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生命システム研究センター  

独立行政法人理化学研究所 生命システム研究センター
多階層生命動態研究チーム


発表論文等PUBLICATIONS

2015 | 2014 | 2013 | 2012 | 2011

2015

 

原著論文

  1. K. Kaneko, C. Furusawa, T. Yomo, "Universal Relationship in Gene-Expression Changes for Cells in Steady-Growth State." Phys. Rev. X, 5, 011014
  2. T. Horinouchi, S. Suzuki, T. Hirasawa, N. Ono, T. Yomo, H. Shimizu, C. Furusawa, "Phenotypic convergence in bacterial adaptive evolution to ethanol stress." BMC Evol. Biol., 15, 180
  3. K. Yoshikawa, S. Aikawa, Y. Kojima, Y. Toya, C. Furusawa, A. Kondo, H. Shimizu, "Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction." PLoS One, 10(12), e0144430
  4. B.W. Ying, Y. Matsumoto, K. Kitahara, S. Suzuki, N. Ono, C. Furusawa, T. Kishimoto, T. Yomo, "Bacterial transcriptome reorganization in thermal adaptive evolution." BMC Genomics, 16(1), 802
  5. C. Furusawa, K. Kaneko, "Global relationships in fluctuation and response in adaptive evolution." Jour. Roy. Soc. Interface, 12(109), 20150482
  6. S. Suzuki, T. Horinouchi, C. Furusawa, "Suppression of antibiotic resistance acquisition by combined use of antibiotics" Jour. Biosci. Bioeng., 120(4), 467-9
  7. S. Kajihata, F. Matsuda, M. Yoshimi, K. Hayakawa, C. Furusawa, A. Kanda, H. Shimizu, "13C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect." Jour. Biosci. Bioeng., 120(2), 140-4
  8. T. Miyamoto, C. Furusawa, K. Kaneko, "Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation." PLoS Comp. Biol., 11(8), e1004476

総説・解説

  1. 古澤力,"進化学に残された謎", 進化の謎をゲノムで解く(監修:長谷部光泰), 学研メディカル秀潤社
  2. 堀之内貴明, 古澤力,"適応進化はどのように起こるのか−進化実験によるアプローチ−", 進化の謎をゲノムで解く(監修:長谷部光泰), 学研メディカル秀潤社

2014

 

原著論文

  1. Shingo Suzuki, Takaaki Horinouchi, and Chikara Furusawa, "Prediction of antibiotic resistance by gene expression profiles." Nature Communications, 5, 5792
  2. Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu, and Chikara Furusawa, "Development of an automated culture system for laboratory evolution" Journal of Laboratory Automation, 19(5), 478-82
  3. Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa and Hiroshi Shimizu, "Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli" Microbial Cell Factories, 13, 64
  4. Satoshi Oono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering" Bioinformatics, 30(7), 981-7
  5. T. Nakajima, S. Kajihata, K. Yoshikawa, F. Matsuda, C. Furusawa, T. Hirasawa, H. Shimizu, "Integrated Metabolic Flux and Omics Analysis of Synechocystis sp. PCC 6803 under Mixotrophic and Photoheterotrophic Conditions" Plant Cell Physiol, 55(9), 1605-12
  6. S. Kajihata, C. Furusawa, F. Matsuda, H. Shimizu, "OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis" Biomed Res Int, 2014, 627014
  7. N. Okahashi, S. Kajihata, C. Furusawa, H. Shimizu, "Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids" Metabolites, 4,(2),408-420
  8. Yuto Yamauchi, Takashi Hirasawa, Masato Nishii, Chikara Furusawa, Hiroshi Shimizu, "Enhanced acetic acid and succinic acid production under microaerobic conditions by?Corynebacterium glutamicum?harboring Escherichia coli transhydrogenase gene pntAB" The Journal of General and Applied Microbiology, 60,(3),112-118
  9. T. Hirasawa, Y. Ida, C. Furusawa, H. Shimizu, "Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction. " Bioengineered, 5,(2),123-128

総説・解説

  1. 堀之内貴明, 古澤力,"適応進化はどのように起こるのか−進化実験によるアプローチ− "細胞工学 Vol.33 No.6 (2014)

