Achievements : Osaka University Shimadzu Omics Innovation Research Laboratories : SHIMADZU CORPORATION

2024.08

Novel mimetic tissue standards for precise quantitative mass spectrometry imaging of drug and neurotransmitter concentrations in rat brain tissues

Anal Bioanal Chem.

Kenichi Watanabe¹
Sayo Takayama¹
Toichiro Yamada¹
Masayo Hashimoto¹
Jun Tadano²
Tetsuya Nakagawa²
Takao Watanabe³
Eiichiro Fukusaki^4,5,6
Izuru Miyawaki¹
Shuichi Shimma^4,5,6

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¹Preclinical Research Unit, Sumitomo Pharma Co., Ltd
²Research Planning & Coordination, Sumitomo Pharma Co., Ltd
³Drug Research Division, Sumitomo Pharma Co., Ltd
⁴Department of Biotechnology, Graduate School of Engineering, Osaka University
⁵Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁶Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University.

2024.Sum.

REACH Project : For Strategic Development of Highly Skilled Human Resources through Academia-Industry Collaboration

Manufacturing & technology, 76 (3), 62-66, 2024

Daisuke Hiramaru
Junko Iida
Hiroaki Nakanishi

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Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University

2024.07

New insights into the characteristic flavor components of traditional sour beers such as Lambic and Flanders Red Ale beers

J Biosci Bioeng . 2024 Jul;138(1):54-62

Kyoya Onishi¹
Masahiro Furuno¹
Asuka Mori¹
Eiichiro Fukusaki^1,2,3

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¹Department of Biotechnology, Graduate School of Engineering, Osaka University
²Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University
³Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University

2024.07

Characteristics of kopyor coconut (Cocos nucifera L.) using sensory analysis and metabolomics-based approach

J Biosci Bioeng. 2024 Jul;138(1):44-53

Mercy Bientri Yunindanova^1,2
Sastia Prama Putri^1,3
Hengky Novarianto⁵
Eiichiro Fukusaki^1,3,4

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¹Department of Biotechnology, Graduate School of Engineering, Osaka University
²Study Program of Agrotechnology, Faculty of Agriculture, Universitas Sebelas Maret
³Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives
⁴Osaka University Shimadzu Omics Innovation Research Laboratories, International Center for Biotechnology
⁵National Research and Innovation Agency (BRIN)

2024.07

Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food

Food Chem . 2024 Jul 15:446:138744

Marvin N. Iman^a
Danielle E. Haslam^b d
Liming Liang^e f
Kai Guo^g
Kaumudi Joshipura^e g
Cynthia M. Pérez^h
Clary Clishⁱ
Katherine L. Tucker^j
JoAnn E. Manson^c
Shilpa N. Bhupathiraju^b d
Eiichiro Fukusaki^a k l
Jessica Lasky-Su^b
Sastia P. Putri^a l

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^aDepartment of Biotechnology, Graduate School of Engineering,
^bChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School
^cDivision of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
^dDepartment of Nutrition, Harvard T.H. Chan School of Public Health,
^eDepartment of Epidemiology, Harvard T.H. Chan School of Public Health
^fDepartment of Biostatistics, Harvard T.H. Chan School of Public Health
^gCenter for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus
^hDepartment of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus
ⁱBroad Institute of Massachusetts Institute of Technology and Harvard,
^jDepartment of Biomedical and Nutritional Sciences, University of Massachusetts Lowell
^kIndustrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University
^lOsaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University

2024.06

Metabolomic characterization of monoclonal antibody-producing Chinese hamster lung (CHL)-YN cells in glucose-controlled serum-free fed-batch operation

Biotechnology and Bioengineering

Puriwat Sukwattananipaat¹
Hirotaka Kuroda^1,2,3
Noriko Yamano-Adachi^1,4,5
Takeshi Omasa^1,4,5

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¹Graduate School of Engineering, Osaka University
²Shimadzu Corp.
³Shimadzu Analytical Innovation Research Laboratories
⁴Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁵Manufacturing Technology Association of Biologics (MAB)

