Shimizu Lab. Graduate School of Information Science and Technology,Osaka University

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Papers

2019

  1. 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,1-13 (2019)
  2. 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)
  3. 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, (2019)
  4. 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)
  5. 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 (2019)
  6. Prediction of rate‐limiting reactions for growth‐associated production using a constraint‐based approach, Kento Tokuyama, Yoshihiro Toya, Hiroshi Shimizu, Biotechnology Journal, 1800431 (2019)
  7. 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).
  8. 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)
  9. 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 Shinizu. Journal of Bioscience Bioengineering, 128(4):424-428 (2019)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)

2018

  1. 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 Biofuel, 11(1):180 (2018)

  2. 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)

  3. 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):7071–7081 (2018)
  4. 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)
  5. 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)
  6. 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, and Fumio Matsuda. Mass Spectrometry, 7(1):A0067 (2018)
  7. 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)
  8. 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, 47:1-9 (2018)
  9. 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)
  10. Integrated analysis of transcriptome and metabolome of Corynebacterium glutamicum during penicillin-induced glutamic acid production, Takashi Hirasawa, Masaki Saito, Katsunori Yoshikawa, Chikara Furusawa, Hiroshi Shmizu. Biotechnology Journal, 13(5):e1700612 (2018)
  11. 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)

2017

  1. 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, 10:307 (2017)
  2. 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)
  3. 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)
  4. 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)
  5. 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.  Jour Biosci Bioeng, 124(3):263-270 (2017)
  6. The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity, Chiaki Takahashi, 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, and Tomoaki Tanaka. Oncogene, 36(36):5145-5157(2017) (IF 7.932)
  7. Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli, Ami Masuda, Yoshihiro Toya, Hiroshi Shimizu. Bioresource Technology, 245, partB:1634-1640 (2017)
  8. Prediction of hopeless peptides unlikely to be selected for targeted proteome analysis, Fumio Matsuda, Atsumi Tomita, Hiroshi Shimizu. Mass Spectrometry, 6(1):A0056 (2017)
  9. Targeted proteome analysis of single-gene deletion strains of Saccharomyces  cerevisiae lacking enzyme in the central carbon metabolism, Fumio Matsuda, Syohei Kinoshita, Shunsuke Nishino, Atsumi Tomita, Hiroshi Shimizu. PlosONE, 12(2):e0172742(2017)
  10. 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(5):791-796(2017)

2016

  1. 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, and Hiroshi Shimizu. Plant and Cell Physiology, 58(3):537-545(2016)
  2. Technical challenges in mass spectrometry-based metabolomics, Fumio Matsuda. Mass Spectrometry,5(2)(2016)
  3. 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)
  4. 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)
  5. 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, 39:1711-1716 (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, Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda. Analytical and Bioanalytical Chemistry, 408:6133-6140 (2016)
  7. Regular expressions of MS/MS spectra for partial annotation of metabolite features, Fumio Matsuda. Metabolomics, 12:113 (2016)
  8. 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)
  9. Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production. Kenshi Hayakawa, Fumio Matsuda, Hiroshi Shimizu. AMB Express, 6:1-8 (2016)
  10. Enhancement of 1,5-diaminopentane production in a recombinant strain of Corynebacgterium glutamicum by Tween 40 addition, Yuta Matsushima, Takashi Hirasawa, Hiroshi Shimizu. Journal of General and Applied Microbiology, 62:42-45 (2016)

2015

  1. 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:e0144430 (2015)
  2. 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)
  3. 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, 79:2073-2080 (2015)
  4. 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)
  5. Design and control of a ray-mimicking soft robot based on morphological features for adaptive deformation, Kenji Urai, Risa Sawada, Natsuki Hiasa, Masashi Yokota, Fabio DallaLibera. AROB Journal, 20:237-243 (2015)
  6. 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, 120:725-731 (2015)
  7. Metabolomic analysis of acid stress response in Saccharomyces cerevisiae, Riyanto Heru Nugroho, Katsunori Yoshikawa, Hiroshi Shimizu. Journal of Bioscience and Bioengineering, 120:396-404 (2015)
  8. 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, 120:532-538 (2015)

2014

  1. 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, 120:280-286 (2014)
  2. SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes, Yoshihiro Toya, Takanori Shiraki, Hiroshi Shimizu. Biotechnology and Bioengineering, 112:759-768 (2014)
  3. Metabolome-genome-wide association study (mGWAS) dissects genetic architecture for generating natural variation in rice secondary metabolism, Fumio Matsuda, Ryo Nakabayashi, Zhigang Yang, Yozo Okazaki, Jun-ichi Yonemaru, Kaworu Ebana, Masahiro Yano,and Kazuki Saito. The Plant Journal, 81:13-23 (2014)
  4. NanoLC-MRM based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra-fast mass spectrometry. Fumio Matsuda, Tairo Ogura, Nobuyuki Okahashi, Atsumi Tomita, Ichiro Hirano, Hiroshi Shimizu. Journal of Bioscience and Bioengineering, 119:117-120 (2014)
  5. Effect of malic enzyme on ethanol production by Synechocystis sp. PCC 6803. Katsunori Yoshikawa, Takashi Hirasawa, Hiroshi Shimizu. Journal of Bioscience and Bioengineering, 119:82-84 (2014)
  6. 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, 55:1605-1612 (2014)
  7. Enhanced acetic acid and succinic acid production under microaerobic conditions by Corynabacterium glutamicum harboroing Escherichia coli transhydrogenase gene pntAB. Yuto Yamauchi, Takashi Hiraswa, Msato Nishii, Chikara Furuasawa, Hiroshi Shimizu. Journal of General and Applied Microbiology, 60:112-118 (2014)
  8. Reliable metabolic flux estimation in Escherichia coli  carbon central metabolism using intracellular free amino acids. Nobuyuki Okahashi, Shuichi Kajihata, Chikara Furusawa, Hiroshi Shimizu. Metabolites, 30:408-420 (2014)
  9. 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)
  10. Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli. Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa, Hiroshi Shimizu. Microbial Cell Factories, 7:64 (2014) 
  11. 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, 10:42-49 (2014)
  12. Development of an automated culture system for laboratory evolution. Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu, Chikara Furusawa. Journal of Laborarory Automation, 19:478-482 (2014)

  13. FastPros: Screening of reaction knockout strategies for metabolic engineering. Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa. Bioinformatics, 30:981-987 (2014)

2013

  1. 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, 5:123-128 (2013).
  2. Metabolic engineering of Saccharomyces cerevisiae for improving succinic acid production based on metabolic profiling, Yuma Ito, Takashi Hirasawa, Hiroshi Shimizu. Bioscience Biotechnology and Biochemistry, 78:151-159 (2013).

  3. Improvement of isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance, Fumio Matsuda, Jun Ishii, Takashi Kondo, Kengo Ida, Hironori Tezuka, Akihiko Kondo. Microbial Cell Factories, 12:119 (2013)
  4. 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, 80:564-573 (2013)
  5. Method for assessing the statistical significance of mass spectral similarities using BLAST statistics, Fumio Matsuda, Hiroshi Tsugawa, Eiichiro Fukusaki. Analytical Chemistry, 85:8291-8297 (2013)
  6. Production of indole alkaloids by metabolic engineering of the tryptophan pathway in rice, Joseph Dubouzet, Fumio Matsuda, Atsushi Ishihara, Hisashi Miyagawa, Kyo Wakasa. Plant Biotechnology Journal, 11:1103-1111 (2013)
  7. ArtPathDesign - Rational heterologous pathway design system for the production of nonnative metabolites, Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu. Journal of Bioscience and Bioengineering, 168:185-193 (2013)
  8. 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, 8:513-514 (2013)
  9. 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)
  10. 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, 8:571-580 (2013)

 

2012

  1. PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation, Tetsuya Sakurai, Yutaka Yamada, Yuji Sawada, Fumio Matsuda, Kenji Akiyama, Kazuo Shinozaki, Masami Yokota Hirai, Kazuki Saito. Plant and Cell Physiolosy, 54:e5 (2013)
  2. Regulation of central carbon metabolism in Saccharomyces cerevisiae by metabolic inhibitors, Fumio Matsuda, Tomokazu Shirai, Jun Ishii, Akihiko Kondo. Journal of Bioscience and Bioengineering, 116:59-64 (2013)
  3. 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, 97:4811-4819 (2013)
  4. 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:e54571 (2013)
  5. 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, 115:221-228 (2013)
  6. An in silico platform for the design of heterologous pathways in nonnative metabolite production, Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu. BMC Bioinformatics, 13:93 (2012)
  7. 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, 11:87 (2012)
  8. 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 , Mol Biosyst, 8(10):2593-2604 (2012)
  9. 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, 113:526-528 (2012)
  10. 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, 113:192-195 (2012)

