Articles

Proceedings

Reviews

Patent/Awards

google scholar citations


Articles

    2013


  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. )

  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)


  7. 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) accepted (2013, Sept).


  8. ArtPathDesign - Rational heterologous pathway design system for the production of nonnative metabolites, Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu*, Jour Biosci Bioeng, vol. 168, No. 2, p. 185-193 (2013. May)


  9. 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, and Hiroshi Shimizu, Journal of Biotechnology, vol. 8, No. 5, p. 513-514 (2013. Apr)


    10. 2012


  10. Chikara Furusawa and Kunihiko Kaneko, "A dynamical-systems view of stem cell biology," Science, 338(6104), 215-217 (2012) )


  11. 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)


  12. Chikara Furusawa and Kunihiko Kaneko, "Adaptation to optimal cell growth through self-organized criticality," Physical Review Letters, 108, 208103 (2012)


  13. 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)


  14. 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)


  15. 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))


  16. 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, and Hiroshi Shimizu, Journal of Bioscience and Bioengineering, Vol. 113, No. 4, p.526-528(2012. Apr)


  17. Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae, Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, and Hiroshi Shimizu, Journal of Bioscience and Bioengineering, Vol. 113, No. 2, p.192-195(2012. Feb)


  18. Molecular Mechanisms and Metabolic Engineering of Glutamate Overproduction in Corynebacterium glutamicum, T. Hirasawa, J. Kim, T. Shirai, C. Furusawa, and H. Shimizu, Subcell Biochem., 64, 261-81 (2012)


    19. 2011


  19. Oscillatory protein expression dynamics endows stem cells with robust differentiation potential, Narito Suzuki, Chikara Furusawa, and Kunihiko Kaneko, PLoS One, vol. 6(11), p. e27232 (2011. Nov)


  20. Evaluating 13C enrichment data of free amino acids for precise metabolic flux analysis, Eiji Mori, Chikara Furusawa, Shuichi Kajihata, Tomokazu Shirai and Hiroshi Shimizu, Biotechnology journal, Vol. 6, No. 11, p.1377-1378(2011. Nov)


  21. 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, and Hiroshi Shimizu, Journal of Bioscience and Bioengineering, Vol. 112, No. 6, p.595-601(2011. Dec)


  22. Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803, Katsunori Yoshikawa, Yuta Kojima, Tsubasa Nakajima, Chikara Furusawa, Takashi Hirasawa and Hiroshi Shimizu, Applied Microbiology and Biotechnology, Vol. 92, No. 2, p.347-358(2011. Oct)


  23. Engineering strategy of yeast metabolism for higher alcohol production, Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, and Akihiko Kondo, Microbial Cell Factories, Vol. 10, No. 1, p.70(2011. Sep)


  24. 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, and Hiroshi Shimizu, Applied Microbiology and Biotechnology, Vol. 91, No. 1, p.143-151(2011. July)


  25. Comparison of sequence reads obtained from three next-generation sequencing platforms, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Bei-wen Ying, Tetsuya Yomo, PLoS One, vol. 6 (5), p. e19534 (2011. May)


  26. Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae, Katsunori Yoshikawa, Tadamasa Tanaka, Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, and Hiroshi Shimizu, Yeast, Vol. 28, No. 5, p.349-361(2011. Mar)


    27. 2010


  27. 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, and Hiroshi Shimizu, BMC Genomics, Vol. 11, No. 1, p.579(2010. Nov)


  28. Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays, Takaaki Horinouchi, Katsunori Yoshikawa, Risa Kawaide, Chikara Furusawa, Yoshihiro Nakao, Takashi Hirasawa, and Hiroshi Shimizu, Journal of Bioscience and Bioengineering, Vol. 110, No. 5, p.602-607(2010. Nov)


  29. 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, Vol.87, No.2, p.391-400(2010. June)


  30. 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, vol. 6, No. 10, e1001164(2010. Oct)


  31. 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, and Hiroshi Shimizu, IET Systems Biology, Vol. 4, No. 1, p.82-89(2010. Jan)


    32. 2009


  32. 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, Vol. 84, No. 6, p.1149-1159(2009. Oct)

  33. Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system, Jianhong Ou, Chikara Furusawa, Tetsuya Yomo, and Hiroshi Shimizu, BioSystems, Vol. 97, Issue 3, p.160-164(2009. Sep)

  34. The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells, Taeko Kobayashi, Hiroaki Mizuno, Itaru Imayoshi, Chikara Furusawa, Katsuhiko Shirahige, and Ryoichiro Kageyama, Genes and Development,Vol. 23, No. 16, p.1870-1875(2009. Aug)

  35. Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae using DNA Microarray, Thai Nho Dinh, Keisuke Nagahisa, Katsunori Yoshikawa, Takashi Hirasawa, Chikara Furusawa and Hiroshi Shimizu, Bioprocess and Biosystems Engineering, Vol. 32, No.5, p.681-688(2009.Aug)

  36. Development and Experimental Verification of a Genome-Scale Metabolic Model for Corynebacterium glutamicum, Yohei Shinfuku, Natee Sorpitiporn, Masahiro Sono, Chikara Furusawa, Takashi Hirasawa and Hiroshi Shimizu, Microbial Cell Factories, vol. 8, NO. 43(2009.Aug)

  37. Chaotic expression dynamics implies pluripotency: when theory and experiment meet, Chikara Furusawa, Kunihiko Kaneko, Biology Direct, vol.4:17(2009. May)

  38. 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, vol. 96, Issue2, p.141-164(2009. May)

  39. 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, Vol. 44, Issue 6, p.647-653(2009. Mar)

  40. Analysis of metabolic network based on conservation of molecular structure, Tomoharu Hogiri, Chikara Furusawa, Yohei Shinfuku, Naoaki Ono, Hiroshi Shimizu, Biosystems, Vol.95, Issue3, P.175-178(2009. Mar)

  41. 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, Vol.9, Issue1, p.32-44(2009. Feb)

  42. 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, Vol.25, No.1, p.36-41(2009. Jan)

  43. 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, Vol.81, No.6, p.1097-1106(2009. Jan)

    44. 2008


  44. 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, Vol.106, No.5, p.507-510(2008. Dec)

  45. 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, Vol. 72, No. 11, p.3063-3066(2008. Nov)

  46. Relevance of Phenotypic Noise to Adaptation and Evolution, Kunihiko Kaneko, Chikara Furusawa, IET Systems Biology, Vol. 2, Issue 5, p.234-246(2008, Sep)

  47. 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, Vol.3, No.7, e2623(2008, July)

  48. Consistency Principle in Biological Dynamical Systems, Kunihiko Kaneko, and Chikara Furusawa, Theory in Biosciences, Vol.127, No.2, p.195-204 (2008, June)

  49. 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, Vol.24, No.10, p.1278-1285 (2008, May)

  50. Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cell, Ou, J., Yamada, T., Nagahisa, K., Hirasawa, T., Furusawa, C., Yomo, T., and Shimizu, H., Molecular BioSystems, Vol.4, p.128-134 (2008, Feb)

  51. A generic mechanism for adaptive growth rate regulation, Furusawa, C., and Kaneko, K., PLoS Computational Biology, Vol.4(1), p.e3 (2008, Jan)

    52. 2007


  52. Analysis of fluctuation in protein abundance without promoter regulation based on Eschrichia coli continuous culture, Yamada, T., Furusawa, C., Nagahisa, K., Kashiwagi, A., Yomo, T. and Shimizu, H., BioSystems, Vol.90, No.3, p.614-622 (2007, Nov)

  53. Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays, Suzuki, S., Ono, N., Furusawa, C., Kashiwagi, A., and Yomo, T., BMC Genomics, Vol.8, p.373 (2007, Oct)

  54. Insight into the sequence specificity of a probe on an Affymetrix GeneChip by titration experiments using only one oligonucleotide, Suzuki, S., Furusawa, C., Ono, N., Kashiwagi, A., Urabe, I., and Yomo, T., Biophysics, Vol.3, p.47-56 (2007, Sep)

  55. Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis, Shirai, T., Fujimura, K., Furusawa, C., Nagahisa, K., Shioya, S. and Shimizu, H., Microbial Cell Factories, Vol.6, No.1, p.19 (2007, July)

  56. Identification of target genes for conferring ethanol stress-tolerance to yeast Saccharomyces cerevisiae based on DNA microarray data analysis, Hirasawa, T., Yoshikawa, K., Nakakura, Y., Nagahisa, K., Furusawa, C., Katakura, Y., Shimizu, H. and Shioya, S., Journal of Biotechnology, Vol.131, p.33-44 (2007, July)

  57. 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(2):415-26 (2007)

  58. Metabolic pathway recruiting through genomic data analysis for industrial application of Saccharomyces cerevisiae, S. Shioya, H. Shimizu, T. Hirasawa, K. Nagahisa, C. Furusawa, G. Pandey, and Y. Katakura, Biochem. Eng. Jour., 36(1), 28-37 (2007)

  59. Comparison of transcriptional responses to osmotic stresses by addition of NaCl and sorbitol in Saccharomyces cerevisiae using DNA microarray ,T. Hirasawa, K. Ashitani, K. yoshikawa, K. nagahisa, C. Furusawa, Y. Katakura, H. Shimizu, and S. Sioya, J. Biosci. Bioeng., 102(6), 568-71 (2007)

    60. 2006


  60. Evolutionary origin of power-laws in a biochemical reaction network: embedding abundance distribution into topology, C. Furusawa and K. