Works by Arita, Masanori

Results: 68

Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.

Published in:

PeerJ, 2025, p. 1, doi. 10.7717/peerj.19566

By:

Zakaria, Douaa;
Sandri, Camillo;
Modesto, Monica;
Spiezio, Caterina;
Scarafile, Donatella;
Cedras, Allen;
Borruso, Luigimaria;
Manghi, Paolo;
Trevisi, Paolo;
Segata, Nicola;
Mattarelli, Paola;
Arita, Masanori

Publication type:

Article

Publishing in the Open Access and Open Science era.

Published in:

Genes to Cells, 2024, v. 29, n. 4, p. 275, doi. 10.1111/gtc.13100

By:

Arita, Masanori;
Pulverer, Bernd;
Uemura, Tadashi;
Sakuma, Chisako;
Hayashi, Shigeo

Publication type:

Article

Open Access and Data Sharing of Nucleotide Sequence Data.

Published in:

Data Science Journal, 2021, v. 20, p. 1, doi. 10.5334/dsj-2021-028

By:

ARITA, MASANORI

Publication type:

Article

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology.

Published in:

Frontiers in Plant Science, 2020, v. 11, p. 1, doi. 10.3389/fpls.2020.00944

By:

Jamil, Ili Nadhirah;
Remali, Juwairiah;
Azizan, Kamalrul Azlan;
Nor Muhammad, Nor Azlan;
Arita, Masanori;
Goh, Hoe-Han;
Aizat, Wan Mohd

Publication type:

Article

InChI isotopologue and isotopomer specifications.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00847-8

By:

Moseley, Hunter N. B.;
Rocca-Serra, Philippe;
Salek, Reza M.;
Arita, Masanori;
Schymanski, Emma L.

Publication type:

Article

Scale-Freeness and Biological Networks.

Published in:

Journal of Biochemistry, 2005, v. 138, n. 1, p. 1, doi. 10.1093/jb/mvi094

By:

Arita, Masanori

Publication type:

Article

Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species.

Published in:

Plant & Cell Physiology, 2015, v. 56, n. 5, p. 843, doi. 10.1093/pcp/pcv008

By:

Donghan Li;
Naoaki Ono;
Tetsuo Sato;
Tadao Sugiura;
Altaf-Ul-Amin, Md;
Daisaku Ohta;
Hideyuki Suzuki;
Masanori Arita;
Ken Tanaka;
Zhiqiang Ma;
Shigehiko Kanaya

Publication type:

Article

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.

Published in:

Bioinformatics, 2006, v. 22, n. 10, p. 1211, doi. 10.1093/bioinformatics/btl067

By:

Hideki Nagasaki;
Masanori Arita;
Tatsuya Nishizawa;
Makiko Suwa;
Osamu Gotoh

Publication type:

Article

Dynamic modeling of genetic networks using genetic algorithm and S-system.

Published in:

Bioinformatics, 2003, v. 19, n. 5, p. 643, doi. 10.1093/bioinformatics/btg027

By:

Kikuchi, Shinichi;
Tominaga, Daisuke;
Arita, Masanori;
Takahashi, Katsutoshi;
Tomita, Masaru

Publication type:

Article

Modeling splicing sites with pairwise correlations.

Published in:

Bioinformatics, 2002, v. 18, p. S27, doi. 10.1093/bioinformatics/18.suppl_2.S27

By:

Arita, Masanori;
Tsuda, Koji;
Asai, Kiyoshi

Publication type:

Article

Mitochondrial genome of Garcinia mangostana L. variety Mesta.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-13706-z

By:

Wee, Ching-Ching;
Nor Muhammad, Nor Azlan;
Subbiah, Vijay Kumar;
Arita, Masanori;
Nakamura, Yasukazu;
Goh, Hoe-Han

Publication type:

Article

Comprehensive Metabolomic Comparison of Five Cereal Vinegars Using Non-Targeted and Chemical Isotope Labeling LC-MS Analysis.