2011

  1. 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, 6:1377-1378 (2011)
  2. 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, 112:595-601 (2011)
  3. 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, 92:347-358 (2011)
  4. Engineering strategy of yeast metabolism for higher alcohol production, Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo. Microbial Cell Factories, 10:70 (2011)
  5. 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, 91:143-151 (2011)
  6. 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, 28:349-361 (2011)
  7. 細胞共生ネットワークの自発的形成メカニズム, 古澤力, 伊地智厚太, 清水浩. 電子情報通信学会論文誌D, J94-D:614-622 (2011)

2010

  1. 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, 11:579 (2010)
  2. 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, 110:602-607 (2010)
  3. Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution, Toshihiko Kishimoto, Leo Iijima, Makoto Tatsumi, Naoaki Ono, Ayana Oyake, Tomomi Hashimoto, Moe Matsuo, Masato Okubo, Shingo Suzuki, Kotaro Mori, Akiko Kashiwagi, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo. PLoS Genetics, 6:e1001164 (2010)
  4. 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, 26:975-992 (2010)
  5. 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, 86:911-920 (2010)
  6. 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, 109:262-266 (2010)
    日本生物工学会 第19回 生物工学論文賞, 100 selected papers ANNUAL REPORT OF OSAKA UNIVERSITY -- Academic Achievements2010-2011
  7. 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, 4:82-89 (2010)

2009

  1. 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, 84:1149-1159 (2009)
  2. Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system, Jianhong Ou, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu, Biosystems, 97:160-164 (2009)
  3. The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells, Taeko Kobayashi, Hiroaki Mizuno, Itaru Imayoshi, Chikara Furusawa, Katsuhiko Shirahige, Ryoichiro Kageyama. Genes and Development, 23:1870-1875 (2009)
  4. 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, 32:681-688 (2009)
  5. 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, Mol Syst Biol, 5(1):306 (2009)
  6. 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, 8:43 (2009)
  7. Chaotic expression dynamics implies pluripotency: when theory and experiment meet, Chikara Furusawa, Kunihiko Kaneko. Biology Direct, 4:17 (2009)
  8. Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum, Kumiko Kihara, Kotaro Mori, Shingo Suzuki, Naoaki Ono, Chikara Furusawa Tetsuya Yomo. Biosystems, 96:141-164 (2009)
  9. 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, 44:647-653(2009)
  10. Analysis of metabolic network based on conservation of molecular structure, Tomoharu Hogiri, Chikara Furusawa, Yohei Shinfuku, Naoaki Ono, Hiroshi Shimizu. Biosystems, 95:175-178 (2009)
  11. 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, 9:32-44 (2009)
  12. 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, 26:17-30 (2009)
  13. 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, 25:36-41 (2009)
  14. 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, 81:1097-1106 (2009)

2008

  1. 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, 106:507-510 (2008)
  2. 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, 35:1205-1215(2008)
  3. 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, 72:3063-3066 (2008)
  4. Relevance of Phenotypic Noise to Adaptation and Evolution, Kunihiko Kaneko, Chikara Furusawa, IET Systems Biology, 2:234-246 (2008)
  5. Distinct roles of two anaplerotic pathways in glutamate production induced by biotin limitation in Corynebacterium glutamicum, Hiroki Sato, Keita Orishimo, Tomokazu Shirai, Takashi Hirasawa, Keisuke Nagahisa, Hiroshi Shimizu, Masaaki Wachi, Journal of Bioscience and Bioengineering, 106:51-58 (2008)
  6. 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, and Hiroshi Shimizu, PloS One, 3:e2623 (2008)
  7. Consistency Principle in Biological Dynamical Systems, Kunihiko Kaneko, Chikara Furusawa. Theory in Biosciences, 127:195-204 (2008)
  8. 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, 24:1278-1285 (2008)
  9. Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cell, Jianhong Ou, Tadashi Yamada, Keisuke Nagahisa, Takashi Hirasawa, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu. Molecular BioSystems, 4:128-134 (2008)
  10. A generic mechanism for adaptive growth rate regulation, Chikara Furusawa, Kunihiko Kaneko. PLoS Computational Biology, 4:e3 (2008)

