研究業績

2024年

1. Matsuyama C, Seike T, Okahashi N, Niide T, Hara KY, Hirono-Hara Y, Ishii J, Shimizu H, Toya Y, Matsuda F. Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin. J Biosci Bioeng. 2024 Jan 27:S1389-1723(23)00352-3. doi: 10.1016/j.jbiosc.2023.12.003. Epub ahead of print. PMID: 38281859.

2023年

1. Matsuda F. Data Processing of Product Ion Spectra: Redundancy of Product Ion Spectra of Small Molecules in Data-Dependent Acquisition Dataset. Mass Spectrom (Tokyo). 2023;12(1):A0138. doi: 10.5702/massspectrometry.A0138. Epub 2023 Dec 8. PMID: 38090113; PMCID: PMC10713281.
2. Sugimura M, Seike T, Okahashi N, Izumi Y, Bamba T, Ishii J, Matsuda F. Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway. Int J Mol Sci. 2023 Nov 15;24(22):16378. doi: 10.3390/ijms242216378. PMID: 38003568; PMCID: PMC10671664.
3. Nishimoto K, Okahashi N, Maruyama M, Izumi Y, Nakatani K, Ito Y, Iida J, Bamba T, Matsuda F. Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment. Sci Rep. 2023 Oct 29;13(1):18549. doi: 10.1038/s41598-023-45764-2. PMID: 37899460; PMCID: PMC10613619.
4. Yatabe F, Seike T, Okahashi N, Ishii J, Matsuda F. Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting. Microb Cell Fact. 2023 Oct 8;22(1):204. doi: 10.1186/s12934-023-02221-z. PMID: 37807050; PMCID: PMC10560415
5. Iwama R, Okahashi N, Suzawa T, Yang C, Matsuda F, Horiuchi H. Comprehensive analysis of the composition of the major phospholipids during the asexual life cycle of the filamentous fungus Aspergillus nidulans. Biochim Biophys Acta Mol Cell Biol Lipids. 2023 Oct;1868(10):159379. doi: 10.1016/j.bbalip.2023.159379. Epub 2023 Aug 31. PMID: 37659899
6. Wada K, Uebayashi K, Toya Y, Putri SP, Matsuda F, Fukusaki E, C Liao J, Shimizu H. Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses. J Gen Appl Microbiol. 2023 Mar 20. doi: 10.2323/jgam.2023.03.002. Epub ahead of print. PMID: 36935115
7. Seike T, Takekata H, Uchida Y, Sakata N, Furusawa C, Matsuda F. Wickerhamiella bidentis sp. nov., a novel yeast species isolated from flowers and insects in Japan. Int J Syst Evol Microbiol. 2023 Mar;73(3). doi: 10.1099/ijsem.0.005739. PMID: 36884375