Published in:

Metabolites (2218-1989), 2022, v. 12, n. 5, p. 427, doi. 10.3390/metabo12050427

By:

Li, Zhihua;
Zhao, Chi;
Dong, Ling;
Huan, Yu;
Yoshimoto, Miwa;
Zhu, Yongqing;
Tada, Ipputa;
Wang, Xiaohang;
Zhao, Shuang;
Zhang, Fengju;
Li, Liang;
Arita, Masanori

Publication type:

Article

Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics.

Published in:

Metabolites (2218-1989), 2019, v. 9, n. 11, p. 251, doi. 10.3390/metabo9110251

By:

Tada, Ipputa;
Tsugawa, Hiroshi;
Meister, Isabel;
Zhang, Pei;
Shu, Rie;
Katsumi, Riho;
Wheelock, Craig E.;
Arita, Masanori;
Chaleckis, Romanas

Publication type:

Article

Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics.

Published in:

Metabolites (2218-1989), 2019, v. 9, n. 6, p. 119, doi. 10.3390/metabo9060119

By:

Tsugawa, Hiroshi;
Satoh, Aya;
Uchino, Haruki;
Cajka, Tomas;
Arita, Makoto;
Arita, Masanori

Publication type:

Article

Isolation of a Highly Thermostable Bile Salt Hydrolase With Broad Substrate Specificity From Lactobacillus paragasseri.

Published in:

Frontiers in Microbiology, 2022, v. 12, p. 1, doi. 10.3389/fmicb.2022.810872

By:

Kusada, Hiroyuki;
Arita, Masanori;
Tohno, Masanori;
Tamaki, Hideyuki

Publication type:

Article

Host-Diet Effect on the Metabolism of Bifidobacterium.

Published in:

Genes, 2021, v. 12, n. 4, p. 609, doi. 10.3390/genes12040609

By:

Satti, Maria;
Modesto, Monica;
Endo, Akihito;
Kawashima, Takeshi;
Mattarelli, Paola;
Arita, Masanori

Publication type:

Article

Critical Involvement of Environmental Carbon Dioxide Fixation to Drive Wax Ester Fermentation in Euglena.

Published in:

PLoS ONE, 2016, v. 11, n. 9, p. 1, doi. 10.1371/journal.pone.0162827

By:

Padermshoke, Adchara;
Ogawa, Takumi;
Nishio, Kazuki;
Nakazawa, Masami;
Nakamoto, Masatoshi;
Okazawa, Atsushi;
Kanaya, Shigehiko;
Arita, Masanori;
Ohta, Daisaku

Publication type:

Article

Rearrangement analysis of multiple bacterial genomes.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3293-4

By:

Noureen, Mehwish;
Ipputa Tada;
Takeshi Kawashima;
Masanori Arita

Publication type:

Article

Differential annotation of converted metabolites (DAC-Met): Exploration of Maoto (Ma-huang-tang)-derived metabolites in plasma using high-resolution mass spectrometry.

Published in:

Metabolomics, 2020, v. 16, n. 5, p. 1, doi. 10.1007/s11306-020-01681-3

By:

Ohbuchi, Katsuya;
Sakurai, Nozomu;
Kitagawa, Hiroyuki;
Sato, Masaru;
Suzuki, Hideyuki;
Kushida, Hirotaka;
Nishi, Akinori;
Yamamoto, Masahiro;
Hanazaki, Kazuhiro;
Arita, Masanori

Publication type:

Article

Data standards can boost metabolomics research, and if there is a will, there is a way.

Published in:

Metabolomics, 2016, v. 12, n. 1, p. N.PAG, doi. 10.1007/s11306-015-0879-3

By:

Rocca-Serra, Philippe;
Salek, Reza M.;
Arita, Masanori;
Correa, Elon;
Dayalan, Saravanan;
Gonzalez-Beltran, Alejandra;
Ebbels, Tim;
Goodacre, Royston;
Hastings, Janna;
Haug, Kenneth;
Koulman, Albert;
Nikolski, Macha;
Oresic, Matej;
Sansone, Susanna-Assunta;
Schober, Daniel;
Smith, James;
Steinbeck, Christoph;
Viant, Mark R.;
Neumann, Steffen

Publication type:

Article

Embedding standards in metabolomics: the Metabolomics Society data standards task group.

