User:Aritalab/Masanori Arita/Publication - Revision history

Adm: /* Refereed Journal Articles */

2020-05-27T02:34:36Z

‎Refereed Journal Articles

Adm: /* Refereed Journal Articles */

2020-05-26T22:34:07Z

‎Refereed Journal Articles

Adm at 13:53, 8 January 2020

2020-01-08T13:53:31Z

Adm: /* Invited Talks and Lectures */

2019-12-09T15:15:04Z

‎Invited Talks and Lectures

Adm: /* Invited Talks and Lectures */

2019-12-09T15:11:56Z

‎Invited Talks and Lectures

Adm: /* 招待講演、トークイベント */

2019-10-02T00:03:00Z

‎招待講演、トークイベント

Adm: /* Invited Talks and Lectures */

2019-10-02T00:01:22Z

‎Invited Talks and Lectures

Adm: /* Refereed Journal Articles */

2019-08-28T07:23:15Z

‎Refereed Journal Articles

Adm: /* Commissioned Reviews, Editorials, Book Chapters */

2019-08-28T07:03:25Z

‎Commissioned Reviews, Editorials, Book Chapters

Adm: /* 招待講演、トークイベント */

2019-06-02T23:52:36Z

‎招待講演、トークイベント

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 ==Refereed Journal Articles==
 {{#repeat:ArticleList/Row|1|
 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
 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

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 ==Refereed Journal Articles==
 {{#repeat:ArticleList/Row|1|
 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
 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
 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
 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

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 ==Refereed Journal Articles==
 {{#repeat:ArticleList/Row|1|
 Maeno S, Tanizawa Y, Kajikawa A, Kanesaki Y, Kubota E, Arita M, Dicks L, Endo A "A pseudo-fructophilic Leuconostoc citreum strain F192-5 isolated from the peel of satsuma mandarin" Applied and Environmental Microbiology, 2019
 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, 2019
-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
+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
-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
+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
-Tanizawa Y, Fujisawa T, Arita M, Nakamura Y "Generating Publication-Ready Prokaryotic Genome Annotations with DFAST" Methods in Molecular Biology, 1962, 215-226, 2019
+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
-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
+Lipidomics Standards Initiative Consortium “Lipidomics needs more standardization” Nature Metabolism 1, 745-747, 2019
-Endo A, Tanizawa Y, Arita M "Isolation and Identification of Lactic Acid Bacteria from Environmental Samples" Methods in Molecular Biology, 1887, 3-13, 2019
+Sato M, Arita M, Kawashima T “Uncovering Ecdysozoa-specific Sphingomyelin Synthase by Phylogenetic Analysis of Metazoan Sequences” Zoological Science 36(4), 316-321, 2019
 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
 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
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 ==Refereed Conference Proceedings==
 {{#repeat:ArticleList/Row|1|
 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
 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
@@ Line 128: / Line 131: @@
 ==Reviews, Editorials, Book Chapters==
 {{#repeat:ArticleList/Row|1|
 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
 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

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 <small>¢ ... support of hotel & participation fee only</small>
 # 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
-# Arita M, Noureen M "Consensis genome structure and cluster analysis strains from NAG" Helicobacter pylori GP workshop, National Cancer Institute (NCI), Rockville, USA, 26 Aug (26-27), 2019
+# 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
 # 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
 # Arita M "Open genome analysis in the post-genomic era" International Workshop on Data Science, Mishima, 15 Nov (12-15), 2018