2022年

1. Morita K, Seike T, Ishii J, Matsuda F, Shimizu H. Improvement of 2,3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae. J Biosci Bioeng. 2022 Mar;133(3):208-212. doi: 10.1016/j.jbiosc.2021.12.007. Epub 2022 Jan 5. PMID: 34998687
2. Morozumi S, Ueda M, Okahashi N, Arita M. Structures and functions of the gut microbial lipidome. Biochim Biophys Acta Mol Cell Biol Lipids. 2022 Mar;1867(3):159110. doi: 10.1016/j.bbalip.2021.159110. Epub 2022 Jan 4. PMID: 34995792
3. Kanazawa S, Shimizu S, Kajihara S, Mukai N, Iida J, Matsuda F. Automated Recommendation of Research Keywords from PubMed That Suggest the Molecular Mechanism Associated with Biomarker Metabolites. Metabolites. 2022 Feb 1;12(2):133. doi: 10.3390/metabo12020133. PMID: 35208208
4. Nishiumi S, Izumi Y, Hirayama A, Takahashi M, Nakao M, Hata K, Saigusa D, Hishinuma E, Matsukawa N, Tokuoka SM, Kita Y, Hamano F, Okahashi N, Ikeda K, Nakanishi H, Saito K, Hirai MY, Yoshida M, Oda Y, Matsuda F, Bamba T. Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories. Metabolites. 2022 Feb 1;12(2):135. doi: 10.3390/metabo12020135. PMID: 35208210
5. Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light- powering microbial proton pump systems. Metab Eng. 2022 Jul;72:227-236. doi: 10.1016/j.ymben.2022.03.012. Epub 2022 Mar 26. PMID: 35346842
6. Lu X, Hackman GL, Saha A, Rathore AS, Collins M, Friedman C, Yi SS, Matsuda F, DiGiovanni J, Lodi A, Tiziani S. Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry. iScience. 2022 Apr 7;25(5):104221. doi: 10.1016/j.isci.2022.104221. PMID: 35494234
7. Okahashi N, Yamada Y, Iida J, Matsuda F. Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform. Metabolites. 2022 Jul 14;12(7):646. doi: 10.3390/metabo12070646. PMID: 35888770
8. Yamamoto J, Chumsakul O, Toya Y, Morimoto T, Liu S, Masuda K, Kageyama Y, Hirasawa T, Matsuda F, Ogasawara N, Shimizu H, Yoshida KI, Oshima T, Ishikawa S. Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production. DNA Res. 2022 May 27;29(3):dsac015. doi: 10.1093/dnares/dsac015. PMID: 35608323
9. Noguchi S, Wakita K, Matsuda F, Shimizu H. 13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia. Metab Eng. 2022 Sep;73:192-200. doi: 10.1016/j.ymben.2022.07.008. Epub 2022 Jul 31. PMID: 35921945
10. Otsuka K, Seike T, Toya Y, Ishii J, Hirono-Hara Y, Hara KY, Matsuda F. Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli. J Biosci Bioeng. 2022 Dec;134(6):484-490. doi: 10.1016/j.jbiosc.2022.08.006. Epub 2022 Sep 25. PMID: 36171161
11. Sano M, Tanaka R, Kamata K, Hirono-Hara Y, Ishii J, Matsuda F, Hara KY, Shimizu H, Toya Y. Conversion of Mevalonate to Isoprenol Using Light Energy in Escherichia coli without Consuming Sugars for ATP Supply. ACS Synth Biol. 2022 Dec 16;11(12):3966-3972. doi: 10.1021/acssynbio.2c00313. Epub 2022 Nov 28. PMID: 36441576
12. Komori S, Okahashi N, Iida J, Matsuda F. Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics. J Biosci Bioeng. 2022 Dec 6:S1389-1723(22)00339-5. doi: 10.1016/j.jbiosc.2022.10.011. Epub ahead of print. PMID: 36494248
13. Jagadeesh V, Yoshida T, Uraji M, Okahashi N, Matsuda F, Vavricka CJ, Tsuge K, Kondo A. Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM-OGAB Method. ACS Synth Biol. 2023 Jan 20;12(1):305-318. doi: 10.1021/acssynbio.2c00565. Epub 2022 Dec 23. PMID: 36563322
14. Matsuda F, Komori S, Yamada Y, Hara D, Okahashi N. Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules. Mass Spectrom (Tokyo). 2022;11(1):A0106. doi: 10.5702/massspectrometry.A0106. Epub 2022 Dec 15. PMID: 36713802

