in rice foliage" BMC Systems Biology 2:51, 2008 (PubMed, Google Scholar )
  70. Kusano M, Fukushima A, Arita M, Jonsson P, Moritz T, Kobayashi M, Hayashi N, Tohge T, Saito K "Unbiased characterization of genotype-dependent metabolic regulations by metabolo mic approach in Arabidopsis thaliana" BMC Systems Biology 1:53, 2007 (PubMed, Google Scholar )
  71. Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O "Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns" Bioinformatics 22(10), 1211-1216, 2006 (PubMed, Google Scholar )
  72. Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O "Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes" Gene 364, 53-62, 2005 (PubMed, Google Scholar )
  73. Arita R, Arita M, Kawai M, Mashima Y, Yamada M "Evaluation of corneal endothelial pump function with a cold stress test" Cornea 24(5), 571-575, 2005 (PubMed, Google Scholar )
  74. Sugimoto M, Kikuchi S, Arita M, Soga T, Nishioka T, Tomita M "Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks" Analytical Chemistry 77(1), 78-84, 2005 (PubMed, Google Scholar )
  75. Arita M, Ohashi Y "Secret signatures inside genomic DNA" Biotechnology Progress 20(5), 1605-1607, 2004 (PubMed, Google Scholar )
  76. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K "Integration of transriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana" Proceedings of the National Academy of Sciences USA 101(27), 10205-10210, 2004 (PubMed, Google Scholar )
  77. Arita M "Computational resources for metabolomics" Briefings in Functional Genomics and Proteomics 3(1), 84-93, 2004 (PubMed, Google Scholar )
  78. Arita M "Comma-free design for DNA words" Communications of the ACM, 47(5), 99-100, 2004 (PubMed, Google Scholar )
  79. Arita M "The metabolic world of Escherichia coli is not small" Proceedings of the National Academy of Sciences USA 101(6), 1543-1547, 2004 (PubMed, Google Scholar )
  80. Yamazaki Y, Kitajima M, Arita M, Takayama H, Sudo H, Yamazaki M, Aimi N, Saito K "Biosynthesis of camptothecin. In silico and in vivo tracer study from [1-13C]glucose" Plant Physiology 134(1), 161-170, 2004 ([1-13Cglucose%22 PubMed], [1-13Cglucose%22 Google Scholar] )
  81. Arita M "In silico Atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism" Genome Research 13(11), 2455-2466, 2003 (PubMed, Google Scholar )
  82. Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M "Dynamic modeling of genetic networks using genetic algorithm and S-system" Bioinformatics 19(5), 643-650, 2003 (PubMed, Google Scholar )
  83. Arita M, Kobayashi S "DNA sequence design using templates" New Generation Computing 20(3), 263-277, 2002 (PubMed, Google Scholar )
  84. Arita M "Graph modeling of metabolism" Journal of Japanese Society for Artificial Intelligence (JSAI), 15(4), 703-710, 2000 (PubMed, Google Scholar )
  85. Arita M "Metabolic reconstruction using shortest paths" Simulation Practice and Theory 8(2), 109-125, 2000 (PubMed, Google Scholar )
  86. Shimada T, Hagiya M, Arita M, Nishizaki S, Tan CL "Knowledge based simulation of regulatory action lambda phage" International Journal of Artificial Intelligence Tools 4(4), 511-524, 1995 (PubMed, Google Scholar )

Refereed Conference Proceedings

  1. Noureen M, Tada I, Kawashima T, Arita M “Rearrangement analysis of multiple bacterial genomes” BMC Bioinformatics 20 (Proceedings GIW 2019 in Australia; Suppl 23), 631, 2019 (PubMed, Google Scholar )
  2. Satti M, Tanizawa Y, Endo A, Arita M "Comparative analysis of probiotic bacteria based on a new definition of core genome" Journal of Bioinformatics and Computational Biology (Proceedings GIW 2017), 16(3):1840012, 2018 (PubMed, Google Scholar )
  3. Tada I, Tanizawa Y, Arita M "Visualization of consensus genome structure without using a reference genome" BMC Genomics (Proceedings APBC 2017), 18(Suppl 2):208, 2017 (PubMed, Google Scholar )