2013

原著論文

  1. Takashi Hirasawa, Katsunori Yoshikawa, Aki Ookubo, Chikara Furusawa, Hiroshi Shimizu, "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," J. Biotech., 168(2), 185-93 (2013)
  2. Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu, "ArtPathDesign: Rational heterologous pathway design system for the production of nonnative metabolites," Journal of Bioscience and Bioengineering, 116(4), 524-527 (2013)
  3. Chikara Furusawa, Kunihiko Kaneko, "Epigenetic feedback regulation accelerates adaptation and evolution," PLoS One, 8(5), e61251 (2013)
  4. Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu, "Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution," Adv. Biochem. Eng. Biotechnol., 131, 1-23 (2013)
  5. Yoshihiro Ida, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu, "Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction," Applied Microbiology and Biotechnology, 97(11), 4811-4819 (2013)
  6. Katsunori Yoshikawa, Takashi Hirasawa, Kenichi Ogawa, Yuki Hidaka, Tsubasa Nakajima, Chikara Furusawa, Hiroshi Shimizu, "Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions," Biotechnology Journal,8(5), 571-580 (2013)
 

国際会議

  1. Chikara Furusawa, " Oscillatory Protein Expression Dynamics Generates Robust and Irreversible Differentiation Dynamics of Stem Cells," The 4th Symposium onSystems and Synthetic Biology(TriSys) (Hong Kong, Nov. 2013)
  2. Chikara Furusawa, " Phenotypic convergence in experimental evolution of antibiotic resistant bacteria,"The 14th International Conference on Systems Biology(ICSB2013) (Copenhagen, Denmark, Sep. 2013)
  3. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," 8th Asian Biophysics Association (ABA) Symposium (Jeju, Korea, May. 2013)
  4. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," iCeMS Symposium on Theoretical and Computational Biology (Kyoto, Japan, Mar. 2013)

2012

原著論文

  1. Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo, "Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays," PLoS One, 8(1), e54571 (2012)
  2. Chikara Furusawa and Kunihiko Kaneko, "A dynamical-systems view of stem cell biology," Science, 338(6104), 215-217 (2012)
  3. Chikara Furusawa and Kunihiko Kaneko, "Adaptation to optimal cell growth through self-organized criticality," Physical Review Letters, 108, 208103 (2012)
  4. Satoshi Ohno, Chikara Furusawa and Hiroshi Shimizu, "In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites," Journal of Bioscience and Bioengineering, 115(2), 221-228 (2012)
  5. Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu, "An in silico platform for the design of heterologous pathways in nonnative metabolite production," BMC Bioinformatics, 13(1), 93 (2012)
  6. Yuki Usui, Takashi Hirasawa, Chikara Furusawa, Tomokazu Shirai, Natsuko Yamamoto, Hirotada Mori, Hiroshi Shimizu, "Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis," Microbial Cell Factories, 11(1),87 (2012)

国際会議

  1. Kazufumi Hosoda, Akihiro Asao, Shingo Suzuki, Tetsuya Yomo, "Experimental evolution of an artificial bacterial mutualism," 13th International Conference on the simulation & synthesis of living systems (Artificial life 13), (Michigan, USA, July 2012)
  2. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," 4th International Congress on Stem Cells and Tissue Formation (Dresden, Germany, July 2012)
  3. Chikara Furusawa, "Temporal oscillation in protein expressions geenrates robust differentiation dynamics of stem cells," 11th Annual Meeting of International Socienty for Stem Cell Research (Yokohama, Japan, June 2012)

総説・解説

  1. Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu,"Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution," Advanced Biochemical Engineering/Biotechnology, 131, 1-23 (2012)
  2. Takashi Hirasawa, Jongpill Kim, Tomokazu Shirai, Chikara Furusawa, Hiroshi Shimizu, "Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum," Subcellular Biochemistry Vol. 64, Reprogramming Microbial Metabolic Pathways, 261-281 (2012)
  3. Katsunori Yoshikawa, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu, "Design of Superior Cell Factories Based on Systems Wide Omics Analysis," Systems Metabolic Engineering, Chapter3, 21-81 (2012)

その他

  1. 受賞:発酵と代謝研究奨励賞, Chikara Furusawa, "in silico 代謝フラックス予測システムの構築とその実験的検証," (2012年10月)
  2. 受賞:第一回Biophysics論文賞 日本生物物理学会, Chikara Furusawa, Takao Suzuki, Akiko Kashiwagi, Tetsuya Yomo, Kunihiko Kaneko, “Ubiquity of log-normal distributions in intra-cellular reaction dynamics,” BIOPHYSICS vol.1, pp.25-31 (2012年9月)

2011

原著論文

  1. Narito Suzuki, Chikara Furusawa, Kunihiko Kaneko, "Oscillatory protein expression dynamics endows stem cells with robust differentiation potential," PLoS One, 6(11), e27232 (2011)
  2. Eiji Mori, Chikara Furusawa, Shuichi Kajihata, Tomokazu Shirai and Hiroshi Shimizu, "Evaluating 13C enrichment data of free amino acids for precise metabolic flux analysis," Biotechnology journal, 6(11), 1377-1378 (2011)
  3. Katsunori Yoshikawa, Yuta Kojima, Tsubasa Nakajima, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu, "Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803," Applied Microbiology and Biotechnology, 92(2), 347-358 (2011)
  4. Motoki Umakoshi, Takashi Hirasawa, Chikara Furusawa, Yasuhiro Takenaka, Yoshimi Kikuchi, Hiroshi Shimizu, "Improving protein secretion of a transglutaminase-secreting Corynebacterium glutamicum recombinant strain on the basis of 13C metabolic flux analysis," Journal of Bioscience and Bioengineering, 112(6), 595-601 (2011)
  5. Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo, "Engineering strategy of yeast metabolism for higher alcohol production," Microbial Cell Factories, 10(1), 70 (2011)
  6. Jongpill Kim, Takashi Hirasawa, Masaki Saito, Chikara Furusawa, Hiroshi Shimizu, "Investigation of phosphorylation status of OdhI protein during penicillin- and Tween 40-triggered glutamate overproduction by Corynebacterium glutamicum," Applied Microbiology and Biotechnology, 91(1), 143-151 (2011)
  7. Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei-Wen Ying, Tetsuya Yomo, "Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli," Molecular Systems Biology, 7, 493 (2011)
  8. Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo, "Comparison of sequence reads obtained from three next-generation sequencing platforms," PLoS One, 6(5), e19534 (2011)

国際会議

  1. Takaaki Horinouchi, Shingo Suzuki, Naoaki Ono, Kuniyasu Tamaoka, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu, Chikara Furusawa "Comprehensive analysis of evolution dynamics in Escherichia coli from parallel experimental evolutions under ethanol stress condition," International Symposium on SYNTHESIZING LIFE AND BIOLOGICAL SYSTEMS (Osaka, Japan, Oct. 2011)
  2. Kazufumi Hosoda, Akihiro Asao, Shingo Suzuki, Tetsuya Yomo, "Synthesizing symbiosis," International Symposium on SYNTHESIZING LIFE AND BIOLOGICAL SYSTEMS (Osaka, Japan, Oct. 2011)
  3. Chikara Furusawa, Takaaki Horinouchi, Shingo Suzuki, Naoaki Ono, Kuniyasu Tamaoka, Takashi Hirasawa, Tetsuya Yomo, and Hiroshi Shimizu, "Genome-Wide resequencing and expression analyses of evolved Escherichia coli strains under ethanol stress," Society for Molecular Biology and Evolution(SMBE2011) (Kyoto, Japan, Juiy 2011)
  4. Naoaki Ono, Chikara Furusawa, Takaaki Horinouchi, Kuniyasu Tamaoka, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu, "Genome-Wide Mutational and Expression Analyses of Evolved Escherichia coli Strains under Ethanol Stress," Asian Congress on Biotechnology (ACB-2011) (Shanghai, China,May 2011)

その他

  1. 受賞:西宮湯川記念賞, Chikara Furusawa, "カオス力学系モデルによる細胞分化の理論的研究," (2011年11月)
  2. 受賞:文部科学大臣表彰 若手科学者賞, Chikara Furusawa, "生物システムにおける普遍的性質に関す
    る研究," (2011年4月)

バナースペース

独立行政法人理化学研究所
生命システム研究センター
多階層生命動態研究チーム

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