Published in:

2015

By:

Salek, Reza;
Arita, Masanori;
Dayalan, Saravanan;
Ebbels, Timothy;
Jones, Andrew;
Neumann, Steffen;
Rocca-Serra, Philippe;
Viant, Mark;
Vizcaíno, Juan-Antonio

Publication type:

Report

Wax ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry: toward understanding of wax ester fermentation under hypoxia.

Published in:

Metabolomics, 2015, v. 11, n. 1, p. 175, doi. 10.1007/s11306-014-0687-1

By:

Furuhashi, Takeshi;
Ogawa, Takumi;
Nakai, Rai;
Nakazawa, Masami;
Okazawa, Atsushi;
Padermschoke, Adchara;
Nishio, Kazuki;
Hirai, Masami;
Arita, Masanori;
Ohta, Daisaku

Publication type:

Article

MRMPROBS suite for metabolomics using large-scale MRM assays.

Published in:

Bioinformatics, 2014, v. 30, n. 16, p. 2379, doi. 10.1093/bioinformatics/btu203

By:

Tsugawa, Hiroshi;
Kanazawa, Mitsuhiro;
Ogiwara, Atsushi;
Arita, Masanori

Publication type:

Article

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species.

Published in:

Plants (2223-7747), 2023, v. 12, n. 4, p. 930, doi. 10.3390/plants12040930

By:

Wee, Ching-Ching;
Nor Muhammad, Nor Azlan;
Subbiah, Vijay Kumar;
Arita, Masanori;
Nakamura, Yasukazu;
Goh, Hoe-Han

Publication type:

Article

Dissemination of local sub-variants of SARS-CoV-2 detected by detailed mutation analysis in wastewater-based epidemiology.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0317076

By:

Honda, Ryo;
Abe, Takashi;
Baba, Tomoya;
Araki, Yui;
Kuroita, Tomohiro;
Iwamoto, Ryo;
Ito, Mayo;
Okamura, Nami;
Yousri, Marie Kenza;
Tamura, Takashi;
Ezaki, Satoshi;
Arita, Masanori

Publication type:

Article

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.

Published in:

DNA Research, 2023, v. 30, n. 5, p. 1, doi. 10.1093/dnares/dsad019

By:

Koshimizu, Shizuka;
Masuda, Sachiko;
Shibata, Arisa;
Ishii, Takayoshi;
Shirasu, Ken;
Hoshino, Atsushi;
Arita, Masanori

Publication type:

Article

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach.

Published in:

BMC Systems Biology, 2011, v. 5, n. 1, p. 1, doi. 10.1186/1752-0509-5-1

By:

Fukushima, Atsushi;
Kusano, Miyako;
Redestig, Henning;
Arita, Masanori;
Saito, Kazuki

Publication type:

Article

Time-resolved metabolomics reveals metabolic modulation in rice foliage.

Published in:

BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-51

By:

Sato, Shigeru;
Arita, Masanori;
Soga, Tomoyoshi;
Nishioka, Takaaki;
Tomita, Masaru

Publication type:

Article

Unbiased characterization of genotype-dependent metabolicregulations by metabolomic approach in Arabidopsis thaliana.

Published in:

BMC Systems Biology, 2007, v. 1, p. 53, doi. 10.1186/1752-0509-1-53

By:

Kusano, Miyako;
Fukushima, Atsushi;
Arita, Masanori;
Jonsson, Pär;
Moritz, Thomas;
Kobayashi, Makoto;
Hayashi, Naomi;
Tohge, Takayuki;
Saito, Kazuki

Publication type:

Article

Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals nichespecific evolution of Fructobacillus spp.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2339-x

By:

Akihito Endo;
Yasuhiro Tanizawa;
Naoto Tanaka;
Shintaro Maeno;
Kumar, Himanshu;
Yuh Shiwa;
Sanae Okada;
Hirofumi Yoshikawa;
Dicks, Leon;
Junichi Nakagawa;
Masanori Arita

Publication type:

Article

Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260<sup>T</sup>, a psychrotrophic lactic acid bacterium isolated from silage.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1435-2

By:

Yasuhiro Tanizawa;
Masanori Tohno;
Eli Kaminuma;
Yasukazu Nakamura;
Masanori Arita

Publication type:

Article

Exploration of polar lipid accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico.