  4. Arita M, Yoshimoto M, Suwa K, Hirai A, Kanaya S, Shibahara N, Tanaka K “Database for crude drugs and kampo medicine” Genome Informatics 25(1) Special Issue JSBi2010, 1-11, 2011 (PubMed, Google Scholar )
  5. Chang CW, Lyu PC, Arita M "Reconstructing phylogeny from metabolic substrate-product relationships" BMC Bioinformatics (Proceedings 9th APBC in Korea) 12(Suppl 1):S27, 2011 (PubMed, Google Scholar )
  6. Arita M, Suwa K, Yoshimoto M, Hirai A, Kanaya S "Ontology checking and integration of crude-drug and kampo information" Proceedings of the 2nd International Conference of Biomedical Engineering and Informatics (BMEI2009), Tianjin China, 3:1304-1307, 2009 (PubMed, Google Scholar )
  7. Horai H, Arita M, Ojima Y, Nihei Y, Kanaya S, Nishioka T "Traceable analysis of multiple-stage mass spectra through precursor-product annotations" Proceedings of German Conference in Bioinformatics (GCB'09) (GI-Edition Lecture Notes in Informatics), Halle, Germany, 157:173-178, 2009 (PubMed, Google Scholar )
  8. Morioka R, Arita M, Sakamoto K, Kawaguchi S, Tei H, Horimoto K "Phase shifts of circadian transcripts in rat suprachiasmatic nucleus" Proceedings of the 2nd International Symposium on Optimization and Systems Biology (OSB2008), Lijiang China, 101-106, 2008 (PubMed, Google Scholar )
  9. Chen LC, Lin YC, Arita M, Tseng VS "A Novel Approach for Handling Missing Values in Microarray Data" Proceedings of the International Computer Symposium (ICS2008) Taipei, 45-50, 2008 (PubMed, Google Scholar )
  10. Wijekoon A, Kusano M, Arita M "Comparison of Gas Chromatography-Mass Spectrometry Data from Different Laboratories using Dynamic Programming" Proceedings of the International Computer Symposium (ICS2008) Taipei, 57-62, 2008 (PubMed, Google Scholar )
  11. Horai H, Arita M, Nishioka T "Comparison of ESI-MS Spectra in MassBank Database" Proceedings of the International Conference on BioMedical Engineering and Informatics (BMEI2008), Hainan China, 1:853-857, 2008 (PubMed, Google Scholar )
  12. Arita M, Tokimatsu T "Detection of monosaccharide types from coordinates" Proceedings of the 18th International Conference on Genome Informatics (Genome Informatics Series Vol.19), Singapore, 3-14, 2007 (PubMed, Google Scholar )
  13. Okada K, Asai K, Arita M "Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions." Proceedings of 5th Asia Pacific Bioinformatics Conference (APBC2007), Hong Kong, 2007 (PubMed, Google Scholar )
  14. Tuji H, Altaf-Ul-Amin Md, Arita M, Nishio H, Shinbo Y, Kurokawa K, Kanaya S "Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms" IPSJ Transactions on Bioinformatics, 47 (SIG17):31-41, 2006 (PubMed, Google Scholar )
  15. Oka H, Arita M "Searching Similar Motifs in Protein Interaction Networks" Proceedings of 1st International Workshop on Biomedical Data Engineering, Tokyo Japan, 52-59, 2005 (PubMed, Google Scholar )
  16. Ueno Y, Arita M, Kumagai T, Asai K "Processing sequence annotation data using the lua programming language" Proceedings of 14th Genome Informatics Workshop (Genome Informatics Series Vol.14), Yokohama Japan, 154-163, 2003 (PubMed, Google Scholar )
  17. Arita M, Tsuda K, Asai K "Modeling splicing sites with pairwise correlations." Bioinformatics (Proceedings 1st European Conference on Computational Biology, Saarbrucken Germany), 18:S27-S34, Oxford Univ Press, 2002 (PubMed, Google Scholar )
  18. Kobayashi S, Kondo T, Arita M "On template method for DNA sequence design" Proceedings of 8th DNA Based Computers, Sapporo Japan, LNCS(2568) 205-214, Springer Verlag, 2002 (PubMed, Google Scholar )
  19. Arita M, Kobayashi S "The power of sequence design" Proceedings of 4th International Conference on Computational Intelligence and Multimedia Applications, Yokosuka Japan, 163-166, IEEE Press, 2001 (PubMed, Google Scholar )
  20. (Journal version listed above, titled "DNA sequence design using templates.") (PubMed, Google Scholar )
