Publication

2024

Original papers

• "Identification of a novel NADPH generation reaction in the pentose phosphate pathway in Escherichia coli using mBFP"
  Koichiro Ueno, Shogo Sawada, Mai Ishibashi, Yoshiki Kanda, Hiroshi Shimizu, Yoshihiro Toya
  (2024).

  • DOI: 10.1128/jb.00276-24
• "A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes."
  Yujiro Hirose, Daniel C Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O Palsson, Victor Nizet
  mSystems (2024).

  • DOI: 10.1128/msystems.00736-24
• "Utilizing ribose 1,5-bisphosphate isomerase and RuBisCO-equipped Escherichia coli Nissle for low-carbon footprint GABA production"
  Sefli Sri Wahyu Effendi, Yoshihiro Toya, Hiroshi Shimizu, Chenfeng Xue, I-Son Ng
  ACS Sustainable Chemistry and Engineering (2024).

  • DOI: 10.1021/acssuschemeng.4c03537
• "Engineering Escherichia coli for efficient glutathione production"
  Hiroki Mori, Misato Matsui, Takahiro Bamba, Yoshimi Hori, Sayaka Kitamura, Yoshihiro Toya, Ryota Hidese, Hisashi Yasueda, Tomohisa Hasunuma, Hiroshi Shimizu, Naoaki Taoka, Shingo Kobayashi
  Metabolic Engineering 84, 180-190 (2024).

  • DOI: https://doi.org/10.1016/j.ymben.2024.07.001
• "Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin"
  Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y. Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda
  Journal of Bioscience and Bioengineering (2024).

  • DOI: 10.1016/j.jbiosc.2023.12.003

Review papers

• "Coupling and uncoupling growth and product formation for producing chemicals"
  Yoshihiro Toya, Hiroshi Shimizu
  Current Opinion in Biotechnology 87, 101133 (2024).

  • URL

Ph.D. theses

• "シアノバクテリアにおける光振動条件や代謝阻害剤が及ぼす光合成への影響の解析"
  今田辰海
  (2024).

Books

• "物質生産のための微生物代謝のin silicoデザイン、微生物を用いた有用物質生産技術の開発第１章第４節"
  戸谷吉博、清水浩
  技術情報協会, １９－２６ (2024).

2023

Original papers

• "Effect of light fluctuations on photosynthesis and metabolic flux in Synechocystis sp. PCC 6803"
  Tatsumi Imada, Chiaki Yamamoto, Masakazu Toyoshima, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology Progress (2023).

  • URL
• "Functional evaluation of non-oxidative glycolysis in Escherichia coli in the stationary phase under microaerobic conditions"
  Kenta Miyoshi, Ryutaro Kawai, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 135, 4, 291-297 (2023).

  • URL
• "Multicolor optogenetics for regulating flux ratio of three glycolytic pathways using EL222 and CcaSR in Escherichia coli "
  Hayato Akagi, Hiroshi Shimizu, Yoshihiro Toya
  Biotechnology and Bioengineering (2023).

  • URL

Review papers

• "光を利用したバイオプロセスの開発に関する研究"
  戸谷 吉博
  生物工学会誌 101, 2, 54-60 (2023).

  • URL

Books

• "13C代謝フラックス解析を利用したイソプロピルアルコール生産大腸菌の代謝改良、微生物を活用した有用物質の製造技術"
  清水浩
  CMC出版 (2023).

2022

Original papers

• "Conversion of mevalonate to isoprenol using light energy in Escherichia coli without consuming sugars for ATP supply"
  Mikoto Sano, Ryo Tanaka, Kentaro Kamata, Yoko Hirono-Hara, Jun Ishii, Fumio Matsuda, Kiyotaka Y Hara, Hiroshi Shimizu, Yoshihiro Toya
  ACS Synthetic Biology 11, 12, 3966–3972 (2022).

  • URL
• "Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli"
  Kensuke Otsuka, Taisuke Seike, Yoshihiro Toya, Jun Ishii, Yoko Hirono-Hara, Kiyotaka Y Hara, Fumio Matsuda
  Journal of Bioscience and Bioengineering 134, 6, 484-490 (2022).

  • URL
• "Logistic regression-guided identification of cofactor specificity-contributing residues in enzyme with sequence datasets partitioned by catalytic properties"
  Sou Sugiki, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu
  ACS Synthetic Biology 11, 12, 3973–3985 (2022).

  • URL
• "13C Metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia"
  Shingo Noguchi, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu
  Metabolic Engineering 73, 192-200 (2022).

  • URL
• "Metabolic pathway design for growth-associated phenylalanine production using synthetically designed mutualism"
  Ryutaro Kawai, Yoshihiro Toya, Hiroshi Shimizu
  Bioprocess and Biosystems Engineering 45, 1539-1546 (2022).

  • URL
• "Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production."
  Junya Yamamoto, Onuma Chumsakul, Yoshihiro Toya, Takuya Morimoto, Shenghao Liu, Kenta Masuda, Yasushi Kageyama, Takashi Hirasawa, Fumio Matsuda, Naotake Ogasawara, Hiroshi Shimizu, Ken-ichi Yoshida, Taku Oshima, Shu Ishikawa
  DNA Research 29, 3, 44574 (2022).

  • URL
• "Metabolic pathway engineering for the non-growth-associated succinate production in Escherichia coli based on flux solution space"
  Yoshihiro Toya, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 134, 1, 29-33 (2022).

  • URL
• "Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems"
  Yoshihiro Toya, Yoko Hirono-Hara, Hidenobu Hirayama, Kentaro Kamata, Ryo Tanaka, Mikoto Sano, Sayaka Kitamura, Kensuke Otsuka, Rei Abe-Yoshizumi, Satoshi P Tsunoda, Hiroshi Kikukawa, Hideki Kandori, Hiroshi Shimizu, Fumio Matsuda, Jun Ishii, Kiyotaka Y Hara
  Metabolic Engineering 72, 227-236 (2022).

  • URL
• "Improvement of 2, 3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae"
  Keisuke Morita, Taisuke Seike, Jun Ishii, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 133, 3, 208-212 (2022).

  • URL
• "Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution"
  Ryutaro Kawai, Yoshihiro Toya, Kenta Miyoshi, Manami Murakami, Teppei Niide, Takaaki Horinouchi, Tomoya Maeda, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu
  Biotechnology and Bioengineering 119, 3, 936-945 (2022).

  • URL

Review papers

• "多様な光に適応する藍藻のシステムバイオロジー"
  清水 浩, 戸谷 吉博
  生物物理 62, 4, 104-109 (2022).
• "バイオによるものづくりに貢献する機械学習・深層学習技術"
  徳山 健斗, 清水 浩
  化学工学会誌 86, 4, 161-164 (2022).
• "データサイエンス駆動型リジン発酵プロセス予測モデリング"
  徳山 健斗, 下平 祥貴, 寺脇 貴弘, 楠瀬 泰弘, 中井 裕章, 辻 雄一郎, 戸谷 吉博, 松田 史生, 清水 浩
  生物工学会誌 100, 2, 80 (2022).
• "発酵生産プロセスにおけるDX：データ駆動型のリジン発酵自律制御システムの開発"
  徳山 健斗, 清水 浩
  バイオサイエンスとインダストリー 80, 1, 26-30 (2022).

Others

• "バイオ系のキャリアデザイン（就職支援OG・OBインタビュー編） Interview 1"
  戸谷 吉博
  生物工学会誌 100, 9, 516-517 (2022).

  • URL

2021

Original papers

• "Reactor control system in bacterial co-culture based on fluorescent proteins using an Arduino-based home-made device"
  Minori Kusuda, Hiroshi Shimizu, Yoshihiro Toya
  Biotechnology Journal 16, 12, 2100169 (2021).

