Publication

2019

Original papers

• "Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC6803"
  Masaharu Maruyama, Hiroki Nishiguchi, Masakazu Toyohima, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience Bioengineering 128, 4, 424-428 (2019).
• "Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms"
  Masakazu Toyoshima, Masumi Sakata, Kazuki Ohnishi, Yuma Tokumaru, Yusuke Kato,Ryutaro Tokutsu, Wataru Sakamoto, Jun Minagawa, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 127, 3, 394-402 (2019).
• "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."
  Nobuyuki Okahashi, Kousuke Maeda, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda
  Metabolic Engineering 51, 43-49 (2019).
• "Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli"
  Kento Tokuyama, Yoshihiro Toya, Fumio Matsuda, Brady Cress, Mattheos A. G. Koffas, Hiroshi Shimizu
  Metabolic Engineering 52, 215-223 (2019).
• "Effect of precise control of flux ratio between the glycolytic pathways on mevalonate production in Escherichia coli."
  Kentaro Kamata, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology and Bioengineering 116, 5, 1080-1088 (2019).
• "Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism"
  Hiroki Nishiguchi, Natsuki Hiasa, Kiyoka Uebayashi, James Liao, Hiroshi Shimizu, Fumio Matsuda
  Metabolic Engineering 52, 273-283 (2019).
• "Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli"
  Rikuto Kamiura, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Biotechnology Letters 41, 743-751 (2019).
• "Flux balance analysis of cyanobacteria reveals selective use of photosynthetic electron transport components under different spectral light conditions"
  Masakazu Toyoshima, Yoshihiro Toya, Hiroshi Shimizu
  Photosynthesis Research 143, 31-43 (2019).
• "13C-Metabolic flux analysis reveals effect of phenol on central carbon metabolism in Escherichia coli"
  Sayaka Kitamura, Yoshihiro Toya, Hiroshi Shimizu
  Frontiers in Microbiology 10, 1010 (2019).

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• "Optogenetic switch for controlling the central metabolic flux of Escherichia coli"
  Sebastian Tommi Tandar, Sachie Senoo, Yoshihiro Toya, Hiroshi Shimizu
  Metabolic Engineering 55, 68-75 (2019).

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• "Prediction of rate-limiting reactions for growth‐associated production using a constraint‐based approach"
  Kento Tokuyama, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology Journal 14, 9, e1800431 (2019).
• "High-yielding rice Takanari has superior photosynthetic response under fluctuating light to a commercial rice Koshihikari"
  Shunsuke Adachi, Yu Tanaka, Atsuko Miyagi, Makoto Kashima, Ayumi Tezuka, Yoshihiro Toya, Shunzo Kobayashi, Satoshi Ohkubo, Hiroshi Shimizu, Maki Kawai-Yamada, Rowan F Sage, Atsushi J Nagano, Wataru Yamori
  Journal of Experimental Botany 70, 19, 5287-5297 (2019).
• "Fragmentation of dicarboxylic and tricarboxylic acids in the Krebs cycle using GC-EI-MS"
  Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda
  Mass Spectrometry 8, 1, A0073 (2019).
• "In vitro production of cysteine from glucose"
  Yohei Hanatani, Makoto Imura, Hironori Taniguchi, Kenji Okano, Yoshihiro Toya, Ryo Iwakiri, Kohsuke Honda
  Applied Microbiology and Biotechnology 103, 19, 8009-8019 (2019).
• "Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative"
  Makoto Imura, Katsuaki Nitta, Ryo Iwakiri, Fumio Matsuda, Hiroshi Shimizu, Eiichiro Fukusaki
  Journal of Bioscience and Bioengineering 129, 1, 52-58 (2019).
• "Light-inducible flux control of triosephosphate isomerase on glycolysis in Escherichia coli"
  Sachie Senoo, Sebastian Tommi Tandar, Sayaka Kitamura, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology and Bioengineering 116, 12, 3292-3300 (2019).
• "Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae"
  Keisuke Morita, Fumio Matsuda, Koji Okamoto, Jun Ishii, Akihiko Kondo, Hiroshi Shimizu
  Microbial Cell Factories 18, 177 (2019).

Review papers

• "計算機工学に基づく代謝設計とその有効性の実証に関する研究"
  清水 浩
  生物工学誌 97, 1, 13-20 (2019).
• "代謝工学におけるバイオインフォマティクスの利用"
  戸谷 吉博, 松田 史生
  生物工学誌 97, 5, 261-264 (2019).

Ph.D. theses

• "Study on molecular breeding of yeast strain for bio-production based on flux balance analysis"
  森田 啓介
  (2019).