  21. Komiya K, Sakamoto K, Gouzu H, Yokoyama S, Arita M, Nishikawa A, Hagiya M "Successive state transitions with I/O interface by molecules." Proceedings of 6th DNA Based Computers, Leiden Netherland, LNCS(2054) 17-26, Springer Verlag, 2001 (PubMed, Google Scholar )
  22. Arita M, Nishikawa A, Hagiya M, Komiya K, Gouzu H, Sakamoto K "Improving sequence design for DNA computing" Proceedings of 5th Gnenetic and Evolutionary Computation Conference (GECCO'00), Las Vegas USA, 875-882, Morgan-Kaufmann, 2000 (PubMed, Google Scholar )
  23. Arita M, Asai K, Nishioka T "Reconstructing metabolic pathways with new enzyme classification" Proceedings of German Conference in Bioinformatics (GCB'00), Heidelberg Germany, 99-106, Logos-Verlag, 2000 (PubMed, Google Scholar )
  24. Arita M "Bio-computing in the 21st century" Proceedings of 5th International Symposium on Artificial Life and Robotics (AROB'00), Ohita Japan, 737-740, 2000 (PubMed, Google Scholar )
  25. Arita M "Metabolic reconstruction using shortest path algorithm" Proceedings of 1st Conference on Modelling and Simulation in Biological, Medical, and Biomedical Engineering (BioMedSim'99), Paris France, 1-4, 1999 (PubMed, Google Scholar )
  26. (Journal version listed above, titled "Metabolic reconstruction using shortest paths.") (PubMed, Google Scholar )
  27. Ueno Y, Asai K, Arita M "Integrating application programs for bioinformatics using a web browser" Proceedings of 10th Genome Informatics Workshop (Genome Informatics Series Vol.10), Tokyo Japan, 166-175, 1999 (PubMed, Google Scholar )
  28. Arita M, Asai K, Nishioka T "Finding precursor compounds in secondary metabolism" Proceedings of 10th Genome Informatics Workshop (Genome Informatics Series Vol.10), Tokyo Japan, 113-120, 1999 (PubMed, Google Scholar )
  29. Hagiya M, Arita M, Kiga D, Sakamoto K, Yokoyama S "Towards parallel evaluation and learning of boolean mu-formulas with molecules" (PubMed, Google Scholar )
  30. DNA Based Computers III, H Rubin and DH Wood (editors), DIMACS series in Discrete Mathematics and Theoretical Computer Science, 48:57-72, American Mathematics Society, 1999 (PubMed, Google Scholar )
  31. Morimoto N, Arita M, Suyama A "Solid phase DNA solution to the Hamiltonian path problem" DNA Based Computers III, H Rubin and DH Wood (editors), DIMACS series in Discrete Mathematics and Theoretical Computer Science, 48:193-206, American Mathematics Society, 1999 (PubMed, Google Scholar )
  32. Arita M, Hagiya M, Suyama A "Joining and rotating data with molecules" Proceedings of IEEE 4th International Conference on Evolutional Computation (ICEC'97), Indianapolis USA, 243-248, IEEE Press, 1997 (PubMed, Google Scholar )
  33. Arita M, Suyama A, Hagiya M "A heuristic approach for Hamiltonian path problem with molecules" Proceedings of 2nd Annual Conference on Genetic Programming, Stanford USA, 457-462, Morgan Kaufmann, 1997 (PubMed, Google Scholar )
  34. Morimoto N, Arita M, Suyama A "Stepwise generation of Hamiltonian path with molecules" Proceedings of 1st International Conference on Biocomputing and Emergent Computation (BCEC'97), Skovde Sweden, 184-192, World Scientific, 1997 (PubMed, Google Scholar )
  35. Shimada T, Hagiya M, Arita M, Nishizaki S, Tan CL "Knowledge based simulation of regulatory action lambda phage" Proceedings of 1st International IEEE Symposium on Intelligence in Neural and Biological Systems (INBS '95), Washington DC. USA, 92-99, IEEE Press, 1995 (PubMed, Google Scholar )
  36. (Journal version listed above, with the same title.) (PubMed, Google Scholar )
  37. Arita M "SIMFLY2: simulation of a fly embryo" Proceedings of 6th Genome Informatics Workshop, Tokyo Japan, 29-38, Universal Academy Press, 1995 (PubMed, Google Scholar )
  38. Arita M, Hagiya M, Shiratori T "GEISHA SYSTEM: an environment for simulating protein interaction" Proceedings of 5th Genome Informatics Workshop, Tokyo Japan, 80-90, Universal Academy Press, 1994 (PubMed, Google Scholar )