Published in:

Bioscience, Biotechnology & Biochemistry, 2014, v. 78, n. 1, p. 14, doi. 10.1080/09168451.2014.877826

By:

Takumi Ogawa;
Takeshi Furuhashi;
Atsushi Okazawa;
Rai Nakai;
Masami Nakazawa;
Tobias Kind;
Oliver Fiehn;
Shigehiko Kanaya;
Masanori Arita;
Daisaku Ohta

Publication type:

Article

Identification of small molecules using accurate mass MS/MS search.

Published in:

Mass Spectrometry Reviews, 2018, v. 37, n. 4, p. 513, doi. 10.1002/mas.21535

By:

Kind, Tobias;
Tsugawa, Hiroshi;
Cajka, Tomas;
Ma, Yan;
Lai, Zijuan;
Mehta, Sajjan S.;
Wohlgemuth, Gert;
Barupal, Dinesh Kumar;
Showalter, Megan R.;
Arita, Masanori;
Fiehn, Oliver

Publication type:

Article

Reconstructing phylogeny from metabolic substrate-product relationships.

Published in:

BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S27

By:

Che-Wei Chang;
Ping-Chiang Lyu;
Arita, Masanori

Publication type:

Article

GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA).

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 131, doi. 10.1186/1471-2105-12-131

By:

Tsugawa, Hiroshi;
Tsujimoto, Yuki;
Arita, Masanori;
Bamba, Takeshi;
Fukusaki, Eiichiro

Publication type:

Article

Consolidating metabolite identifiers to enablecontextual and multi-platform metabolomicsdata analysis.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 214, doi. 10.1186/1471-2105-11-214

By:

Redestig, Henning;
Kusano, Miyako;
Fukushima, Atsushi;
Matsuda, Fumio;
Saito, Kazuki;
Arita, Masanori

Publication type:

Article

Computational resources for metabolomics.

Published in:

Briefings in Functional Genomics & Proteomics, 2004, v. 3, n. 1, p. 84, doi. 10.1093/bfgp/3.1.84

By:

Arita, Masanori

Publication type:

Article

Comparative analysis of probiotic bacteria based on a new definition of core genome.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 3, p. N.PAG, doi. 10.1142/S0219720018400127

By:

Satti, Maria;
Tanizawa, Yasuhiro;
Endo, Akihito;
Arita, Masanori

Publication type:

Article

Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06580-0

By:

Konno, Naoki;
Maeno, Shintaro;
Tanizawa, Yasuhiro;
Arita, Masanori;
Endo, Akihito;
Iwasaki, Wataru

Publication type:

Article

MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.

Published in:

Frontiers in Genetics, 2015, v. 5, p. 1, doi. 10.3389/fgene.2014.00471

By:

Hiroshi Tsugawa;
Erika Ohta;
Yoshihiro Izumi;
Atsushi Ogiwara;
Daichi Yukihira;
Takeshi Bamba;
Eiichiro Fukusaki;
Masanori Arita;
Vizcaino, Juan Antonio

Publication type:

Article

DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D45, doi. 10.1093/nar/gkae882

By:

Kodama, Yuichi;
Ara, Takeshi;
Fukuda, Asami;
Tokimatsu, Toshiaki;
Mashima, Jun;
Kosuge, Takehide;
Tanizawa, Yasuhiro;
Tanjo, Tomoya;
Ogasawara, Osamu;
Fujisawa, Takatomo;
Nakamura, Yasukazu;
Arita, Masanori

Publication type:

Article

The international nucleotide sequence database collaboration (INSDC): enhancing global participation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D62, doi. 10.1093/nar/gkae1058

By:

Karsch-Mizrachi, Ilene;
Arita, Masanori;
Burdett, Tony;
Cochrane, Guy;
Nakamura, Yasukazu;
Pruitt, Kim D;
Schneider, Valerie A;
of the International Nucleotide Sequence Database Collaboration, on behalf

Publication type:

Article

DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata.