2024.05

13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation

Metab Eng Commun . 2024 May 27:18:e00239

Takeo Taniguchi¹
Nobuyuki Okahashi^1,2,3
Fumio Matsuda^1,2,3

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¹Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
²Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University.
³Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University

2024.04

New insights into the characteristic flavor components of traditional sour beers such as Lambic and Flanders Red Ale beers

J Biosci Bioeng. 2024 Apr 22:S1389-1723(24)00111-7

Kyoya Onishi¹
Masahiro Furuno¹
Asuka Mori¹
Eiichiro Fukusaki^1,2,3

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¹Department of Biotechnology, Graduate School of Engineering, Osaka University
²Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University
³Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University,

2024.04

Identification and enzymatic properties of arginine decarboxylase from Aspergillus oryzae

Appl Environ Microbiol. 2024 Apr 16:e0029424

Yui Murakami¹
Soichiro Ikuta²
Wakao Fukuda²
Naoki Akasaka^1,3
Jun-Ichi Maruyama^4,5
Shuichi Shinma^6,7,8
Eiichiro Fukusaki^6,7,8
Shinsuke Fujiwara^1,2

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¹Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University
²Department of Biosciences, School of Biological and Environmental Sciences
³Laboratory for Circular Bioeconomy Development, Office of Society-Academia Collaboration for Innovation, Kyoto University
⁴Department of Biotechnology, The University of Tokyo
⁵Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
⁶Department of Biotechnology, Graduate School of Engineering, Osaka University
⁷Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University
⁸Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University.

2024.03

Development of a Mass Spectrometry Imaging Method to Evaluate the Penetration of Moisturizing Components Coated on Surgical Gloves into Artificial Membranes

Mass Spectrom (Tokyo) . 2024;13(1):A0145

Erika Nagano¹
Kazuki Odake¹
Toru Akiyoshi²
Shuichi Shimma ^1,3,4,5

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¹Research and Development Department, Miruion Corporation
²Marketing Department, Cardinal Health K.K.
³Department of Biotechnology, Graduate School of Engineering, Osaka University
⁴Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁵Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University

2024.03

Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin

J Biosci Bioeng. 2024 Mar;137(3):187-194.

Chinatsu Matsuyama¹
Taisuke Seike¹
Nobuyuki Okahashi^1,2
Teppei Niide¹
Kiyotaka Y. Hara³
Yoko Hirono-Hara⁴
Jun Ishii⁵
Hiroshi Shimizu¹
Yoshihiro Toya¹
Fumio Matsuda^1,2

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¹Graduate School of Information Science and Technology, Osaka University
²Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University
³Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka
⁴396Bio Inc.
⁵Engineering Biology Research Center, Kobe University

2024.03

Rice grain structural characteristics of sake rice cultivar Hakutsurunishiki for daiginjo-shu brewing

Biosci Biotechnol Biochem. 2024 Mar 22;88(4):445-452

Yoshihiro Tamada^1,2
Takuya Asai¹
Takafumi Kubodera¹
Takahiro Akashi¹
Eiichiro Fukusaki^2,3,4
Shuichi Shimma^2,3,4

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¹Hakutsuru Sake Brewing Co., Ltd.
²Department of Biotechnology, Graduate School of Engineering, Osaka University
³Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University
⁴Institute for Open and Transdisciplinary Research Initiatives, Osaka University

2024.02

Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food

Food Chem. 2024 Feb 16:446:138744.

Marvin N. Iman^{a 1}
Danielle E. Haslam^{b d 1}
Liming Liang^{e f}
Kai Guo^g
Kaumudi Joshipura^{e g}
Cynthia M. Pérez^h
Clary Clishⁱ
Katherine L. Tucker^j
JoAnn E. Manson^c
Shilpa N. Bhupathiraju^{b d 2}
Eiichiro Fukusaki^{a k l 2}
Jessica Lasky-Su^{b 2}
Sastia P. Putri^{a l 2}

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^aDepartment of Biotechnology, Graduate School of Engineering, Osaka University,
^bChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School
^cDivision of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School
^dDepartment of Nutrition, Harvard T.H. Chan School of Public Health
^eDepartment of Epidemiology, Harvard T.H. Chan School of Public Health
^fDepartment of Biostatistics, Harvard T.H. Chan School of Public Health,
^gCenter for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus
^hDepartment of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus
ⁱBroad Institute of Massachusetts Institute of Technology and Harvard
^jDepartment of Biomedical and Nutritional Sciences, University of Massachusetts Lowell
^kIndustrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University
^lOsaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University
¹These authors contributed equally: Marvin N. Iman, Danielle E. Haslam.
²Joint senior authors, contributed equally: Shilpa N. Bhupathiraju, Eiichiro Fukusaki, Jessica Lasky-Su, Sastia P. Putri.