Reviews, Editorials, Book Chapters

  1. Tanizawa Y, Fujisawa T, Arita M, Nakamura Y "Generating Publication-Ready Prokaryotic Genome Annotations with DFAST" Methods in Molecular Biology, 1962, 215-226, 2019 (PubMed, Google Scholar )
  2. Endo A, Tanizawa Y, Arita M "Isolation and Identification of Lactic Acid Bacteria from Environmental Samples" Methods in Molecular Biology, 1887, 3-13, 2019 (PubMed, Google Scholar )
  3. Endo A, Maeno S, Tanizawa Y, Kneifel W, Arita M, Dicks L, Salminen S "Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes" Applied and Environmental Microbiology, 84(19), 2018 (PubMed, Google Scholar )
  4. Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O "Identification of small molecules using accurate mass MS/MS search" Mass Spectrometry Reviews, 37(4):513-532, 2018 doi: 10.1002/mas.21535 (PubMed, Google Scholar )
  5. Carroll AJ, Salek RM, Arita M, Kopka J, Walther D. "Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends" Frontiers in Bioengineering and Biotechnology, 4:63, 2016 (PubMed, Google Scholar )
  6. Salek RM, Arita M, Dayalan S, Ebbels T, Jones AR, Neumann S, Rocca-Serra P, Viant MR, Vizcaino JA. "Embedding standards in metabolomics: the Metabolomics Society data standards task group" Metabolomics, 11(4), 782-783, 2015 (PubMed, Google Scholar )
  7. Arita M "From metabolic reactions to networks and pathways" Methods in Molecular Biology 804:93-106, Springer Verlag, 2012 (File:FromReactionsToPathways.pdf) (PubMed, Google Scholar )
  8. Arita M, Hagiya M, Takinoue M, Tanaka F "DNA Memory" In Handbook of Natural Computing (Volume II, Molecular Computation), Springer Verlag, 2011 (PubMed, Google Scholar )
  9. Arita M "What can metabolomics learn from genomics and proteomics?" Current Opinion in Biotechnology 20, 610-615, 2009 (PubMed, Google Scholar )
  10. Fukushima A, Kusano M, Redestig H, Arita M, Saito K "Integrated omics approaches in plant systems biology" Current Opinion in Chemical Biology 13, 532–538, 2009 (PubMed, Google Scholar )
  11. Arita M, Fujiwara Y, Nakanishi Y "Map Editor for the Atomic Reconstruction of Metabolism (ARM)" Chapter II.3 In Plant Metabolomics (Eds. K Saito, RA Dixon, L Willmitzer) Biotechnology in Agriculture and Forestry Vol.57, Springer Verlag, 129-140, 2006 (PubMed, Google Scholar )
  12. Shinbo Y, Nakamura Y, Altaf-Ul-Amin Md, Asahi H, Kurokawa K, Arita M, Saito K, Ohta D, Shibata D, Kanaya S "KNApSAcK: A Comprehensive Species-Metabolite Relationship Database" Chapter II.6 In Plant Metabolomics (Eds. K Saito, RA Dixon, L Willmitzer) Biotechnology in Agriculture and Forestry Vol.57, Springer Verlag, 165-184, 2006 (PubMed, Google Scholar )
  13. Arita M "Scale-freeness and biological networks" Journal of Biochemistry, 138, 1-4, Oxford Univ Press, 2005 (PubMed, Google Scholar )
  14. Arita M, Robert M, Tomita M "All systems go: launching cell simulation fueled by integrated experimental biology data" Current Opinion in Biotechnology, 16(3), 344-349, Elsevier, 2005 (PubMed, Google Scholar )
  15. Arita M "Introduction to the ARM Database: Database on Chemical Transformations in Metabolism for Tracing Pathways" Chapter 13 (pp.193-211) In Metabolomics: The Frontier of Systems Biology (Tomita M and Nishioka T eds.) Springer verlag, 2005 (PubMed, Google Scholar )
  16. Arita M "Writing Information Into DNA" In Aspects of Molecular Computing (Jonoska N, Paun G, and Rozenberg G eds.), LNCS(2950), 23-35, Springer Verlag, 2004 (File:WritingInformationIntoDNA.pdf) (PubMed, Google Scholar )

総説、書籍

研究以外の連載や本はこちらを御覧ください。

  1. 有田正規、遠藤 明仁, 多田 一風太, 谷沢 靖洋, 遠野 雅徳「データベースから発見されたガセリ菌のサブグループ」化学と生物, 56(7), 459-460, 2018
  2. 有田正規、津川裕司　「化学とメタボロミクス」 化学, 72(2), 26-30, 2017
  3. 津川裕司、有田正規　「生体内の低分子代謝産物を網羅的に捉えるための新技術」化学と生物, 54(3), 151-153, 2016
  4. 有田 正規,...,望月 敦史(代表) 計11名「数学協働プログラム提言　数理生命科学」 文部科学省 科学技術試験研究委託事業「数理・生命科学」WG（統計数理研究所） 12/26, 2014
  5. 美宅 成樹ほか　「大容量情報時代の次世代生物学」 日本学術会議 報告 (バイオインフォマティクス分科会), 9/17, 2014