@@ Line 187: / Line 187: @@
 <small>¢ ... support of hotel & participation fee only</small>
 # 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
-# Arita M "Cheminformatics for Predicting Structures from Mass Spectra" 1st Annual Conference of Chinese Society of Metabolomics (plenary), Shanghai, China, April 20 (19-21), 2019
+# Arita M, Noureen M "Consensis genome structure and cluster analysis strains from NAG" Helicobacter pylori GP workshop, National Cancer Institute (NCI), Rockville, USA, 26 Aug (26-27), 2019
-# Arita M "Open genome analysis in the post-genomic era" International Workshop on Data Science, Mishima, November 15 (12-15), 2018
+# 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
-# Arita M "Computational Metabolomics" 6th Annual Korea Metabolomics Society (plenary), Seoul, Korea, April 6 (5-6), 2018
+# Arita M "Open genome analysis in the post-genomic era" International Workshop on Data Science, Mishima, 15 Nov (12-15), 2018
-# Arita M "Distribution of Glycosphingolipids Revealed by LipidBank" International Life Science Integration Workshop, Tokyo, March 5 (5-6), 2018 ¢
+# Arita M "Computational Metabolomics" 6th Annual Korea Metabolomics Society (plenary), Seoul, Korea, 6 Apr (5-6), 2018
-# Arita M "Identifying Metabolites with Theoretical References" The 26th International KOGO Annual Conference (plenary), Seoul, Korea, Sep 6 (6-8), 2017
+# Arita M "Distribution of Glycosphingolipids Revealed by LipidBank" International Life Science Integration Workshop, Tokyo, 5 Mar (5-6), 2018 ¢
-# Arita M "Prediction of Molecular Structures from their Spectra" The 4th International Conference on Plant Metabolism (ICPM 2017), July 17 (16-20), 2017
+# Arita M "Identifying Metabolites with Theoretical References" The 26th International KOGO Annual Conference (plenary), Seoul, Korea, 6 Sep (6-8), 2017
-# Arita M "Computational Mass Spectrometry" SLING workshop `Mass spectrometry-based lipidomics of human blood plasma' National University of Singapore, May 2, 2017 (teleconference talk)
+# Arita M "Prediction of Molecular Structures from their Spectra" The 4th International Conference on Plant Metabolism (ICPM 2017), 17 Jul (16-20), 2017
-# Arita M "Comprehensive Acquisition of MS/MS Spectra Benefits Database Research" 6th International Singapore Lipid Symposium, December 1 (Nov30-Dec1), 2015 ¢
+# Arita M "Computational Mass Spectrometry" SLING workshop `Mass spectrometry-based lipidomics of human blood plasma' National University of Singapore, 2 May, 2017 (teleconference talk)
-# Arita M "Impact of Metabolome Database in Plant Science" The 38th Naito Conference "Molecule-based biological systems", October 8 (7-10), Sapporo, Japan, 2014
+# Arita M "Comprehensive Acquisition of MS/MS Spectra Benefits Database Research" 6th International Singapore Lipid Symposium, 1 Dec (Nov30-Dec1), 2015 ¢
-# Arita M "MassBank Past, Present and Future" Norman Massbank Workshop, September 17 (-18), Duebendorf, Switzerland, 2014 (no travel support)
+# Arita M "Impact of Metabolome Database in Plant Science" The 38th Naito Conference "Molecule-based biological systems", 8 Oct (7-10), Sapporo, Japan, 2014
-# Arita M "Genetic, Protein, and Metabolic Networks: Which Choice Is Amenable to Modelling" International Conference on Mathematical Modeling and Applications (ICMMA 2013), November 28 (26-28), Tokyo, Japan, 2013
+# Arita M "MassBank Past, Present and Future" Norman Massbank Workshop, 17 Sep (17-18), Duebendorf, Switzerland, 2014 (no travel support)
-# Arita M "Cyberinfrastructure for metabolomics and synthetic biology" International Symposium on Biotechnology for Green Growth, October 24 (-26), Kobe, Japan, 2012 ¢
+# 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
-# Arita M "What can metabolomics learn from genomics and proteomics?" International Conference of Research and Application on Traditional Complementary and Alternative Medicine (TCAM), June 22 (21-23), Muhammadiyah University of Surakarta (Indonesia), 2012
+# Arita M "Cyberinfrastructure for metabolomics and synthetic biology" International Symposium on Biotechnology for Green Growth, 24 Oct (24-26), Kobe, Japan, 2012 ¢
-# Arita M "Update on Lipid Databank and other lipidomics initiatives" EMBL-EBI Industry Programme & MetaboLights Project Workshop May 22, Hinxton, 2012
+# 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
-# Arita M "Wiki-based Databases: Integration of knowledge through the web" C-NAIR Seminar Nasional, Gadjah Mada University (Indonesia) Dec 5, 2011 (no travel support)
+# Arita M "Update on Lipid Databank and other lipidomics initiatives" EMBL-EBI Industry Programme & MetaboLights Project Workshop, 22 May, Hinxton, 2012
-# Arita M "Structural Classification for PKS in Aspergilli" IUMS2011 (International Union of Microbiological Societies Congress), Sep 9 (6-10), Sapporo, 2011 (no travel support)
+# 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)
-# Arita M "Knowledge Management using a Wiki-based System and its Application to Mass Spectra" EBI Seminar, April 19, EBI, Hinxton UK, 2011
+# Arita M "Structural Classification for PKS in Aspergilli" IUMS2011 (International Union of Microbiological Societies Congress), 9 Sep (6-10), Sapporo, 2011 (no travel support)
 # Arita M "Wiki-based platform for PKS in Aspergilli" Pacifichem, Dec 19 (15-20), Honolulu (Hawaii), 2010 ¢
 # 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)]

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 ==招待講演、トークイベント==
 # 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
 # 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

@@ Line 1: / Line 1: @@
 ==Refereed Journal Articles==
 {{#repeat:ArticleList/Row|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
 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
@@ Line 9: / Line 13: @@
 Tanaka W, Arita M "Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry" Mass Spectrometry (Tokyo), 7(1):A0066, 2018
 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
-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
+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
-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
+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
 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
 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

@@ Line 122: / Line 122: @@
 }}
-==Commissioned Reviews, Editorials, Book Chapters==
+==Reviews, Editorials, Book Chapters==
 {{#repeat:ArticleList/Row|1|
 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
-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  doi: 10.1002/mas.21535
+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
 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
 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

@@ Line 227: / Line 227: @@
 # 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
 # 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
-# 有田 正規 「遺伝子から見た地球生命」静岡県教育研究会, 8/8, 三島, 2018
+# 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
 # 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
 # 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