2021年

1. Yoshikawa K, Ogawa K, Toya Y, Akimoto S, Matsuda F, Shimizu H. Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803. Commun Biol. 2021 Mar 16;4(1):343. doi: 10.1038/s42003-021-01875-y. PMID: 33727624
2. Nagata M, Toyonaga K, Ishikawa E, Haji S, Okahashi N, Takahashi M, Izumi Y, Imamura A, Takato K, Ishida H, Nagai S, Illarionov P, Stocker BL, Timmer MSM, Smith DGM, Williams SJ, Bamba T, Miyamoto T, Arita M, Appelmelk BJ, Yamasaki S. Helicobacter pylori metabolites exacerbate gastritis through C-type lectin receptors. J Exp Med. 2021 Jan 4;218(1):e20200815. doi: 10.1084/jem.20200815. PMID: 32991669; PMCID: PMC7527975.
3. Isogai S, Okahashi N, Asama R, Nakamura T, Hasunuma T, Matsuda F, Ishii J, Kondo A. 2021. Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases. Metab Eng Commun. 2021 Mar 19;12:e00169. doi: 10.1016/j.mec.2021.e00169. eCollection 2021 Jun. PMID: 33868922
4. Okahashi N, Ueda M, Matsuda F, Arita M. 2021. Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry. Metabolites. 2021 Mar 26;11(4):197. doi: 10.3390/metabo11040197. PMID: 33810392
5. 馬場健史，平山明由，松田史生，津川裕司/編、メタボロミクス実践ガイド サンプル調製からデータ解析まで、あなたに合った実験デザインと達人テクニック、2021年、実験医学別冊
6. Okahashi N, Ueda M, Yasuda S, Tsugawa H, Arita M. Global profiling of gut microbiota-associated lipid metabolites in antibiotic-treated mice by LC-MS/MS-based analyses. STAR Protoc. 2021 Apr 21;2(2):100492. doi: 10.1016/j.xpro.2021.100492. eCollection 2021 Jun 18. PMID: 33997812
7. Seike T, Sakata N, Matsuda F, Furusawa C. Elevated Sporulation Efficiency in Fission Yeast Schizosaccharomyces japonicus Strains Isolated from Drosophila. J Fungi (Basel). 2021 Apr 29;7(5):350. doi: 10.3390/jof7050350. PMID: 33947067
8. Seike T, Narazaki Y, Kaneko Y, Shimizu H, Matsuda F. Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance. J Fungi (Basel). 2021 Apr 15;7(4):302. doi: 10.3390/jof7040302. PMID: 33921057
9. Tokuyama K, Shimodaira Y, Kodama Y, Matsui R, Kusunose Y, Fukushima S, Nakai H, Tsuji Y, Toya Y, Matsuda F, Shimizu H. Soft-sensor development for monitoring the lysine fermentation process. J Biosci Bioeng. 2021 Aug;132(2):183-189. doi: 10.1016/j.jbiosc.2021.04.002. Epub 2021 May 3. PMID: 33958301
10. Sheng J, Kohno S, Okada N, Okahashi N, Teranishi K, Matsuda F, Shimizu H, Linn P, Nagatani N, Yamamura M, Harada K, Horike SI, Inoue H, Yano S, Kumar S, Kitajima S, Ajioka I, Takahashi C. Treatment of Retinoblastoma 1-Intact Hepatocellular Carcinoma With Cyclin-Dependent Kinase 4/6 Inhibitor Combination Therapy. Hepatology. 2021 Oct;74(4):1971-1993. doi: 10.1002/hep.31872. Epub 2021 Aug 25. PMID: 33931882
11. Yatabe F, Okahashi N, Seike T, Matsuda F. Comparative 13 C-metabolic flux analysis indicates elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains. Biotechnol J. 2022 Mar;17(3):e2000438. doi: 10.1002/biot.202000438. Epub 2021 May 25. PMID: 33983677
12. 松田史生、がん代謝の数理学的解析による仮説生成と検証、実験医学 2021年7月号 Vol.39 No.11
13. Toyoshima M, Sakata M, Ueno Y, Toya Y, Matsuda F, Akimoto S, Shimizu H. Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803. J Proteomics. 2021 Aug 30;246:104306. doi: 10.1016/j.jprot.2021.104306. Epub 2021 Jun 19. PMID: 34157441
14. Matsuda F, Maeda K, Taniguchi T, Kondo Y, Yatabe F, Okahashi N, Shimizu H. mfapy: An open-source Python package for 13C-based metabolic flux analysis. Metab Eng Commun. 2021 Jul 17;13:e00177. doi: 10.1016/j.mec.2021.e00177. eCollection 2021 Dec. PMID: 34354925
15. Yoshida E, Kojima M, Suzuki M, Matsuda F, Shimbo K, Onuki A, Nishio Y, Usuda Y, Kondo A, Ishii J. Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis. Sci Rep. 2021 Nov 11;11(1):22126. doi: 10.1038/s41598-021-01469-y. PMID: 34764337
16. Yonekura-Sakakibara K, Yamamura M, Matsuda F, Ono E, Nakabayashi R, Sugawara S, Mori T, Tobimatsu Y, Umezawa T, Saito K. Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis. Plant Cell. 2021 Mar 22;33(1):129-152. doi: 10.1093/plcell/koaa014. PMID: 33751095
17. Abdelrahman M, Nishiyama R, Tran CD, Kusano M, Nakabayashi R, Okazaki Y, Matsuda F, Chávez Montes RA, Mostofa MG, Li W, Watanabe Y, Fukushima A, Tanaka M, Seki M, Saito K, Herrera-Estrella L, Tran LP. Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2105021118. doi: 10.1073/pnas.2105021118. PMID: 34815339;

2020年

1. Imura M, Nitta K, Iwakiri R, Matsuda F, Shimizu H, Fukusaki E. Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative. J Biosci Bioeng. 2020 Jan;129(1):52-58. doi: 10.1016/j.jbiosc.2019.07.007. Epub 2019 Sep 16. PMID: 31537452.
2. Matsuda F, Maeda K, Okahashi N. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Sci Rep. 2020 Jan 14;10(1):286. doi: 10.1038/s41598-019-57146-8. PMID: 31937835; PMCID: PMC6959353.
3. Negoro H, Matsumura K, Matsuda F, Shimizu H, Hata Y, Ishida H. Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 2020 Jun;104(11):4971-4983. doi: 10.1007/s00253-020-10573-4. Epub 2020 Apr 4. PMID: 32248437.
4. Siriwach R, Matsuda F, Yano K, Hirai MY. Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of _Arabidopsis thaliana_. Metabolites. 2020 Apr 18;10(4):159. doi: 10.3390/metabo10040159. PMID: 32325728; PMCID: PMC7241242.
5. Tsugawa H, Ikeda K, Takahashi M, Satoh A, Mori Y, Uchino H, Okahashi N, Yamada Y, Tada I, Bonini P, Higashi Y, Okazaki Y, Zhou Z, Zhu ZJ, Koelmel J, Cajka T, Fiehn O, Saito K, Arita M, Arita M. A lipidome atlas in MS-DIAL 4. Nat Biotechnol. 2020 Oct;38(10):1159-1163. doi: 10.1038/s41587-020-0531-2. Epub 2020 Jun 15. PMID: 32541957.
6. Tokuyama K, Shimodaira Y, Terawaki T, Kusunose Y, Nakai H, Tsuji Y, Toya Y, Matsuda F, Shimizu H. Data science-based modeling of the lysine fermentation process. J Biosci Bioeng. 2020 Oct;130(4):409-415. doi: 10.1016/j.jbiosc.2020.06.011. Epub 2020 Jul 22. PMID: 32709563.
7. Noguchi S, Ishikawa H, Wakita K, Matsuda F, Shimizu H. Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells. Sci Rep. 2020 Aug 3;10(1):13065. doi: 10.1038/s41598-020-70000-6. PMID: 32747645; PMCID: PMC7400513.
8. Toyoshima M, Tokumaru Y, Matsuda F, Shimizu H. Assessment of Protein Content and Phosphorylation Level in _Synechocystis_ sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis. Molecules. 2020 Aug 6;25(16):3582. doi: 10.3390/molecules25163582. PMID: 32781706; PMCID: PMC7466104.
9. Kanazawa S, Noda A, Ito A, Hashimoto K, Kunisawa A, Nakanishi T, Kajihara S, Mukai N, Iida J, Fukusaki E, Matsuda F. Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks. J Biosci Bioeng. 2020 Oct 10:S1389-1723(20)30362-5. doi: 10.1016/j.jbiosc.2020.09.013. Epub ahead of print. PMID: 33051155.
10. Nishiguchi H, Liao J, Shimizu H, Matsuda F. Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of _Synechocystis_ sp. PCC 6803 metabolism. Metab Eng Commun. 2020 Nov 27;11:e00153. doi: 10.1016/j.mec.2020.e00153. PMID: 33312875; PMCID: PMC7721636.
11. Yasuda S, Okahashi N, Tsugawa H, Ogata Y, Ikeda K, Suda W, Arai H, Hattori M, Arita M. Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses. iScience. 2020 Nov 23;23(12):101841. doi: 10.1016/j.isci.2020.101841. PMID: 33313490; PMCID: PMC7721639.
12. 岡橋伸幸, 上田政宏, 有田誠, "第1編 第2章 第2節 マイクロバイオームのリピドミクス",ヒトマイクロバイオー Vol.2,(2020),エヌ・ティー・エス
13. 西本和生, 丸山正晴, 岡橋伸幸, 松田史生, "Effects of Organic Solvents on Cancer Metabolism" (2020) J. Mass Spectrom. Soc. Jpn. Vol.68, No.6

2019年

1. Toyoshima M, Sakata M, Ohnishi K, Tokumaru Y, Kato Y, Tokutsu R, Sakamoto W, Minagawa J, Matsuda F, Shimizu H. Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms. J Biosci Bioeng. 2019 Mar;127(3):394-402. doi: 10.1016/j.jbiosc.2018.09.001. Epub 2018 Sep 28. PMID: 30274798.
2. Tokuyama K, Toya Y, Matsuda F, Cress BF, Koffas MAG, Shimizu H. Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli. Metab Eng. 2019 Mar;52:215-223. doi: 10.1016/j.ymben.2018.12.002. Epub 2018 Dec 6. PMID: 30529031.
3. Nishiguchi H, Hiasa N, Uebayashi K, Liao J, Shimizu H, Matsuda F. Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism. Metab Eng. 2019 Mar;52:273-283. doi: 10.1016/j.ymben.2019.01.004. Epub 2019 Jan 8. PMID: 30633975.
4. Kamiura R, Toya Y, Matsuda F, Shimizu H. Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli. Biotechnol Lett. 2019 Jul;41(6-7):743-751. doi: 10.1007/s10529-019-02672-8. Epub 2019 Apr 5. PMID: 30953309.
5. Maruyama M, Nishiguchi H, Toyoshima M, Okahashi N, Matsuda F, Shimizu H. Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC 6803. J Biosci Bioeng. 2019 Oct;128(4):424-428. doi: 10.1016/j.jbiosc.2019.03.016. Epub 2019 Apr 10. PMID: 30979614.
6. Ueda K, Mizuuchi R, Matsuda F, Ichihashi N. A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Qβ Replicase. Chembiochem. 2019 Sep 16;20(18):2331-2335. doi: 10.1002/cbic.201900120. Epub 2019 Aug 5. Erratum in: Chembiochem. 2019 Dec 2;20(23):2968. PMID: 31037814.
7. Kamiura R, Matsuda F, Ichihashi N. Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution. J Biosci Bioeng. 2019 Nov;128(5):558-563. doi: 10.1016/j.jbiosc.2019.05.005. Epub 2019 Jun 7. PMID: 31182278.
8. Morita K, Matsuda F, Okamoto K, Ishii J, Kondo A, Shimizu H. Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae. Microb Cell Fact. 2019 Oct 15;18(1):177. doi: 10.1186/s12934-019-1226-6. PMID: 31615527; PMCID: PMC6794801.
9. Izumi Y, Matsuda F, Hirayama A, Ikeda K, Kita Y, Horie K, Saigusa D, Saito K, Sawada Y, Nakanishi H, Okahashi N, Takahashi M, Nakao M, Hata K, Hoshi Y, Morihara M, Tanabe K, Bamba T, Oda Y. Inter-Laboratory Comparison of Metabolite Measurements for Metabolomics Data Integration. Metabolites. 2019 Oct 31;9(11):257. doi: 10.3390/metabo9110257. PMID: 31683650; PMCID: PMC6918145.
10. Okahashi N, Kawana S, Iida J, Shimizu H, Matsuda F. Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC- EI-MS/MS. Mass Spectrom (Tokyo). 2019;8(1):A0073. doi: 10.5702/massspectrometry.A0073. Epub 2019 Aug 30. PMID: 32010541; PMCID: PMC6920549.
11. 安田柊, 岡橋伸幸, 上田政宏, 有田誠, "腸内細菌のリポクオリティと生体制御",(2019) The Lipid, Vol. 30, No. 4, 51-57

2018年

1. Murase Y, Nakanishi H, Tsuji G, Sunami T, Ichihashi N. In Vitro Evolution of Unmodified 16S rRNA for Simple Ribosome Reconstitution. ACS Synth Biol. 2018 Feb 16;7(2):576-583. doi: 10.1021/acssynbio.7b00333. Epub 2017 Oct 31. PMID: 29053248.
2. Tokuyama K, Toya Y, Horinouchi T, Furusawa C, Matsuda F, Shimizu H. Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain. Biotechnol Bioeng. 2018 Jun;115(6):1542-1551. doi: 10.1002/bit.26568. Epub 2018 Mar 8. PMID: 29457640.
3. Nagai H, Masuda A, Toya Y, Matsuda F, Shimizu H. Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis. Metab Eng. 2018 May;47:1-9. doi: 10.1016/j.ymben.2018.02.012. Epub 2018 Feb 27. PMID: 29499375.
4. Ueda K, Nakajima T, Yoshikawa K, Toya Y, Matsuda F, Shimizu H. Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803. J Biosci Bioeng. 2018 Jul;126(1):38-43. doi: 10.1016/j.jbiosc.2018.01.020. Epub 2018 Feb 28. PMID: 29499995.
5. Narazaki Y, Nomura Y, Morita K, Shimizu H, Matsuda F. Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases. J Biosci Bioeng. 2018 Sep;126(3):317-321. doi: 10.1016/j.jbiosc.2018.03.008. Epub 2018 Apr 7. PMID: 29636254.
6. Ohnishi M, Anegawa A, Sugiyama Y, Harada K, Oikawa A, Nakayama Y, Matsuda F, Nakamura Y, Sasaki R, Shichijo C, Hatcher PG, Fukaki H, Kanaya S, Aoki K, Yamazaki M, Fukusaki E, Saito K, Mimura T. Molecular Components of Arabidopsis Intact Vacuoles Clarified with Metabolomic and Proteomic Analyses. Plant Cell Physiol. 2018 Jul 1;59(7):1353-1362. doi: 10.1093/pcp/pcy069. PMID: 29660082.
7. Tokumaru Y, Uebayashi K, Toyoshima M, Osanai T, Matsuda F, Shimizu H. Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of _Synechocystis_ sp. PCC 6803. Molecules. 2018 May 1;23(5):1051. doi: 10.3390/molecules23051051. PMID: 29723969; PMCID: PMC6102573.
8. Tsuji G, Sunami T, Ichihashi N. Production of giant unilamellar vesicles by the water-in-oil emulsion-transfer method without high internal concentrations of sugars. J Biosci Bioeng. 2018 Oct;126(4):540-545. doi: 10.1016/j.jbiosc.2018.04.019. Epub 2018 May 21. PMID: 29793863.
9. Hayakawa K, Matsuda F, Shimizu H. 13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production. Microb Cell Fact. 2018 May 31;17(1):82. doi: 10.1186/s12934-018-0935-6. PMID: 29855316; PMCID: PMC5977476.
10. Uebayashi K, Shimizu H, Matsuda F. Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol. 2018 Aug;102(16):7071-7081. doi: 10.1007/s00253-018-9128-9. Epub 2018 Jun 7. PMID: 29882163.
11. Ogawa K, Yoshikawa K, Matsuda F, Toya Y, Shimizu H. Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions. J Biosci Bioeng. 2018 Nov;126(5):596-602. doi: 10.1016/j.jbiosc.2018.05.015. Epub 2018 Jun 19. PMID: 29907527.
12. Araki C, Okahashi N, Maeda K, Shimizu H, Matsuda F. Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells. Mass Spectrom (Tokyo). 2018;7(1):A0067. doi: 10.5702/massspectrometry.A0067. Epub 2018 Jun 14. PMID: 29922569; PMCID: PMC6002601.
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