  6. 有田 正規「理系総合のための生命科学 第3版」羊土社 2013 (27章 生物情報科学)
  7. 有田 正規（編）「使えるデータベース・ウェブツール」実験医学別冊 9月 29(15), 羊土社, 2011
  8. 有田 正規 「代謝産物の検索に役立つデータベース：化合物の素性・素行を調べるウェブサイト」 実験医学9月号 Vol.28(14), 2301-2303, 2010
  9. 有田 正規, 蓬莱 尚幸, 尾嶌 雄也, 二瓶 義人, 金谷 重彦, 西岡 孝明 「化合物情報とマススペクトルを活用するためのウェブ基盤」 CICSJ Bulletin, 27(2), 48-50, 日本化学会 情報化学部会, 2009
  10. 有田正規, 諏訪和大 「Wikiによるフラボノイドのデータベース」実験医学増刊,「バイオデータベースとソフトウェア最前線」, 4月, 1148-1154, 羊土社, 2008
  11. 福島敦史, 草野都, 有田正規, 斉藤和季 「植物メタボロミクス―代謝プロファイルからシステム解析へ」 実験医学, 1月号, 羊土社, 2008
  12. 有田正規　「生体ネットワークをどう研究するべきか」　数理科学5月号(527)79-83, サイエンス社, 2007
  13. 時松敏明, 有田正規　「代謝マップビューワで見るフラボノイド」　細胞工学, 25(12), 1388-1393, 2006
  14. 小林徹也, 有田正規, 森下喜弘, 合原一幸 「細胞内現象のシステム的理解―今理論に何が求められているのか？」 システム/制御/情報 50(8), システム制御情報学会誌 2006
  15. 杉峰伸明, 大塚一路, 有田正規, 合原一幸「ネットワーク的思考で生命現象をよみとく」（特集「意識・脳・身体の接続へ」）科学 76(3), 岩波書店 2006
  16. 有田 正規 「スケールフリーにご用心」 蛋白質核酸酵素 12月号増刊「ゲノムから生命システムへ」50(16 Suppl), 2294-2299, 共立出版, 2005
  17. 有田 正規、田口 良 「メタボロームによる脂質代謝パスウェイ解析」 実験医学増刊号 「ダイナミックに新展開する脂質研究 」23(6), 151-157, 羊土社, 2005
  18. 有田 正規 「代謝マップを電子化するARMプロジェクト」CICSJ Bulletin, 22(4), 64-67, 日本化学会 情報化学部会, 2004
  19. 有田 正規 「代謝ネットワークの解析法」 バイオインダストリー 特集「システム生物学の最前線」21(9), 34-39, シーエムシー出版, 2004
  20. 有田 正規 「ARMデータベース」（執筆分担） 冨田勝、西岡孝明（編） 「メタボローム研究の最前線」, シュプリンガー東京, 2003
  21. 有田 正規 「代謝の電子化と高分子への応用」 炎症と免疫 11(6), 46-51, 先端医学社 2003
  22. 有田 正規 「代謝の電子化プロジェクト」 蛋白質核酸酵素 48(7), 823-828, 共立出版, 2003
  23. 有田 正規 「代謝は原子レベルで記述しよう －電子化の意義と将来性－」 JITAニュース March, 16-19, 日本産業技術振興協会, 2003
  24. 有田 正規 「ベイジアンネットとバイオインフォマティクス」 人工知能学会誌 17(5), 539-545, 2002
  25. 有田 正規 「代謝の電子化と有用物質の生産」 実験医学 9月号 1868-1872, 羊土社, 2002
  26. 「DNAコンピュータ」（執筆分担。第4章配列設計担当） 萩谷昌己、横森貴（編）, 培風館, 148-164, 2002
  27. 有田 正規 「代謝ネットワークの情報解析」 日本計算工学会誌 6(1), 10-12, 2001
  28. 有田 正規 「パスウェイマップの探索」 日本シミュレーション学会誌, vol.20(2), 16-20, 2001
  29. 萩谷 昌己, 有田 正規 「分子計算とその物理的基礎」 日本物理学会誌, Vol.56, 6月号, 403-410, 2001
  30. 有田 正規 「遺伝子ネットワークと確率モデル」 ベイジアンネットチュートリアル予稿集 (BN2001), 50-53, 2001
  31. 有田 正規 「グラフで見る代謝」 IPSJ Symposium Series Vol.2000, No.5, 149-156, 2000
  32. 西川 明男, 有田 正規, 三好 直人, 萩谷 昌己 「DNA計算の塩基配列設計におけるバランスの指標について」 IPSJ Symposium Series Vol.2000, No.16, 67-69, 2000
  33. 有田 正規, 西岡 孝明 「生体内化学反応の階層分類」 バイオインダストリー 特集「バイオインフォマティクス」, 17(7), 45-50, シーエムシー出版 2000 (再掲: DNAチップ応用技術 II 第6章, 227-236, シーエムシー出版 2001)
  34. 有田 正規 「DNA計算における配列設計」 数理科学 特集「分子コンピューティング」, No.445 七月号, 32-38, サイエンス社 2000 (再掲：数理科学 SGCライブラリ31 「分子コンピュータの現状と展望」 萩谷昌己編著, II章3, サイエンス社 2004)
  35. 有田 正規 「代謝系の再構築」（執筆分担。第4章の1担当） ポストシークエンスのゲノム科学シリーズ 「ゲノム情報生物学」 高木利久、冨田勝（編）, 148-164, 中山書店 2000
  36. 角野宏司, 有田正規, 萩谷昌己, 白取知樹 「Computing-as-Editing(CAEP)に基づいた数式処理システムのユーザ・インタフェース」 インタラクティブシステムとソフトウェアIII, レクチャーノート/ソフトウェア学, 12, 161-170, 近代科学社 1995

Invited Talks and Lectures

¢ ... support of hotel & participation fee only

  1. Arita M "Data sharing and the power of omics integration" 6th Global Forum of Leaders for Agricultural Science and Technology (GLAST), Chengdu, China, Nov 12 (12-14), 2019
  2. Arita M, Noureen M "Consensis genome structure and cluster analysis strains from NAG" Helicobacter pylori Genome Project workshop, National Cancer Institute (NCI), Rockville, USA, 26 Aug (26-27), 2019
  3. Arita M "Cheminformatics for Predicting Structures from Mass Spectra" 1st Annual Conference of Chinese Society of Metabolomics (plenary), Shanghai, China, 20 Apr (19-21), 2019
  4. Arita M "Open genome analysis in the post-genomic era" International Workshop on Data Science, Mishima, 15 Nov (12-15), 2018
  5. Arita M "Computational Metabolomics" 6th Annual Korea Metabolomics Society (plenary), Seoul, Korea, 6 Apr (5-6), 2018
  6. Arita M "Distribution of Glycosphingolipids Revealed by LipidBank" International Life Science Integration Workshop, Tokyo, 5 Mar (5-6), 2018 ¢
  7. Arita M "Identifying Metabolites with Theoretical References" The 26th International KOGO Annual Conference (plenary), Seoul, Korea, 6 Sep (6-8), 2017
  8. Arita M "Prediction of Molecular Structures from their Spectra" The 4th International Conference on Plant Metabolism (ICPM 2017), 17 Jul (16-20), 2017