  • URL
• "An open-source Python package for 13C-based metabolic flux analysis"
  Fumio Matsuda, Kohsuke Maeda, Takeo Taniguchi, Yuya Kondo, Futa Yatabe, Nobuyuki Okahashi, Hiroshi Shimizu
  Metabolic Engineering Communications, 13, e00177 (2021).
• "Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803"
  Masakazu Toyoshima, Masumi Sakata, Yoshifumi Ueno, Yoshihiro Toya, Fumio Matsuda, Seiji Akimoto, Hiroshi Shimizu
  Journal of Proteomics 246, 104306 (2021).
• "Soft-sensor development for monitoring the lysine fermentation process"
  Kento Tokuyama, Yoshiki Shimodaira, Yohei Kodama, Ryuzo Matsui, Yasuhiro Kusunose, Shunsuke Fukushima, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 132, 2, 183-189 (2021).
• "Treatment of RB1-intact hepatocellular carcinoma with CDK4/6 inhibitor combination therapy"
  Jindan Sheng, Susumu Kohno, Nobuhiro Okada, Nobuyuki Okahashi, Kana Teranishi, Fumio Matsuda, Hiroshi Shimizu, Paing Linn, Naoko Nagatani, Minako Yamamura, Kenichi Harada, Shin-ichi Horike, Hiroshi Inoue, Seiji Yano, Sharad Kumar, Shunsuke Kitajima, Itsuki Ajioka, Chiaki Takahashi
  Hepatology (2021).
• "Random transfer of Ogataea polymorpha genes into Saccharomyces cerevisiae revealed a complex background of heat tolerance"
  Taisuke Seike, Yuki Narazaki, Yoshinobu Kaneko, Hiroshi Shimizu, Fumio Matsuda
  Journal of Fungi 7, 4, 302 (2021).
• "Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803"
  Katsunori Yoshikawa1, Kenichi Ogawa, Yoshihiro Toya, Seiji Akimoto , Fumio Matsuda, Hiroshi Shimizu
  Communications Biology 4, 343 (2021).

  • URL
• "Thioredoxin pathway in Anabaena sp. PCC 7120: case of the NADPH-thioredoxin reductase C"
  Frederic Deschoenmaeker, Shoko Mihara, Tatsuya Niwa, Hideki Taguchi, Ken-Ichi Wakabayashi, Masakazu Toyoshima, Hiroshi Shimizu, Toru Hisabori
  The Journal of Biochemistry mvab014 (2021).
• "Role of type I NADH dehydrogenase in Synechocystis sp. PCC 6803 under phycobilisome excited red light"
  Masakazu Toyoshima, Chiaki Yamamoto, Yoshifumi Ueno, Yoshihiro Toya, Seiji Akimoto, Hiroshi Shimizu
  Plant Science 304, 110798 (2021).

Review papers

• "バイオプロセス運転の最適化と自動化"
  清水 浩
  生物工学会誌 99, 538-542 (2021).
• "Recent advances in metabolic engineering-integration of in silico design and experimental analysis of metabolic pathways"
  Hiroshi Shimizu, Yoshihiro Toya
  Journal of Bioscience and Bioengineering 132, 5, 429-436 (2021).
• "フラックス解析のいろいろ"
  戸谷 吉博
  生物工学会誌 99, 1, 36 (2021).

Ph.D. theses

• "酵素反応測定と代謝フラックス解析に基づく代謝経路の律速反応の推定に関する研究"
  北村 さや香
  (2021).
• "In vitroモデル細胞を用いた代謝フラックス変化とがん細胞の増殖や生存との関係に関する研究"
  野口 真悟
  (2021).

Books

• "第Ⅳ部、3. 光合成のカギとなる段階を探せ"
  清水 浩, 豊島 正和
  光合成 (朝倉書店), 174-178 (2021).

2020

Original papers

• "Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism"
  Hiroki Nishiguchi, James Liao, Hiroshi Shimizu, Fumio Matsuda
  Metabolic Engineering Communications 11, e00153 (2020).
• "Estimation of linear and cyclic electron flows in photosynthesis based on 13C-metabolic flux analysis"
  Chiaki Yamamoto, Masakazu Toyoshima, Sayaka Kitamura, Yoshifumi Ueno, Seiji Akimoto, Yoshihiro Toya, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 131, 3, 277-282 (2020).
• "Identification of a rate-limiting step in a metabolic pathway using the kinetic model and in vitro experiment"
  Sayaka Kitamura, Hiroshi Shimizu, Yoshihiro Toya
  Journal of Bioscience and Bioengineering 131, 3, 271-276 (2020).

  • URL
• "Assessment of protein content and phosphorylation level in Synechocystis sp. PCC 6803 under various growth conditions using quantitative phosphoproteomic analysis"
  Masakazu Toyoshima, Yuma Tokumaru, Fumio Matsuda, Hiroshi Shimizu
  Molecules 25, 16, 3582 (2020).
• "Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells,"
  Shingo Noguchi, Hirokazu Ishikawa, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu
  Scientific Reports 10, 1, 13065 (2020).
• "Data science-based modeling of the lysine fermentation process"
  Kento Tokuyama, Yoshiki Shimodaira, Takahiro Terawaki, Yasuhiro Kusunose, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 130, 4, 409-415 (2020).
• "Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae"
  Hiroaki Negoro, Kengo Matsumura, Fumio Matsuda, Hiroshi Shimizu, Yoji Hata, Hiroki Ishida
  Applied Microbiology and Biotechnology 102, 20, 8909-8920 (2020).
• "Transcription factor ArcA is a flux sensor for the oxygen consumption rate in Escherichia coli"
  Naoya Nochino, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology Journal 15, 6, e1900353 (2020).

  • URL

Review papers

• "シアノバクテリア由来の光応答スイッチの大腸菌代謝工学への利用"
  戸谷 吉博
  生物工学会誌 98, 11, 608-610 (2020).
• "Flux controlling technology for central carbon metabolism for efficient microbial bio-production"
  Yoshihiro Toya, Hiroshi Shimizu
  Current Opinion in Biotechnology 64, 169-174 (2020).
• "光照射により代謝フラックスをコントロールする技術の開発"
  戸谷 吉博, 清水 浩
  バイオサイエンスとインダストリー 78, 1, 30-31 (2020).

Ph.D. theses

• "網羅的遺伝子発現解析を用いたシアノバクテリアの強光耐性機構に関する研究"
  小川 健一
  (2020).

2019

Original papers

• "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).
• "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).
• "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).
• "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).
• "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).
• "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).
• "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).
• "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).
• "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).

  • URL
• "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).

  • URL
• "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).
• "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).
• "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).
• "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).
• "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).
• "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).
• "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).

Review papers

• "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).
• "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).