2024.01

A Bayesian approach for constituent estimation in nucleic acid mixture models

Front. Anal. Sci., 08 Jan 2024, 10.3389/frans.2023.1301602

Taichi Tomono^1,2,3
Satoshi Hara¹
Yusuke Nakai²
Kazuma Takahara²
Junko Iida^3,4
Takashi Washio¹

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¹Department of Reasoning for Intelligence, The Institute of Scientific and Industrial Research, Osaka University, Ōsaka, Japan
²AI Solution Unit, Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
³Shimadzu Analytical Innovation Research Laboratories, Osaka University, Ōsaka, Japan
⁴Life Science Business Department, Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan

2023.11

Applicability of supercritical fluid chromatography for oligonucleotide analysis: A proof-of-concept study

J Chromatogr A 1708(2023) 464333.

Momoka　Hayashida^1,2,3
Risa Suzuki³
Shinnosuke Horie^2,3,4
Junichi Masuda³
Takao Yamaguchi¹
Satoshi Obika¹

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¹Graduate School of Pharmaceutical Sciences, Osaka University
²Shimadzu Analytical Innovation Research Laboratories
³Shimadzu Corporation
⁴Shimadzu Europa GmbH

2023.10

Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment

Sci. Rep. (2023) 13:18549

Kazuki Nishimoto¹
Nobuyuki Okahashi^1,2,3
Masaharu Maruyama¹
Yoshihiro Izumi⁴
Kohta Nakatani⁴
Yuki Ito^2,5
Junko Iida^2,5
Takeshi Bamba⁴
Fumio Matsuda^1,2,3

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¹Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
²Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University
³Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁴Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University
⁵Analytical and Measuring Instruments Division, Shimadzu Corporation

2023.02

Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics

J Biosci Bioeng, 135(2) 102-108

Shuka Komori¹
Nobuyuki Okahashi^{1 2 3}
Junko Iida^{2 4}
Fumio Matsuda^{1 2 3}

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¹Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
²Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University
³Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁴Analytical and Measuring Instruments Division, Shimadzu Corporation

2022.07

Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform

Metabolites 2022, 12(7), 646

Nobuyuki Okahashi^{1 2 3}
Yuki Yamada¹
Junko Iida^{2 4}
Fumio Matsuda^{1 2 3}

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¹Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
²Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University
³Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University
⁴Analytical and Measuring Instruments Division, Shimadzu Corporation

2022.01

Automated Recommendation of Research Keywords from PubMed That Suggest the Molecular Mechanism Associated with Biomarker Metabolites

Metabolites

Shinji Kanazawa^1,2,3
Satoshi Shimizu¹
Shigeki Kajihara¹
Norio Mukai¹
Junko Iida^1,2
Fumio Matsuda^3,4

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¹Shimadzu Corporation
²Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University
³Graduate School of Information Science and Technology, Osaka University
⁴Institute for Open and Transdisciplinary Research Initiatives, Osaka University

2021.05

Evaluation of change in metabolome caused by comprehensive diabetes treatment: A prospective observational study of diabetes inpatients with gas chromatography/mass spectrometry-based non-target metabolomic analysis

journal of diabetes investigation

Naohiro Taya¹
Naoto Katakami^1,2
Kazuo Omori¹
Shoya Arakawa³
Shigero Hosoe¹
Hirotaka Watanabe¹
Mitsuyoshi Takahara^1,4
Kazuyuki Miyashita¹
Hitoshi Nishizawa¹
Taka-Aki Matsuoka¹
Masahiro Furuno³
Takeshi Bamba⁵
Junko Iida^6,7
Eiichiro Fukusaki³
Iichiro Shimomura¹