  9. Arita M "Computational Mass Spectrometry" SLING workshop `Mass spectrometry-based lipidomics of human blood plasma' National University of Singapore, 2 May, 2017 (teleconference talk)
  10. Arita M "Comprehensive Acquisition of MS/MS Spectra Benefits Database Research" 6th International Singapore Lipid Symposium, 1 Dec (Nov30-Dec1), 2015 ¢
  11. Arita M "Impact of Metabolome Database in Plant Science" The 38th Naito Conference "Molecule-based biological systems", 8 Oct (7-10), Sapporo, Japan, 2014
  12. Arita M "MassBank Past, Present and Future" Norman Massbank Workshop, 17 Sep (17-18), Duebendorf, Switzerland, 2014 (no travel support)
  13. Arita M "Genetic, Protein, and Metabolic Networks: Which Choice Is Amenable to Modelling" International Conference on Mathematical Modeling and Applications (ICMMA 2013), 28 Nov (26-28), Tokyo, Japan, 2013
  14. Arita M "Cyberinfrastructure for metabolomics and synthetic biology" International Symposium on Biotechnology for Green Growth, 24 Oct (24-26), Kobe, Japan, 2012 ¢
  15. Arita M "What can metabolomics learn from genomics and proteomics?" International Conference of Research and Application on Traditional Complementary and Alternative Medicine (TCAM), 22 June (21-23), Muhammadiyah University of Surakarta (Indonesia), 2012
  16. Arita M "Update on Lipid Databank and other lipidomics initiatives" EMBL-EBI Industry Programme & MetaboLights Project Workshop, 22 May, Hinxton, 2012
  17. Arita M "Wiki-based Databases: Integration of knowledge through the web" C-NAIR Seminar Nasional, Gadjah Mada University (Indonesia) 5 Dec, 2011 (no travel support)
  18. Arita M "Structural Classification for PKS in Aspergilli" IUMS2011 (International Union of Microbiological Societies Congress), 9 Sep (6-10), Sapporo, 2011 (no travel support)
  19. Arita M "Knowledge Management using a Wiki-based System and its Application to Mass Spectra" EBI Seminar, 19 Apr, EBI, Hinxton UK, 2011
  20. Arita M "Wiki-based platform for PKS in Aspergilli" Pacifichem, Dec 19 (15-20), Honolulu (Hawaii), 2010 ¢
  21. Arita M "Circulating information and knowledge through a cyber-infrastructure" Mass Spectrometry Informatics in Systems Biology (MSiB) Oct 28-29, Helsinki, 2010 [JSPS Japan-Finland Bilateral Workshop (self-organized)]
  22. Arita M "Integration of Flavonoid Information through Wiki" Satellite Symposium of 4th International Conference on Polyphenols and Health (ICPH2009), Dec 11 (7-11), Yorkshire England, 2009 ¢
  23. Arita M "Web-based Resources for Metabolomics", Tutorial at the CBI-KSBSB joint conference (Bioinfo2009), Nov 4 (4-6), Haeundae Busan Korea, 2009 ¢
  24. Arita M "Data Management of Cross-disciplinary Information using Wiki", 16th International Conference on Cytochrome P450, June 21 (21-25), Okinawa Japan, 2009
  25. Arita M "Metabolic Pathway Analysis using Wiki", The Sixth International Aspergillus Meeting (Asperfest 6), March 15-17, Monterey USA, 2009 ¢
  26. Arita M "Wiki-based Database of Secondary Metabolites", JSPS-KOSEF Joint Seminar -Pioneering researches on fungal molecular biology-, November 19-20, Kanazawa Japan, 2008
  27. Arita M "Computational Analysis of Metabolism" iPlant Mechanistic modeling grand challenge workshop, November 7-10, Biosphere2 Arizona USA, 2008
  28. Arita M "Software Tools to Study Flavonoids", Systems Biology and Bioinformatics Symposium (SBBS07), March 27-29 Taipei Taiwan, 2007
  29. Arita M "Databaes for Flavonoids and Measurement in Arabidopsis", 2nd International Symposium on Environmental Metabolomics, March 24-25, University of Louisville(KY), USA, 2007
  30. Arita M "Metabolic Pathway Chart for Flavonoid", 2nd Taiwan-Japan Bilateral Symposium on Bioinformatics, Nov 7-9, Tainan Taiwan, 2006
  31. Arita M " Atomic-level analysis of metabolism and mass spectral database", Invited Lecture Course, May9-14, Center for Regulatory, Environmental, Analytical Metabolomics, University of Louisville(KY), USA, 2006
  32. Arita M "Metabolomics in Japan and the Need for a Metabolic Map Editor", 1st Japan-Taiwan Bilateral Symposium on Bioinformatics, March 13-17, Tokyo Japan, 2006 ¢
  33. Arita M "ARM Database for Interactive Metabolic Maps", 1st International BioPAX Symposium, November 18, Tokyo Japan, 2005 ¢
  34. Arita M "Map Editor for the Atomic Reconstruction of Metabolism", 1st Louisville Symposium on Environmental Metabolomics, November 5-6, Louisville (KY) USA, 2005
  35. Arita M "Interpretation of Metabolic Networks", 50th NIBB Conference, Structure and Dynamics of Complex Biological Networks, February 8-10, Okazaki Japan, 2005
  36. Arita M "Scale-free Network and Biological Network", Invited Lecture Course, June 9 - 13, Centre National de la Recherche Scientifique, Marseille, France, 2004
  37. Arita M "Computer Applications for Metabolome Analysis", ICSB2002 Satellite Meeting "Metabolome Analysis and Systems Biology", December 16, Stockholm Sweden, 2002 ¢
  38. Arita M "Computer Applications for Comprehensive Metabolite Analysis", Cambridge Healthtech Institute's Second Annual Metabolic Profiling: Pathways in Discovery, December 2 - 3, Research Triangle Park (North Carolina) USA, 2002
  39. Arita M "Atomic Representation of Metabolism", Invited Lecture Course, June26 - July 2, Department of Computer Science, University of Helsinki, Finland, 2002
  40. Arita M "Atomic Reconstruction of Metabolism (ARM) Project", Workshop on Protein Interaction and Clinical Data Analysis, May 28 - 31, National University of Singapore, 2002
  41. Hagiya M. and Arita M "Several Approaches to Bio-simulation", International Symposium on Human Genome Project and Computer Science Sanjo Hall, March 9-10, Tokyo University, 1995 ¢

招待講演、トークイベント

  1. 有田 正規 「バイオインフォマティクスが推し進めるバイオの世界」バイオインフォマティクスフォーラム, 8/24, 那覇, 2019
  2. 有田 正規 「データ時代における学術出版とデータベース」第90回日本医学図書館協会総会, 5/31, 2019
  3. 有田 正規 「学術データは誰のものか」日本医学会第五回研究倫理教育研修会, 5/30, 東京, 2019
  4. 有田 正規 「元素から眺める地球・生命・食事」静岡県保育所連合会東部支部総会, 5/14, 沼津, 2019
  5. 有田 正規 「生薬情報のデータベース」薬用資源の持続的利用促進に関する研究会, 11/21, 草津（滋賀）, 2018
  6. 有田 正規 「遺伝子から見た地球生命」静岡県教育研究会夏季研究大会（理科）, 8/8, 三島, 2018
  7. 有田 正規 「生命科学データ共有のあり方」Japan Open Science Summit, 6/19, 東京, 2018
  8. 有田 正規 「DNAレベルからみたミシマサイコ」ミシマサイコの会 3/24 三島 2018
  9. 有田 正規 「たべものは体の中でどうなるか」三島遺伝学講座 3/4 三島 2018
  10. 有田 正規 「これからのスペクトルデータベース」日本質量分析学会第65回質量分析総合討論会（基調講演） 5/17 つくば 2017
  11. 有田 正規 津川裕司 「MS2スペクトルのフラグメンテーション解析と前駆体構造予測」日本分子生物学会年会 シンポジウム「生命システムを俯瞰するための質量分析情報解析技術とデータベースの活用」 11/30 横浜 2016
  12. 有田 正規 「クリエイティブは毒か薬か」 三島市クリエイティブファクトリー　「うるまの部屋」第一回 9/16 2016
  13. 有田 正規 「Comprehensive lipidomics and Mass/LipidBank databases」日本分子生物・生化学会大会（BMB2015）シンポジウム「リピドミクスから見えてきた脂質の新機能 –基礎から臨床まで-」12/4 神戸 2015
  14. 有田 正規 「科学者から見た学術のオープン化」林和弘氏、有田正規氏講演会「オープンな知がイノベーションを生む -オープンサイエンスの潮流と図書館の可能性-」(東大新図書館トークイベント14) 10/17 東京 2015
  15. 有田 正規 「代謝の杜:分子の食物連鎖」地域イベント伊豆経済大学 9/22 三島 2015
  16. 有田 正規 津川 裕司 「ノンターゲットMS/MSによる藻類脂質の網羅的解析とデータベース化」 健康・長寿研究談話会（旧ホスファチジルセリン研究会）11/7 品川 2014
  17. 有田 正規 "Database for Biology: which data deserve maintaining?" 第52回日本生物物理学会年会 シンポジウム「大容量生命情報時代の新しい生物学とは？」(兼オーガナイザ)　9/27 (25-27) 札幌 2014
  18. 有田 正規 津川 裕司 「藻類メタボロミクス：植物との違い」日本植物学会第78回大会シンポジウム「バイオリソースとゲノム情報から考える藻類研究の未来形」 9/12 (12-14) 東京 2014
  19. 有田 正規 「マススペクトルのデータベースを使いこなす」第31回日本植物細胞分子生物学会　バイオインフォマティクス講習会 9/12 (10-12) 札幌 2013
  20. 有田 正規 「和漢薬データベースの構築」日本薬学会第133年会　シンポジウム "和漢薬の科学基盤：共同研究による先駆的統合的解明" 3/29 (27-30) 横浜 2013
  21. 有田 正規　「ポリケチド合成酵素の進化解析」革新的バイオマテリアル実現のための高機能化ゲノムデザイン技術開発キックオフシンポジウム 10/30 東京 2012
  22. 有田 正規 「Knowledge Management using a Wiki-based System」 細胞を作る研究会 4.0 10/27(-28) 大阪 2011
  23. 有田 正規　「コミュニティとして機能するためのインフラストラクチャ」第84会日本生化学会大会シンポジウム "ゲノムデザインの最前線" 9/22 (21-24) 京都 2011
  24. 有田 正規　「ウェブを通じた生薬知識のアウトリーチ」南方資源利用技術研究会 11/26 那覇 2010
  25. 長谷川禎彦 有田正規 「細胞内のノイズと遺伝子スイッチ」細胞を作る研究会 3.0 11/12(-13) 駒場 2010
  26. 有田 正規 「Wikiを通じて学会をまとめよう　代謝データベースを例に」 第20回記念微生物資源ワークショップ 11/14 (13-14) 修善寺 2009