Ph.D. theses

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

2018

Original papers

• "Characterization of oil-producing yeast Lipomyces starkeyi on glycerol carbon source based on metabolomics and 13C-labeling."
  Yuki Maruyama, Yoshihiro Toya, Hiroshi Kurokawa, Yuka Fukano, Atsushi Sato, Hiroyasu Umemura, Kaoru Yamada, Hideaki Iwasaki, Norio Tobori, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 102, 20, 8909-8920 (2018).
• "A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae"
  Jun Ishii, Keisuke Morita, Kengo Ida, Hiroko Kato, Shohei Kinoshita, Shoko Hataya, Hiroshi Shimizu, Akihiko Kondo, Fumio Matsuda
  Biotechnology for Biofuels 11, 180 (2018).
• "Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions"
  Kenichi Ogawa, Katsunori Yoshikawa, Fumio Matsuda, Yoshihiro Toya, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 126, 5, 596-602 (2018).
• "Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains"
  Kiyoka Uebayashi, Hiroshi Shimizu, Fumio Matsuda
  Applied Microbiology and Biotechnology 102, 16, 7071-81 (2018).
• "13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production"
  Kenshi Hayakawa, Fumio Matsuda, Hiroshi Shimizu
  Microbial Cell Factories 17, 82 (2018).
• "Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803"
  Yuma Tokumaru, Kiyoka Uebayashi, Masakazu Toyoshima, Takashi Osanai, Fumio Matsuda, Hiroshi Shimizu
  Molecules 23, 5, 1051 (2018).
• "Mass spectrometry-based method to study inhibitor-induced metabolic redirection in the central metabolism of cancer cells"
  Chie Araki, Nobuyuki Okahashi, Kousuke Maeda, Hiroshi Shimizu, Fumio Matsuda
  Mass Spectrometry 7, 1, A0067 (2018).
• "Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases"
  Yuki Narazaki, Yuta Nomura, Keisuke Morita, Hiroshi Shimizu, Fumio Matsuda
  Journal of Bioscience and Bioengineering 126, 3, 317-321 (2018).
• "Metabolic engineering of a mevalonate-producing Escherichia coli strain based on thermodynamic analysis"
  Hikaru Nagai, Ami Masuda, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Metabolic Engineering 47, 43474 (2018).
• "Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain"
  Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu
  Biotechnology and Bioengineering 115, 6, 1542-1551 (2018).
• "Integrated analysis of transcriptome and metabolome of Corynebacterium glutamicum during penicillin-induced glutamic acid production"
  Takashi Hirasawa, Masaki Saito, Katsunori Yoshikawa, Chikara Furusawa, Hiroshi Shimizu
  Biotechnology Journal 13, 5, e1700612 (2018).
• "Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803"
  Kentaro Ueda, Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 126, 1, 38-43 (2018).
• "Optimal 13C-labeling of glycerol carbon source for precise flux estimation in Escherichia coli"
  Yoshihiro Toya, Shugo Ohashi, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 125, 3, 301-305 (2018).

Review papers

• "Editorial overview: Recent progress in analytical technologies for design-build-test-learn cycle in biotechnology"
  Hiroshi Shimizu, Fumio Matsuda
  Current Opinion in Biotechnology 54, 145-147 (2018).

Ph.D. theses

• "Genome-scale metabolic design for improved target production of Escherichia coli based on flux balance analysis"
  徳山 健斗
  (2018).
• "13C代謝フラックス解析に基づいた微生物のNADPH再生および消費の収支に関する研究"
  和田圭介
  (2018).

Books

• "第25章 培養動物細胞の13C代謝フラックス解析"
  岡橋 伸幸, 松田 史生, 清水 浩
  代謝センシング-健康,食,美容,薬,そして脳の代謝を知る- (シーエムシー出版), 218-228 (2018).

2017

Original papers

• "Identification of alcohol stress tolerance genes of Synechocystis sp. PCC 6803 by using adaptive laboratory evolution"
  Takuya Matsusako, Yoshihiro Toya, Katsunori Yoshikawa, Hiroshi Shimizu
  Biotechnology for Biofuels 10, 1, 307 (2017).
• "Prediction of cross-resistance and collateral sensitivity by gene expression profiles and genomic mutations"
  Takaaki Horinouchi, Shingo Suzuki, Hazuki Kotani, Kumi Tanabe, Natsue Sakata, Hiroshi Shimizu, Chikara Furusawa
  Scientific Report 7, 14009 (2017).
• "Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with 13C-metabolic flux analysis"
  Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu
  Biotechnolgy and Bioengineering 114, 12, 2782-2793 (2017).
• "Heterologous expression of bacterial phosphoenol pyruvate carboxylase and Entner-Doudoroff pathway in Saccharomyces cerevisiae for improvement of isobutanol production"
  Keisuke Morita, Yuta Nomura, Jun Ishii, Fumio Matsuda, Akihiko Kondo, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 124, 3, 263-270 (2017).
• "The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity"
  Shunsuke Kitajima, Akiyo Yoshida, Susumu Kohno, Sawako Suzuki, Naoko Nagatani, Fengkai Li, Yuuki Nishimoto, Nobunari Sasaki, Hayato Muranaka, Yuansong Wan, Tran Thai, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu, Takumi Nishiuchi, Yutaka Suzuki, Kana Tominaga, Noriko Gotoh, Misa Suzuki, Mark Ewen, David Barbie, Osamu Hirose, Tomoaki Tanaka, Chiaki Takahashi
  Oncogene 36, 36, 5145-5157 (2017).
• "Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli"
  Ami Masuda, Yoshihiro Toya, Hiroshi Shimizu
  Bioresource Technology 245, Pt B, 1634-1640 (2017).
• "Prediction of hopeless peptides unlikely to be selected for targeted proteome analysis"
  Fumio Matsuda, Atsumi Tomita, Hiroshi Shimizu
  Mass Spectrometry 6, 1, A0056-A0056 (2017).
• "Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism"
  Fumio Matsuda, Syohei Kinoshita, Shunsuke Nishino, Atsumi Tomita, Hiroshi Shimizu
  PLoS One 12, 2, e0172742 (2017).
• "Metabolic engineering of Synechocystis sp. PCC 6803 for enhanced ethanol production based on flux balance analysis"
  Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu
  Bioprocess and Biosystems Engineering 40, 791-796 (2017).
• "Metabolic flux analysis of Synechocystis sp. PCC6803 ΔnrtABCD mutant reveals a mechanism for metabolic adaptation to nitrogen-limited conditions"
  Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Plant and Cell Physiology 58, 3, 537-545 (2017).

Review papers

• "Learning from quantitative data to understand central carbon metabolism"
  Fumio Matsuda, Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology Advances 35, 8, 971-980 (2017).

Ph.D. theses

• "出芽酵母の代謝解析とその応用による物質生産性向上に関する研究"
  早川 謙嗣
  (2017).
• "遊離代謝物質に基づく物質生産大腸菌およびがん細胞の13C代謝フラックス解析に関する研究"
  岡橋 伸幸
  (2017).

Books

• "Chapter 7, Omics integrations for the state analysis of microbial processes"
  Hiroshi Shimizu, Chikara Fursawa, Takashi Hirasawa, Katsunori Yoshikawa, Yoshihiro Toya, Tomokazu Shirai, Fumio Matsuda
  BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 5: Applied Bioengineering: Innovations and Future Directions, 201-236 (2017).
• "Chapter 8, Control of Microbial Processes"
  Kazuyuki Shimizu, Hiroshi Shimizu, Toshiomi Yoshida
  BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 5: Applied Bioengineering: Innovations and Future Directions, 237- 258 (2017).

2016

Original papers

• "Metabolic Adaptation to Nutritional Stress in Human Colorectal Cancer"
  Miyo Masaaki, Konno Masamitsu, Nishida Naohiro, Sueda Toshinori, Noguchi Kozo, Matsui Hidetoshi, Colvin Hugh, Kawamoto Koichi, Koseki Jun, Haraguchi Naotsugu, Nishimura Junichi, Hata Taishi, Gotoh Noriko, Matsuda Fumio, Satoh Taroh, Mizushima Tsunekazu, Shimizu Hiroshi, Doki Yuichiro, Mori Masaki, Ishii Hideshi
  Scientific Reports 6, 38415 (2016).
• "Combinatorial deletions of glgC and phaCE enhance ethanol production in Synechocystis sp. PCC 6803"
  Katsunori Namakoshi, Tubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu
  Journal of Biotechnology 239, -, 13-19 (2016).
• "13C-metabolic flux analysis for mevalonate producing Escherichia coli"
  Keisuke Wada, Yoshihiro Toya, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 123, 2, 177-182 (2016).
• "Positive effects of proline addition on the central metabolism of wild-type and lactic acid-producing Saccharomyces cerevisiae strains"
  Riyanto Heru Nugroho, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu
  Bioprocess and Biosystems Engineering 39, 11, 1711-1716 (2016).
• "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"
  Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda
  Analytical and Bioanalytical Chemistry 408, 22, 6133-6140 (2016).
• "Investigation of useful carbon tracers for 13C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions"
  Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu
  Metabolic Engineering Communications 3, -, 187-195 (2016).
• "Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production"
  Kenshi Hayakawa, Fumio Matsuda, Hiroshi Shimizu
  AMB Express 6, 1, 44569 (2016).
• "Enhancement of 1,5-diaminopentane production in a recombinant strain of Corynebacterium glutamicum by Tween 40 addition"
  Yuta Matsushima, Takashi Hirasawa, Hiroshi Shimizu
  Journal of General and Applied Microbiology 62, 1, 42-45 (2016).