Published in:

Nucleic Acids Research, 2024, v. 52, n. D1, p. D67, doi. 10.1093/nar/gkad1046

By:

Ara, Takeshi;
Kodama, Yuichi;
Tokimatsu, Toshiaki;
Fukuda, Asami;
Kosuge, Takehide;
Mashima, Jun;
Tanizawa, Yasuhiro;
Tanjo, Tomoya;
Ogasawara, Osamu;
Fujisawa, Takatomo;
Nakamura, Yasukazu;
Arita, Masanori

Publication type:

Article

The international nucleotide sequence database collaboration.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D121, doi. 10.1093/nar/gkaa967

By:

Arita, Masanori;
Karsch-Mizrachi, Ilene;
Cochrane, Guy

Publication type:

Article

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W205, doi. 10.1093/nar/gkw415

By:

Sriyudthsak, Kansuporn;
Mejia, Ramon Francisco;
Arita, Masanori;
Masami Yokota Hirai

Publication type:

Article

Genome sequence of Aspergillus luchuensis NBRC 4314.

Published in:

DNA Research, 2016, v. 23, n. 6, p. 507, doi. 10.1093/dnares/dsw032

By:

Osamu Yamada;
Masayuki Machida;
Akira Hosoyama;
Masatoshi Goto;
Toru Takahashi;
Taiki Futagami;
Youhei Yamagata;
Michio Takeuchi;
Tetsuo Kobayashi;
Hideaki Koike;
Keietsu Abe;
Kiyoshi Asai;
Masanori Arita;
Nobuyuki Fujita;
Kazuro Fukuda;
Ken-ichi Higa;
Hiroshi Horikawa;
Takeaki Ishikawa;
Koji Jinno;
Yumiko Kato

Publication type:

Article

SVD-based Anatomy of Gene Expressions for Correlation Analysis in Arabidopsis thaliana.

Published in:

DNA Research, 2008, v. 15, n. 6, p. 367, doi. 10.1093/dnares/dsn025

By:

Fukushima, Atsushi;
Wada, Masayoshi;
Kanaya, Shigehiko;
Arita, Masanori

Publication type:

Article

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Published in:

Nature Methods, 2015, v. 12, n. 6, p. 523, doi. 10.1038/nmeth.3393

By:

Tsugawa, Hiroshi;
Cajka, Tomas;
Kind, Tobias;
Ma, Yan;
Higgins, Brendan;
Ikeda, Kazutaka;
Kanazawa, Mitsuhiro;
VanderGheynst, Jean;
Fiehn, Oliver;
Arita, Masanori

Publication type:

Article

Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast.

Published in:

Comparative & Functional Genomics, 2012, p. 1, doi. 10.1155/2012/653174

By:

Peng, Chien-Hua;
Lin, Shu-Hsi;
Peng, Shih-Chi;
Lyu, Ping-Chiang;
Arita, Masanori;
Tang, Chuan-Yi

Publication type:

Article

Knockout of the SREBP system increases production of the polyketide FR901512 in filamentous fungal sp. No. 14919 and lovastatin in Aspergillus terreus ATCC20542.

Published in:

Applied Microbiology & Biotechnology, 2018, v. 102, n. 3, p. 1393, doi. 10.1007/s00253-017-8685-7

By:

Itoh, Hiroya;
Miura, Ai;
Matsui, Makoto;
Arazoe, Takayuki;
Nishida, Keiji;
Kumagai, Toshitaka;
Arita, Masanori;
Tamano, Koichi;
Machida, Masayuki;
Shibata, Takashi

Publication type:

Article