  27. 有田 正規 「和漢薬の知識流通を促すウェブ基盤の構築」 第30回和漢医薬学総合研究所特別セミナー「和漢薬とインフォマティクス」 10/9, 富山 2009
  28. 有田 正規 「和漢薬Wikiデータベースの開発」 第26回和漢医薬学会学術大会 メインテーマ企画「生薬とデータベース」 8/29 (29-30), 幕張 2009
  29. 有田 正規 「メタボロミクス解析におけるインフォマティクス」 日本薬物動態学会第２回ビジョン・シンポジウム 6/6 (5-6), 本郷 2009
  30. 有田 正規 「Wikiによるマススペクトルの共有と知識抽出」 日本質量分析学会 第57回質量分析総合討論会ワークショップ 「マススペクトルを日本発のツールで解析、整理しよう」 5/14, 大阪 2009
  31. 有田 正規 「Wikiによるオミクスデータ管理と知識発見」 農芸化学会大会シンポジウム「OMICSを基盤とした生物機能の戦略的高度化と物質生産」3/29 福岡 2009
  32. 有田 正規 「百科事典とデータベースを区別できない生物学者」 BMB2008 日本分子生物・生化学会合同年会シンポジウム「最新メタボロミクス事情と植物科学への貢献」(兼オーガナイザ)　 12/12 神戸 2008
  33. 有田 正規 「バイオデータベースのあるべき姿」 第五回　コンビナトリアル・バイオエンジニアリング会議 11/7 大阪 2008
  34. 有田 正規 「メタボロームデータベースを統合する：*Bankと*Wiki」 第2回メタボロームシンポジウム(兼実行委員) 10/30 鶴岡 2008
  35. 有田 正規　「Wiki をもちいたデータベース設計」 高度好熱菌丸ごと一匹プロジェクト 第7回連携研究会 9/13, Spring-8普及棟 2008
  36. 有田 正規 「ウィキによるフラボノイドのデータベース」 日本植物生理学会年会 シンポジウム「データベースの中に築く生物像」 3/20, 札幌 2008
  37. 有田 正規 「化学構造と植物種をつなぐフラボノイドデータベース」 日本化学会 化学と生物学を統合する情報学に関するシンポジウム 12/7, 東京 2007
  38. 有田　正規　「メタボロミクス　－代謝を研究する新しいOmics分野－」 高度好熱菌丸ごと一匹プロジェクト第六回連携研究会　8/4, Spring-8普及棟 2007
  39. 有田 正規 「マススペクトルデータベースMassBankの検索技法」 日本質量分析学会 質量分析総合討論会ワークショップ 「ケミカルバイオロジーとマススペクトルデータベース」 5/15, 広島 2007
  40. 有田　正規 「原子レベルでみる代謝ネットワーク」 京大理　数学教室　研究集会「スケールフリーネットワークとランダムグラフ」　1/27, けいはんな 2007
  41. 有田 正規 「化学構造データベースから代謝経路へ」 奈良先端大 植物科学研究教育推進ユニットワークショップ 「植物研究にいかに役立てるか、『システム生物学』」 12/12, 奈良 2006
  42. 有田 正規 「インタラクティブ代謝マップによるメタボローム解析」 日本医用マススペクトル学会 シンポジウム 「メタボローム解析への質量分析の応用」9/29, 名古屋 2006
  43. 有田　正規　「バクテリアの代謝はどこまでわかっているか」 高度好熱菌丸ごと一匹プロジェクト第五回連携研究会　8/12, Spring-8普及棟 2006
  44. 有田 正規 「メタボロームのための代謝パスウェイ電子マップ 」 日本質量分析学会 質量分析総合討論会シンポジウム 「メタボロミクスとバイオインフォマティクス」5/26, 大阪 2006
  45. 有田 正規 「メタボロームは本当に網羅的か」 日本分子生物学会 年会シンポジウム 12/7, 福岡 2005
  46. 有田 正規「バイオインフォマティクスの環境バイオへの適用可能性」 環境バイオ・新規提案検討国際ワークショップ －微生物集団機能の高効率利用・デザイン化技術の創出のために－ 10/21, 東京 2005
  47. 有田 正規「生体ネットワークの大域情報と局所情報をつなぐソフトウェア」 第10回分生研シンポジウム「情報生物学」9/22, 東京 2005
  48. 有田 正規「代謝のネットワークとスケールフリー性」 日本数理生物学会 第15回大会シンポジウム 「複雑ネットワークの展開」 9/16, 横浜 2005
  49. 有田 正規 「メタボロームのための代謝パスウェイ電子マップ」 日本質量分析学会 質量分析総合討論会シンポジウム 「メタボロームとＭＳ」5/26, 大宮 2005
  50. 有田 正規 「マップエディタを用いたオンデマンドの代謝解析」 日本農芸化学会シンポジウム「モノづくりの代謝工学」 3/29, 札幌 2005
  51. 有田 正規 「代謝のネットワーク解析：大域的特徴から分子構造変化まで」 (財)新世代研究所 中性子生体ナノマシン・バイオナノ合同研究会 1/28, 東海村 2005
  52. 有田 正規 「お気楽マップエディタによる代謝解析」 日本分子生物学会 年会ワークショップ 「メタボローム研究の新展開」 12/10, 神戸 2004
  53. 有田 正規 「生物ネットワークとスケールフリー性」 日本生化学会 全国大会シンポジウム 「分子ネットワークのシステム特性」 10/16, 横浜 2004
  54. 有田 正規 「脂質代謝を原子レベルで表現するデータベース」 日本脂質栄養学会 第13回大会 9/3, 酒田 2004
  55. 有田 正規 「インタラクティブ代謝マップに基づくメタボローム解析」 日本質量分析学会 質量分析総合討論会シンポジウム 「メタボロームとＭＳ」6/4, 名古屋 2004
  56. 有田 正規 「代謝の電子化と機能予測」 新資源生物変換研究会シンポジウム 12/5, 東京 2003
  57. 有田 正規 「代謝データベースとその盲点」 日本生化学会 全国大会シンポジウム 「メタボローム研究の最前線」 10/15, 横浜 2003
  58. 有田 正規 「代謝の電子化プロジェクト」 日本質量分析学会 質量分析総合討論会シンポジウム 「ポストゲノム時代を担う若手研究者」 5/16, つくば 2003
  59. 有田 正規 「ARMプロジェクト： 細胞内代謝の電子化技術」 基礎生物学研究所研究会「生命科学におけるInformaticsと Mathematics」　3/11-12, 岡崎 2003
  60. 有田 正規 「大腸菌の代謝経路再構築」 JST異分野研究者交流フォーラム 3/1-2, 大仁 2002
  61. 有田 正規 「計算論的バイオテクノロジー」 計測自動制御学会 第7回創発システムシンポジウム「創発夏の学校」, 8/24-26, 富山, 2001

Meeting series and Workshops

  • AYRCOB Conference Series (http://ayrcob.org/) 2008-2016
  • International Metabolomics Society
    • Board Member (2014 Oct-2016 Sep)
    • Organization and talks
      • Workshop "Data Sharing and Standardisation" (SF, 29 Jun, 2015; Dublin, 27 Jun 2016; Brisbane, 26 Jun, 2017)
      • NSF-JST "Metabolomics for a Low Carbon Society", San Francisco, 28 Jun 2015
      • JST-NSF "Metabolomics Measurement Technology and Application" Tsuruoka, 23 Jun 2014
  • Annual Metabolome Symposium (domestic) 2006-2018
    • Mishima meeting (2015)
  • NII Shonan meeting "Computational metabolomics", March 20-23, Shonan, 2017 (organizer)
  • NIG International Symposium (commemorating DDBJ 30th) "Life, Environment and Evolution revealed by Genomes" (general chair)
  • ROIS International Workshop on Data Science (DSWS2018) "Present & Future of Open Data & Open Science" (local organizer)
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