Review papers

• "計算機シミュレーションを利用した代謝デザイン技術－有用物質生産の効率化を目的とした代謝経路の改変"
  戸谷 吉博
  化学と生物 (2016).
• "Recent advances in amino acid production by microbial cells"
  Takashi Hirasawa, Hiroshi Shimizu
  Current Opinion in Biotechnology 42, 133-146 (2016).

Books

• "Chapter 11. Glutamic acid fermentation: Discovery of glutamic acid-producing microorganisms, analysis of the production mechanism, metabolic engineering and industrial production process"
  Takashi Hirasawa, Hiroshi Shimizu
  BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 4: Indsutrial Biotechnology Products and Processes, 339-360 (2016).

2015

Original papers

• "Construction of a genome-scale metabolic model of Arthrospira platensis NIES-39 and metabolic design for cyanobacterial bioproduction"
  Katsunori Yoshikawa, Shimpei Aikawa, Yuta Kojima, Yoshihiro Toya, Chikara Furusawa, Akihiko Kondo, Hiroshi Shimizu
  PLoS One 10, 12, e0144430 (2015).
• "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism"
  Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek, Andrea Rocco
  PLoS One 10, 10, e0139507 (2015).
• "Phenotypic Convergence in Bacterial Adaptive Evolution to Ethanol Stress"
  Takaaki Horinouchi, Shingo Suzuki, Takashi Hirasawa, Naoaki Ono, Tetsuya Yomo, Hiroshi Shimizu, Chikara Furusawa
  BMC Evolutionary Biology 15, 180 (2015).
• "Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations"
  Nobuyuki Okahashi, Susumu Kohno, Shunsuke Kitajima, Fumio Matsuda, Chiaki Takahashi, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 120, 6, 725-31 (2015).
• "Enhanced dipicolinic acid production during the stationary phase in Bacillus subtilis by blocking acetoin synthesis"
  Yoshihiro Toya, Takashi Hirasawa, Shu Ishikawa, Onuma Chumsakul, Takuya Morimoto, Shenghao Liu, Kenta Masuda, Yasushi Kageyama, Katsuya Ozaki, Naotake Ogasawara, Hiroshi Shimizu
  Bioscience, Biotechnology, and Biochemistry 79, 12, 2073-80 (2015).
• "13C-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae"
  Kenshi Hayakawa, Shuichi Kajihata, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 120, 5, 532-8 (2015).
• "Metabolomic analysis of acid stress response in Saccharomyces cerevisiae"
  Riyanto Heru Nugroho, Katsunori Yoshikawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 120, 4, 396-404 (2015).
• "13C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect"
  Shuichi Kajihata, Fumio Matsuda, Mika Yoshimi, Kenshi Hayakawa, Chikara Furusawa, Akihisa Kanda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 120, 2, 140-144 (2015).
• "Absolute quantitation of glycolytic intermediates reveals thermodynamic shifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes"
  Shunsuke Nishino, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 120, 3, 280-6 (2015).
• "SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes"
  Yoshihiro Toya, Takanori Shiraki, Hiroshi Shimizu
  Biotechnology and Bioengineering 112, 4, 759-768 (2015).
• "Nano-scale liquid chromatography coupled to tandem mass spectrometry using the multiple reaction monitoring mode based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra fast mass spectrometry"
  Fumio Matsuda, Tairo Ogura, Atsumi Tomita, Ichiro Hirano, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 119, 1, 117-20 (2015).
• "Effect of malic enzyme on ethanol production by Synechocystis sp. PCC 6803"
  Katsunori Yoshikawa, Takashi Hirasawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 119, 1, 82-84 (2015).

Review papers

• "代謝デザインと13C同位体標識を用いた代謝フラックス解析の物質生産への応用"
  清水 浩, 松田 史生, 戸谷 吉博
  化学と生物 53, 7, 455-461 (2015).

Ph.D. theses

• "微生物育種に向けた多重遺伝子破壊の探索手法の開発"
  大野 聡
  (2015).
• "13C代謝フラックス解析ソフトウェアの開発と真核生物への応用"
  梶畠 秀一
  (2015).
• "シアノバクテリアの代謝フラックス解析法の開発と異なる栄養条件におけるSynechocystis sp. PCC6803の代謝解析"
  仲嶋 翼
  (2015).
• "Metabolomics study of Saccharomyces cerevisiae under acid stress condition"
  Riyanto Heru Nugroho
  (2015).

2014

Original papers

• "Integrated Metabolic Flux and Omics Analysis of Synechocystis sp. PCC 6803 under Mixotrophic and Photoheterotrophic Conditions"
  Tsubasa Nakajima, Shuichi Kajihata, Katsunori Yoshikawa, Fumio Matsuda, Chikara Furusawa, Hiroshi Shimizu
  Plant and Cell Physiology 55, 9, 1605-1612 (2014).
• "Enhanced acetic acid and succinic acid production under microaerobic conditions by Corynabacterium glutamicum harboring Escherichia coli transhydrogenase gene pntAB"
  Yuto Yamauchi, Takashi Hiraswa, Msato Nishii, Chikara Furuasawa, Hiroshi Shimizu
  Journal of General and Applied Microbiology 60, 3, 112-118 (2014).
• "Reliable metabolic flux estimation in Escherichia coli central carbon metabolism using intracellular free amino acids"
  Nobuyuki Okahashi, Shuichi Kajihata, Chikara Furusawa, Hiroshi Shimizu
  Metabolites 30, 4(2), 408-420 (2014).
• "OpenMebius: An open source software for isotopically nonstationary 13C-based metabolic flux analysis"
  Shuichi Kajihata, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu
  BioMed Research International, 627014 (2014).
• "Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli Journal: Microbial Cell Factories"
  Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa, Hiroshi Shimizu
  Microbial Cell Factories 7, 13, 64 (2014).
• "13C-Metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain"
  Yoshihiro Toya, Takashi Hirasawa, Takuya Morimoto, Kenta Masuda, Yasushi Kageyama, Katsuya Ozaki, Naotake Ogasawara, Hiroshi Shimizu
  Journal of Biotechnology 10, 179, 42-49 (2014).
• "Development of an automated culture system for laboratory evolution"
  Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu, Chikara Furusawa
  Journal of Laborarory Automation 19, 5, 478-82 (2014).
• "FastPros: Screening of reaction knockout strategies for metabolic engineering"
  Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa
  Bioinformatics 30, 7, 981-7 (2014).
• "Addendum, Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction"
  Takashi Hirasawa, Yoshihiro Ida, Chikara Furusawa, Hiroshi Shimizu
  Bioengineered 5, 2, 123-128 (2014).
• "Metabolic engineering of Saccharomyces cerevisiae for improving succinic acid production based on metabolic profiling"
  Yuma Ito, Takashi Hirasawa, Hiroshi Shimizu
  Bioscience, Biotechnology, and Biochemistry 78, 1, 151-9 (2014).