2007

  1. Analysis of fluctuation in protein abundance without promoter regulation based on Eschrichia coli continuous culture, Tadashi Yamada, Chikara Furusawa, Keisuke Nagahisa, Akiko Kashiwagi, Tetsuya Yomo, Hiroshi Shimizu. Biosystems, 90:614-622 (2007)
  2. Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Akiko Kashiwagi, Tetsuya Yomo. BMC Genomics, 8:373 (2007)
  3. Insight into the sequence specificity of a probe on an Affymetrix GeneChip by titration experiments using only one oligonucleotide, Shingo Suzuki, Chikara Furusawa, Naoaki Ono, Akiko Kashiwagi, Itaru Urabe, Tetsuya Yomo. Biophysics, 3:47-56 (2007)
  4. Reduction of lactate production in Lactococcus lactis, a combined strategy: metabolic engineering by introducing the foreign alanine dehydrogenasegene and hemin addition, Agustin Krisna Wardani, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya. World Journal of Microbiology and Biotechnology, 23:947-953 (2007)
  5. 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, 6:19 (2007)
  6. 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, 131:33-44 (2007)
  7. Universal Statistics for Chemical Abundances in Reproducing Cell, Chikara Furusawa, Kunihiko Kaneko. Journal of Korean Physical Society, 50:142-149 (2007)
  8. Kinetic modeling of kefiran production in mixed culture of Lactobacillus kefiranofaciens and Saccharomyces cerevisiae, Benjamas Cheirsilp, Hiroshi Shimizu, Suteaki Shioya, Process Biochemistry, 42:570-579 (2007)
  9. 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, 103:451-456 (2007)
  10. Extracting hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA micro array 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, 75:415-426 (2007)
  11. Analysis of fluctuation in protein abundance without promoter regulation based on Eschrichia coli continuous culture, Tadashi Yamada, Chikara Furusawa, Keisuke Nagahisa, Akiko Kashiwagi, Tetsuya Yomo, Hiroshi Shimizu. Biosystems, 90:614-622 (2007)

2006

  1. 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, 70:346-357 (2006)
  2. 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, 91:2941-2950 (2006)
  3. Precise metabolic flux analysis of coryneform bacteria with gas spectrometry --mass spectrometry and verification of nuclear magnetic resonance, Tomokazu Shirai, Kunihiro Matsuzakim, Masanori Kuzumoto, Keisuke Nagahisa, Chikara Furusawa, Suteaki Shioya, Hiroshi Shimizu. Journal of Bioscience and Bioengineering, 102:413-424 (2006)
  4. 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, 73:540-558 (2006)
  5. 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, Yoshii Katakura. Biochemical Engineering Journal, 36:28-37 (2006)
  6. 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, 102:568-571 (2006).
  7. 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, 23:947-953 (2006)
  8. Evolutionary origin of power-laws in a biochemical reaction network: Embedding abundance distribution into topology, Chikara Furusawa, Kunihiko Kaneko. Physical Review E, 73:011912 (2006)
  9. 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, 70:346-357 (2006)
  10. An evolutionary relationship between genetic variation and phenotypic fluctuation, Kunihiko Kaneko, Chikara Furusawa. Journal of Theoretical Biology, 240:78-86 (2006)

2005

  1. Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture, Shinsuke Tada, Takumi Era, Chikara Furusawa, Hedetoshi Sakurai, Satomi Nishikawa, Masaki Kinoshita, Kazuki Nakao, Tsutomu Chiba, Shin-Ichi Nishikawa. Development, 132:4363 (2005)
  2. Comparative study of flux redistribution of metabolic pathway in glutamate production in two strains of coryneform bacteria, Tomokazu Shirai, Akinori Nakato, Noriyuki Izutani,Keisuke Nagahisa, Suteaki Shioya, Eiichiro Kimura,Yutaka Kawarabayashi, Akihiko Yamagishi, Takashi Gojobori, Hiroshi Shimizu. Metabolic Engineering, 7:59-69 (2005)
  3. Development of Co-Culture Systems of Lactic Acid Bacteria and Yeasts for Bioproduction, Hiroshi Shimizu, Benjamas Cheirsilp, Suteaki Shioya. Japanese Journal Lactic Acid Bacteria, 16:2-10 (2005)
  4. Ubiquity of Log-normal Distribution in Intra-cellular Reaction Dynamics, Chikara Furusawa, Takao Suzuki, Akiko Kashiwagi, Tetsuya Yomo, Kunihiko Kaneko. Biophysics, 1:25-31 (2005)
  5. Selection of Initial Conditions for Recursive Production of Multicellular Organisms, Hiroshi Yoshida, Chikara Furusawa, Kunihiko Kaneko. Journal of Theoretical Biology, 233:501-514 (2005)

2004

  1. Metabolic flux control analysis of branch points: an improved approach to obtain flux control coefficients from large perturbation data, Joseph J. Heijnen, Walter M. van Gulik, Hiroshi Shimizu, Gregory Stephanopoulos. Metabolic Engineering, 6:391-400 (2004)
  2. 清水浩, 増田康之, 永久圭介, 古澤力, 塩谷捨明. 生分解性高分子生産プロセスにおけるモデル予測制御, 計測自動制御学会誌43:691-695 (2004)

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