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¹Department of Metabolic Medicine, Osaka University Graduate School of Medicine
²Department of Metabolism and Atherosclerosis, Osaka University Graduate School of Medicine
³Laboratory of Bioresource Engineering, Department of Biotechnology, Graduate School of Engineering, Osaka University
⁴Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University
⁵Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University
⁶Shimadzu Corporation
⁷Osaka University Shimadzu Omics Innovation Research Laboratories, Graduate School of Engineering, Osaka University

2021.02

Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks

Journal of Bioscience and Bioengineering

Shinji Kanazawa^1,2,3
Akira Noda¹
Arisa Ito²
Kyoko Hashimoto²
Akihiro Kunisawa¹
Tsuyoshi Nakanishi¹
Shigeki Kajihara¹
Norio Mukai¹
Junko Iida^1,2
Eiichiro Fukusaki⁴
Fumio Matsuda³

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¹Shimadzu Corporation
²Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University
³Graduate School of Information Science and Technology, Osaka University
⁴Graduate School of Engineering, Osaka University

2019.08

Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC-EI-MS/MS

Mass Spectrometry

Nobuyuki Okahashi¹
Shuichi Kawana²
Junko Iida^2,3
Hiroshi Shimizu¹
Fumio Matsuda¹

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¹Graduate School of Information Science and Technology, Osaka University
²Shimadzu Corporation
³Osaka University Shimadzu Analytical Innovation Research Laboratory, Osaka University

2018.09

Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells

Metabolic Engineering (2018)

Nobuyuki Okahashi¹
Kousuke Maeda¹
Shuichi Kawana²
Junko Iida^2,3
Hiroshi Shimizu¹
Fumio Matsuda¹

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¹Graduate School of Information Science and Technology, Osaka University
²Shimadzu Corporation
³Osaka University Shimadzu Analytical Innovation Research Laboratory, Osaka University

2018.08

FK960 binding proteins, quinone oxidoreductase2 and pyridoxal kinase were identified by LC-MS/MS for drug discovery of Alzheimer's treatment

Trends in Research (2018), DOI:10.15761/TR.1000113

Zenzaburo Tozuka^1,2,3
Akihiro Kunisawa²
Fumiyuki Shirai^3,4
Yoshinori Ishii^3,4

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¹Graduate School of Pharmaceutical Science, Osaka University
²Osaka University Shimadzu Analytical Innovation Research Laboratory, Osaka University
³Fujisawa Pharmaceutical Co., Ltd.
⁴Astellas Pharma Inc.

2018.07

Multi omics by LC-MS/MS to search small molecule ligands of nuclear receptors to control transcription of pharmaceutical active proteins for drug discovery

Trends in Research (2018), DOI: 10.15761/TR.1000111

Zenzaburo Tozuka¹
Akihiro Kunisawa¹

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¹Osaka University Shimadzu Analytical Innovation Research Laboratory, Osaka University

2018.01

Free D-amino acids produced by commensal bacteria in the colonic lumen

Scientific Reports (2018), DOI:10.1038/s41598-018-36244-z

Mitsuharu Matsumoto¹
Akihiro Kunisawa^2,3
Takanari Hattori^2,3
Shuichi Kawana²
Yusuke Kitada¹
Hazuki Tamada¹
Shinichi Kawano^2,3
Yoshihiro Hayakawa²
Junko Iida^2,3
Eiichiro Fukusaki^3,4

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¹Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd
²Shimadzu Corporation
³Osaka University Shimadzu Analytical Innovation Research Laboratory, Osaka University
⁴Graduate School of Information Science and Technology, Osaka University

2016.6

GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to 13C-metabolic flux analysis of Escherichia coli central metabolism

Analytical and Bioanalytical Chemistry, June, 2016, in press.

Nobuyuki Okahashi¹
Shuichi Kawana²
Junko Iida^2,3
Hiroshi Shimizu¹
Fumio Matsuda¹

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¹Graduate School of Information Science and Technology, Osaka University
²Shimadzu Co.
³Graduate School of Engineering, Osaka University