Review papers

• "代謝シミュレーションによる細胞内代謝のデザインと工学的応用"
  松田 史生, 吉川 勝徳, 清水 浩
  生物工学会誌 92, 11, 593-597 (2014).

Books

• "Chapter 17 Glutamic Acid"
  Takashi Hirasawa, Hiroshi Shimizu
  Bioprocessing of Renewable Resources to Commodity Bioproducts (Weiley), 473-495 (2014).

2013

Original papers

• "A vector library for silencing central carbon-metabolism genes with antisense RNAs in Escherichia coli."
  Nobutaka Nakashima, Satoshi Ohno, Katsunori Yoshikawa, Hiroshi Shimizu, Tomohiro Tamura
  Applied and Environmental Microbiology 80, 2, 564-73 (2013).
• "ArtPathDesign -Rational heterologous pathway design system for the production of　nonnative metabolites"
  Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 116, 4, 524-527 (2013).
• "Genome-wide identification of the targets for genetic manipulation to improve L-lactate production by Saccharomyces cerevisiae by using a single-gene deletion strain collection"
  Takashi Hirasawa, Masakado Takekuni, Katsunori Yoshikawa, Aki Ookubo, Chikara Furusawa, Hiroshi Shimizu
  Journal of Biotechnology 168, 2, 185-193 (2013).
• "Time-resolved metabolomics of a novel trebouxiophycean alga using 13CO2 feeding"
  Takuro Ito, Masahiro Sugimoto, Yoshihiro Toya, Yoshitaka Ano, Norihide Kurano, Tomoyoshi Soga, Masaru Tomita
  Journal of Bioscience and Bioengineering 116, 3, 408-415 (2013).
• "Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions"
  Katsunori Yoshikawa, Takashi Hirasawa, Kenichi Ogawa, Yuki Hidaka, Tsubasa Nakajima, Chikara Furusawa, Hiroshi Shimizu
  Biotechnology Journal 8, 5, 513-514 (2013).
• "Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction"
  Yoshihiro Ida, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 97, 11, 4811-4819 (2013).
• "Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays"
  Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo
  PLoS One 8, 1, e54571 (2013).
• "In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites"
  Satoshi Ohno, Chikara Furusawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 115, 2, 221-228 (2013).
• "Systems metabolic engineering for the production of bio‐nylon precursor"
  Hiroshi Shimizu
  Biotechnology Journal 8, 5, 513-514 (2013).
• "Flux analysis and metabolomics for systematic metabolic engineering of microorganisms"
  Yoshihiro Toya, Hiroshi Shimizu
  Biotechnology Advances 31, 6, 818-826 (2013).
• "Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction"
  Takashi Hirasawa, Yoshihiro Ida, Chikara Furuasawa, Hiroshi Shimizu
  Bioengineered 5, 3, 123-128 (2013).

Review papers

• "生命現象の数理表現と生命システムデザイン"
  清水 浩
  生物工学会誌 91, 12, 712-716 (2013).
• "Flux analysis and metabolomics for systematic metabolic engineering of microorganisms"
  Toya Yoshihiro, Shimizu Hiroshi
  Biotechnology Advances 31, 6, 818-826 (2013).

Ph.D. theses

• "出芽酵母を用いた物質生産のための代謝設計に関する研究"
  井田 祥弘
  (2013).
• "Development of computational method for heterologous pathways design"
  Sunisa Chatsurachai
  (2013).
• "遊離アミノ酸および中間代謝物質の13C標識情報に基づく代謝フラックス解析に関する研究"
  森 英詞
  (2013).

2012

Original papers

• "Molecular Mechanisms and Metabolic Engineering of Glutamate Overproduction in Corynebacterium glutamicum"
  Takashi Hirasawa, Jongpill Kim, Tomokazu Shirai, Chikara Furusawa, Hiroshi Shimizu
  Reprogramming Microbial Metabolic Pathways 64, 261-281 (2012).
• "Systems Metabolic Engineering: The Creation of Microbial Cell Factories by Rational Metabolic Design and Evolution"
  Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu
  Advances in biochemical engineering/biotechnology 131, 44584 (2012).
• "An in silico platform for the design of heterologous pathways in nonnative metabolite production"
  Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu
  BMC Bioinformatics 13, 1, 93 (2012).
• "Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis"
  Yuki Usui, Takashi Hirasawa, Chikara Furusawa, Tomokazu Shirai, Natsuko Yamamoto, Hirotada Mori, Hiroshi Shimizu
  Microbial Cell Factories 11, 1, 87 (2012).
• "Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data"
  Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita, Kazuyuki Shimizu
  Molecular BioSystems 8, 10, 2593-2604 (2012).
• "Understanding the mechanism of heat stress tolerance caused by high trehalose accumulation in Saccharomyces cerevisiae using DNA microarray"
  Siraje Arif Mahmud, Takashi Hirasawa, Chikara Furusawa, Katsunori Yoshikawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 113, 4, 526-528 (2012).
• "Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae"
  Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 113, 2, 192-195 (2012).

Review papers

• "光合成微生物システムバイオロジー"
  吉川 勝徳, 古澤 力, 平沢 敬, 清水 浩
  生物工学会誌 90, 10, 627-628 (2012).
• "代謝工学の創成と発展、-代謝解析とオミクス研究との融合"
  清水 浩, 古澤 力, 平沢 敬, 吉川 勝徳, 小野 直亮, 戸谷 吉博, 白井 智量
  生物工学会誌 90, 10, 619-620 (2012).
• "Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses (出芽酵母における複数の環境ストレスに対するトレハロース蓄積の効果の差異)"
  Siraje Arif Mahmud, 平沢敬, 清水浩
  生物工学会誌 90, 2, 80 (2012).

Books

• "Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution"
  Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu
  Advanced Biochemical Engineering/Biotechnology (Springer), 1-23 (2012).
• "Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum (Springer)"
  Takashi Hirasawa, Jongpill Kim, Tomokazu Shirai, Chikara Furusawa, Hiroshi Shimizu
  Subcellular Biochemistry Vol. 64, Reprogramming Microbial Metabolic Pathways (Springer), 261-281 (2012).
• "Chapter3, Design of Superior Cell Factories Based on Systems Wide Omics Analysis"
  Katsunori Yoshikawa, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Systems Metabolic Engineering (Springer), 57-82 (2012).
• "第2節　ゲノムスケール代謝デザインとフラックス解析による微生物細胞創製"
  清水 浩, 古澤 力, 白井 智量, 吉川 勝徳, 平沢 敬
  合成生物工学の隆起 ―有用物質の新たな生産法構築をめざして― 第3章 オミクス解析の視点 (シーエムシー出版), 57-66 (2012).
• "第12章 ゲノム・生物情報工学"
  清水 浩
  遺伝子工学 (化学同人), 170-181 (2012).

2011

Original papers

• "Evaluating 13C enrichment data of free amino acids for precise metabolic flux analysis."
  Eiji Mori, Chikara Furusawa, Shuichi Kajihata, Tomokazu Shirai, Hiroshi Shimizu
  Biotechnology Journal 6, 11, 1377-1378 (2011).
• "Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803"
  Katsunori Yoshikawa, Yuta Kojima, Tsubasa Nakajima, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 92, 2, 347-358 (2011).

  • URL
• "Improving protein secretion of a transglutaminase-secreting Corynebacterium glutamicum recombinant strain on the basis of 13C metabolic flux analysis"
  Motoki Umakoshi, Takashi Hirasawa, Chikara Furusawa, Yasuhiro Takenaka, Yoshimi Kikuchi, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 112, 6, 595-601 (2011).

  • URL
• "Engineering strategy of yeast metabolism for higher alcohol production"
  Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo,
  Microbial Cell Factories 10, 1, 70 (2011).

  • URL
• "Investigation of phosphorylation status of OdhI protein during penicillin- and Tween 40-triggered glutamate overproduction by Corynebacterium glutamicum"
  Jongpill Kim, Takashi Hirasawa, Masaki Saito, Chikara Furusawa, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 91, 1, 143-151 (2011).

  • URL
• "Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae."
  Katsunori Yoshikawa, Tadamasa Tanaka, Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Yeast 28, 5, 349-361 (2011).

Review papers

• "Metabolic flux analysis and visualization"
  Yoshihiro Toya, Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
  Journal of Proteome Research 10, 8, 3313-3323. (2011).

Ph.D. theses

• "長期植え継ぎ培養を用いた大腸菌のエタノールストレスへの適応に関する研究"
  堀之内 貴明
  (2011).

2010

Original papers

• "Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress"
  Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu
  BMC Genomics 11, 1, 579 (2010).
• "Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays"
  Takaaki Horinouchi, Katsunori Yoshikawa, Risa Kawaide, Chikara Furusawa, Yoshihiro Nakao, Takashi Hirasawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 110, 5, 602-607 (2010).
• "13C-Metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites"
  Yoshihiro Toya, Nobuyoshi Ishii, Kenji Nakahigashi, Takashi Hirasawa, Tomoyoshi Soga, Masaru Tomita, Kazuyuki Shimizu
  Biotechnology Progress 26, 4, 975-992 (2010).

  • URL
• "Requirement of de novo synthesis of the OdhI protein in penicillin-induced glutamate production by Corynebacterium glutamicum"
  Jongpill Kim, Hirohisa Fukuda, Takashi Hirasawa, Keisuke Nagahisa, Kazuo Nagai, Masaaki Wachi, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 86, 3, 911-920 (2010).
• "Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses"
  Siraje Arif Mahmud, Takashi Hirasawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 109, 3, 262-266 (2010).
• "Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways"
  Tadashi Yamada, Jianhong Ou, Chikara Furusawa, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu
  IET Systems Biology 4, 1, 82-89 (2010).

Review papers

• "Saccharomyces cerevisiae and DNA microarray analyses: what did we learn from it for a better understanding and exploitation of yeast biotechnology"
  Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 87, 2, 391-400 (2010).
• "Development of a Prediction System for Metabolic Fluxes based on Genome Information"
  Yohei Shinfuku, Natee Sorpitiporn, Masahiro Sono, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu
  ソフトウエアバイオロジー 9, 18-21 (2010).

Ph.D. theses

• "A study of the effect of trehalose accumulation on environmental stresses in Saccharomyces cerevisiae"
  Siraje Arif Mahmud
  (2010).
• "Metabolic engineering approaches for glutamate production in Corynebacterium glutamicum"
  Jong Pill Kim
  (2010).

2009

Original papers

• "Investigating the effectiveness of DNA microarray analysis for identifying the genes involved in L-lactate production by Saccharomyces cerevisiae"
  Takashi Hirasawa, Aki Ookubo, Katsunori Yoshikawa, Keisuke Nagahisa, Chikara Furusawa, Hideki Sawai, Hiroshi Shimizu
  Applied Microbiology and Biotechnology 84, 6, 1149-1159 (2009).
• "Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system"
  Jianhong Ou, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu
  BioSystems 97, 3, 160-164 (2009).
• "Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae using DNA Microarray"
  Thai Nho Dinh, Keisuke Nagahisa, Katsunori Yoshikawa, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu
  Bioprocess and Biosystems Engineering 32, 5, 681-688 (2009).
• "Systematic phenome analysis of Escherichia coli multiple‐knockout mutants reveals hidden reactions in central carbon metabolism"
  Kenji Nakahigashi,Yoshihiro Toya, Nobuyoshi Ishii, Tomoyoshi Soga, Miki Hasegawa, Hisami Watanabe, Yuki Takai, Masayuki Honma, Hirotada Mori, Masaru Tomita
  Molecular Systems Biology 5, 1, 306 (2009).
• "Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum"
  Yohei Shinfuku, Natee Sorpitiporn, Masahiro Sono, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Microbial Cell Factories 8, 1, 43 (2009).
• "Proteomic analysis of responses to osmotic stress in laboratory and sake-brewing strains of Saccharomyces cerevisiae"
  Takashi Hirasawa, Kazuyuki Yamada, Keisuke Nagahisa, Thai Nho Dinh, Chikara Furusawa, Yoshio Katakura, Suteaki Shioya, Hiroshi Shimizu
  Process Biochemistry 44, 6, 647-653 (2009).
• "Analysis of metabolic network based on conservation of molecular structure"
  Tomoharu Hogiri, Chikara Furusawa, Yohei Shinfuku, Naoaki Ono, Hiroshi Shimizu
  BioSystems 95, 3, 175-178 (2009).
• "Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae"
  Katsunori Yoshikawa, Tadamasa Tanaka, Chikara Furusawa, Keisuke Nagahisa, Takashi Hirasawa, Hiroshi Shimizu
  FEMS Yeast Research 9, 1, 32-44 (2009).
• "Effect of trehalose accumulation on response to saline stress in Saccharomyces cerevisiae"
  Siraje Arif Mahmud, Keisuke Nagahisa, Takashi Hirasawa, Katsunori Yoshikawa, Kengo Ashitani, Hiroshi Shimizu
  Yeast 26, 1, 17-30 (2009).
• "Model-based analysis of non-specific binding for　background correction of high-density oligonucleotide　microarrays"
  Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo
  Bioinfromatics 25, 1, 36-41 (2009).
• "Effect of odhA overexpression and odhA antisense RNA expression on Tween-40-triggered glutamate production by Corynebacterium glutamicum"
  Jongpill Kim, Takashi Hirasawa, Yoshiyasu Sato, Keisuke Nagahisa, Chikara Furusawa, Hiroshi Shimizu
  Applied Microbiology Biotechnology 81, 6, 1097-1106 (2009).

Review papers

• "乳酸生産能を付与した酵母の網羅的遺伝子発現情報に基づいた生産性向上のための育種"
  平沢 敬, 大久保 亜紀, 吉川 勝徳, 古澤 力, 清水 浩
  ソフトウエアバイオロジー 8, 54-61 (2009).

Ph.D. theses

• "細胞育種に向けた遺伝子発現と表現型の網羅的情報の解析"
  吉川 勝徳
  (2009).
• "Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae"
  Thai Nho Dinh
  (2009).
• "Study of promoter activation via single cell analysis"
  Jianhong Ou
  (2009).

2008

Original papers

• "Genome-wide analysis of the effects of location and number of stress response elements on gene expression in Saccharomyces cerevisiae"
  Katsunori Yoshikawa, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 106, 5, 507-510 (2008).
• "Characterization of new isolated Ralstonia eutropha strain A-04 and kinetic study of biodegradable copolyester poly(3-hydroxybutyrate-co-4-hydroxybutyrate) production"
  Suchada Chaprateep, Yoshio Katakura, Sirirat Visetkoop, Hiroshi Shimizu, Songsri Kulpreecha, Suteaki Shioya
  Journal of Industrial Microbiology and Biotechnology 35, 11, 1205-1215 (2008).
• "Improvement of L-lactate production by CYB2 gene disruption in a recombinant Saccharomyces cerevisiae strain under low pH condition"
  Aki Ookubo, Takashi Hirasawa, Katsunori Yoshikawa, Keisuke Nagahisa, Chikara Furusawa, Hiroshi Shimizu
  Bioscience, Biotechnology, and Biochemistry 72, 11, 3063-3066 (2008).
• "Distinct roles of two anaplerotic pathways in glutamate production induced by biotin limitation in Corynebacterium glutamicum"
  Hiroki Sato, Keita Orishimo, Tomkazu Shirai, Takashi Hirasawa, Keisuke Nagahisa, Hiroshi Shimizu, Masaaki Wachi
  Journal of Bioscience and Bioengineering 106, 1, 51-58 (2008).
• "Adaptation of Saccharomyces cerevisiae cells to high ethanol concentration and changes in fatty acid composition of membrane and cell size"
  Thai Nho Dinh, Keisuke Nagahisa, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu
  PloS One 3, 7, e2623 (2008).
• "An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays."
  Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Tomoharu Agata, Akiko Kashiwagi, Hiroshi Shimizu, Tetsuya Yomo
  Bioinformatics 24, 10, 1278-1285 (2008).
• "Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells."
  Jianhong Ou, Tadashi Yamada, Keisuke Nagahisa, Takashi Hirasawa, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu
  Molecular BioSystems 4, 2, 128-134 (2008).

Review papers

• "微生物代謝のシステムバイオロジー ―オミックス解析からシミュレーションへ―"
  戸谷吉博, 石井伸佳, 冨田勝
  バイオインダストリー 25, 44-51 (2008).
• "Beer Volatile Compounds and Their Application to Low-Malt Beer Fermentation"
  Michiko Kobayashi, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 106, 4, 317-323 (2008).
• "バイオ情報を基盤とする有用生物創製の時代を拓く代謝情報工学"
  清水 浩, 古澤 力, 平沢 敬
  バイオサイエンスとインダストリー 66, 8, 426-432 (2008).
• "ビール醸造におけるアルコール濃度と揮発性成分の同時制御法,"
  小林 倫子, 清水 浩, 塩谷 捨明
  ソフトウエアバイオロジー 7, 44-47 (2008).
• "ガスクロマトグラフ-質量分析計によるコリネ型細菌の精密な代謝フラックス解析と核磁気共鳴を用いた解析結果の検証"
  白井 智量, 松崎 匡浩, 葛本 雅宣, 永久 圭介, 古澤 力, 塩谷 捨明, 清水 浩
  生物工学会誌 86, 1, 14 (2008).

Ph.D. theses

• "代謝ネットワークに見られる遺伝子発現の環境応答と揺らぎの解析"
  山田 忠司
  (2008).

Books

• "メタボロミクスの先端技術と応用, 第14章メタボロームデータを用いた代謝フラックス解析 (シーエムシー出版)"
  清水 浩, 古澤 力, 白井 智量
  (2008).

2007

Original papers

• "Analysis of fluctuation in protein abundance without promoter regulation based on Escherichia coli continuous culture"
  Tadashi Yamada, Chikara Furusawa, Keisuke Nagahisa, Akiko Kashiwagi, Tetsuya Yomo, Hiroshi Shimizu
  Biosystems 90, 3, 614-622 (2007).
• "Metabolic pathway rerouting through genomic data analysis for industrial application of Saccharomyces cerevisiae"
  Suteaki Shioya, Hiroshi Shimizu, Takashi Hirasawa, Keisuke Nagahisa, Chikara Furusawa, Gaurav Pandey, Yoshio Katakura
  Biochemical Engineering Journal 36, 1, 28-37 (2007).
• "Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis"
  Yoshihiro Toya, Nobuyoshi Ishii, Takashi Hirasawa, Miki Naba, Kenta Hirai, Kaori Sugawara, Saori Igarashi, Kazuyuki Shimizu, Masaru Tomita, Tomoyoshi Soga
  Journal of Chromatography 1159, 134-141 (2007).
• "Reduction of lactate production in Lactococcus lactis, a combined strategy: metabolic engineering by introducing the foreign alanine dehydrogenase gene and hemin addition"
  Agustin Krisna Wardani, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya
  World Journal of Microbiology and Biotechnology 23, 7, 947-953 (2007).
• "Identification of target genes for conferring ethanol stress-tolerance to yeast Saccharomyces cerevisiae based on DNA microarray data analysis"
  Takashi Hirasawa, Katsunori Yoshikawa, Yuki Nakakura, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Hiroshi Shimizu, Suteaki Shioya
  Journal of Biotechnology 131, 1, 34-44 (2007).
• "Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis"
  Tomokazu Shirai, Koki Fujimura, Chikara Furusawa, Keisuke Nagahisa, Suteaki Shioya, Hiroshi Shimizu
  Microbial Cell Factories 6, 1, 44731 (2007).
• "Analysis of hemin effect on lactate reduction in Lactococcus lactis"
  Machiko Nagayasu, Agustin Krisna Wardani, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 103, 6, 529-534 (2007).
• "Physiological analysis of yeast cells by flow cytometry during serial-repitching of low-malt beer fermentation"
  Michiko Kobayashi, Hiroshi Shimizu, Suteaki Shioya,
  Journal of Bioscience and Bioengineering 103, 5, 451-456 (2007).
• "Extracting hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using self- organizing map: biosynthesis of amino acids"
  Gaurav Pandey, Katsunori Yoshikawa, Takashi Hirasawa, Keisuke Nagahisa, Yoshio Katakura, Chikara Furusawa, Hiroshi Shimizu, Suteaki Shioya
  Applied Microbiology and Biotechnology 75, 2, 415-426 (2007).
• "Kinetic modeling of kefiran production in mixed culture of Lactobacillus kefiranofaciens and Saccharomyces cerevisiae"
  Benjamas Cheirsilp, Hiroshi Shimizu, Suteaki Shioya
  Process Biochemistry 42, 4, 570-579 (2007).
• "Multiple high throughput analyses monitor the response of E. coli to perturbations"
  Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita
  Science 316, 5824, 593-597 (2007).

Review papers

• "バイオ情報工学の展開"
  清水 浩
  ソフトウエアバイオロジー 6, 3月7日 (2007).

Ph.D. theses

• "コリネ型細菌のグルタミン酸生産における代謝解析に関する研究"
  白井 智量
  (2007).

Books

• "Production of glutamate and glutamate-related amino acids: molecular mechanism analysis and metabolic engineering, Amino Acid Biosynthesis – Pathways, Regulation and Metabolic Engineering"
  Hiroshi Shimizu, Takashi Hirasawa
  Microbiology Monographs (Springer) 5, 1-38 (2007).

2006

Original papers

• "Comparison of transcriptional responses to osmotic stresses induced by NaCl and sorbitol additions in Saccharomyces cerevisiae using DNA microarray"
  Takashi Hirasawa, Kengo Ashitani, Katsunori Yoshikawa, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 102, 6, 568-571 (2006).
• "Simultaneous control of apparent extract and volatile compounds concentrations in low-malt beer fermentation"
  Michiko Kobayashi, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya
  Applied Microbiology Biotechnology 73, 3, 549-558 (2006).
• "Precise metabolic flux analysis of coryneform bacteria with gas spectrometry-mass spectrometry and verification of nuclear magnetic resonance"
  Tomokazu Shirai, Kunihiro Matsuzaki, Masanori Kuzumoto, Keisuke Nagahisa, Chikara Furusawa, Suteaki Shioya, Hiroshi Shimizu
  Journal of Bioscience and Bioengineering 102, 5, 413-424 (2006).
• "Characterization and enzymatic degradation of microbial copolyester P(3HB-co-3HV)s produced by metabolic reaction model-based system"
  Suchada Chanprateep, Hiroshi Shimizu, Suteaki Shioya
  Polymer Degradation and Stability 91, 12, 2941-2950 (2006).
• "Comparative analysis of transcriptional responses to saline stress in the laboratory and brewing strains of Saccharomyces cerevisiae with DNA microarray"
  Takashi Hirasawa, Yuki Nakakura, Katsunori Yoshikawa, Kengo Ashitani, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Hiroshi Shimizu, Suetaki Shioya
  Applied Microbiology and Biotechnology 70, 3, 346-357 (2006).
• "Robustness of the cascade pH and DO control in a symbiotic nisin production process system of L-lactis and K. marxianus"
  Agustin Krisna Wardani, Sunao Egawa, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 101, 3, 274-276 (2006).
• "Computational prediction of impact of rerouting the carbon flux in metabolic pathway on cell growth and nisin production by Lactococcus lactis"
  Agustin Krisna Wardani, Sunao Egawa, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya
  Biochemical Engineering Journal 28, 3, 220-230 (2006).

Review papers

• "情報科学を基盤とする有用生物創製にむけて"
  清水 浩, 平沢 敬, 永久 圭介, 古澤 力, 片倉 啓雄, 塩谷 捨明
  ソフトウェアバイオロジー 5, 39-42 (2006).
• "Downregulation of pyruvate kinase gene (pyk) in a glutamate producing Corynebacterium glutamicum strain"
  Navaporn Posayapisit, Keisuke Nagahisa, Hiroshi Shimizu
  Report of The 1st UNESCO Postgraduate Inter-University Course in Biotechnology, 2004-2005, 139-149 (2006).

Books

• "代謝フラックス解析"
  清水 浩
  バイオインフォマティクス事典, バイオインフォマティクス学会編 (共立出版), 709-711 (2006).
• "代謝制御解析"
  清水 浩
  バイオインフォマティクス事典, バイオインフォマティクス学会編 (共立出版), 716-717 (2006).
• "４章メタボリックエンジニアリング"
  清水 浩
  バイオプロダクション, 化学工学会バイオ部会編 (コロナ社), 57-62 (2006).

2005

Original papers

• "Application of a mathematical model and differential evolution algorithm approach to optimization of bacteriocin production by Lactococcus lactis C7"
  Sompop Moonchai, Weeranuch Madlhoo, Kanidtha Jariyachavalit, Hiroshi Shimizu, Suteaki Shioya, Somhchai Chauvatcharin
  Bioprocess and Biosystems Engineering 28, 1, 15-26 (2005).
• "On-line estimation and control of apparent extract concentration in low-malt beer fermentation"
  Michiko Kobayashi, Toshinari Hiroshima, Keisuke Nagahisa, Hiroshi Shimizu, Suetaki Shioya
  Journal of the Institute of Brewing 111, 2, 128-136 (2005).
• "DNA microarray analysis on Saccharomyces cerevisiae under high carbon dioxide concentration in fermentation process"
  Keisuke Nagahisa, Toshiharu Nakajima, Katsunori Yoshikawa, Takashi Hirasawa, Yoshio Katakura, Chikara Furusawa, Suteaki Shioya, Hiroshi Shimizu
  Biotechnology and Bioprocess Engineering 10, 5, 451-461 (2005).
• "Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria"
  Tomokazu Shirai, Akinori Nakato, Noriyuki Izutani,Keisuke Nagahisa, Suteaki Shioya, Eiichiro Kimura,Yutaka Kawarabayashi, Akihiko Yamagishi, Takashi Gojobori, Hiroshi Shimizu
  Metabolic Engineering 7, 2, 59-69 (2005).

Review papers

• "生分解性高分子ポリヒドロキシアルカノエート生産菌の代謝モデル構築"
  清水 浩
  長瀬科学技術財団研究報告書 16, 99-104 (2005).
• "バイオインフォマティクスデータを統合する代謝情報工学"
  清水 浩
  生産と技術 57, 2, 55-58 (2005).
• "Analysis of Complex Bionetworks and Creation of Industrially Useful Organisms based on Bioinformatic Data"
  Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 2月6日 (2005).
• "Proteome analysis on adaptation of yeast cells to a high osmotic pressure stress"
  Keisuke Nagahisa, Kazuyuki Yamada, Yuki Nakakura, Takashi Hirasawa, Yoshio Katakura, Suteaki Shioya, Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 7月11日 (2005).
• "DNA microarray analysis with an integrating method of self-organizing map and hierarchical clustering."
  Katsunori Yoshikawa, Gaurav Pandey, Takashi Hirasawa, Yoshio Katakura, Keisuke Nagahisa, Chikara Furusawa, Suteaki Shioya, Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 12月15日 (2005).
• "Metabolic Pathway Modification Based on DNA Microarray Data in the Yeast Saccharomyces cerevisiae"
  Takashi Hirasawa, Yuki Nakakura, Zhao Hui, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Suteaki Shioya, Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 16-23 (2005).
• "Analysis of Metabolic Flow Control in Glutamate Production by Coryneform Bacteria"
  Tomokazu Shirai, Masanori Kuzumoto, Takashi Hirasawa, Yoshio Katakura, Keisuke Nagahisa, Chikara Furusawa, Suteaki Shioya, Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 24-30 (2005).
• "Dynamic Behavior of Cell Distribution in Continuous Culture of Escherichia coli"
  Tadashi Yamada, Kohei Maeoka, Akiko Kashiwagi, Keisuke Nagahisa, Chikara Furusawa, Suteaki Shioya, Tetsuya Yomo, Hiroshi Shimizu
  ソフトウェアバイオロジー 4, 31-36 (2005).

Books

• "７章 培養工学, 7.5.3 代謝工学的手法と培養操作の実際"
  清水 浩
  生物工学ハンドブック, 日本生物工学会編, 444-449 (2005).

2004

Review papers

• "8.4 生物情報"
  清水 浩
  化学工学年鑑2004 (2004).
• "乳酸菌と酵母の共培養による有用物質生産"
  塩谷 捨明, Benjamas Cheirsilp, 江川 直, Agustin K. Wardani, 永久 圭介, 夛田 志緒里, 片倉 啓雄, 清水 浩
  生物工学会誌 82, 9, 438-439 (2004).

Books

• "Analysis of responses of complex bionetworks to changes in environmental conditions"
  Hiroshi Shimizu, Takashi Hirasawa, Keisuke Nagahisa, Suteaki Shioya
  Lecture Note Series of Computer Science Vol. 3141, Biologically Inspired Approaches to Advanced Information Technology (Springer), 13-27 (2004).

2003

Original papers

• "Enhanced kefiran production by mixed culture of Lactobacillus kefiranofaciens and Saccharomyces cerevisiae"
  Benjamas Cheirsilp, Hiroshi Shimizu, Suteaki Shioya
  Journal of Biotechnology 100, 1, 43-53 (2003).

Review papers

• "Interactions between Lactobacillus kefiranofaciens and Saccharomyces cerevisiae in mixed culture for kefiran production"
  Benjamas Cheirsilp, Hirofumi Shoji, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 96, 3, 279-284 (2003).
• "Clustering gene expression pattern and extracting relationship in gene network based on artificial neural networks"
  Jihua Huang, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 96, 5, 421-428 (2003).

2002

Original papers

• "Classification of fermentation performance by multivariate analysis based on mean hypothesis testing"
  Jihua Huang, Hidenori Nanami, Akihisa Kanda, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 94, 3, 251-257 (2002).
• "Data preprocessing and output evaluation of an autoassociative neural network model for online fault detection in virginiamycin production"
  Jihua Huang, Hiroshi Shimizu, Suteaki Shioya
  Journal of Bioscience and Bioengineering 94, 1, 70-77 (2002).
• "Model predictive controller for biodegradable polyhydroxyalkanoate production in fed-batch culture"
  Suchada Chanprateep, Kensuke Kikuya, Hiroshi Shimizu, Suteaki Shioya
  Journal of Biotechnology 95, 2, 157-169 (2002).