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生命システム研究センター  

RIKEN Quantitative Biology Center (QBiC)Laboratory for Multiscale Biosystem Dynamics



PUBLICATIONS

2013 | 2012 | 2011

2013

 

Original Papers

  1. Satoshi Oono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering" Bioinformatics, in press
  2. 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)
  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)
 

International Conference

  1. 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)
  2. 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

Original Papers

  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)

International Conference

  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)

Reviews

  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)

2011

Original Papers

  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)

International Conference

  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)

バナースペース





Laboratory for Multiscale Biosystem Dynamics
RIKEN Quantitative Biology Center (QBiC)

Team Leader:
Chikara Furusawa

    

Address:
OLABB, Osaka University, 6-2-3
Furuedai, Suita, Osaka
565-0874,JAPAN

Phone:+81-6-6155-0456 FAX:+81-6-6155-0112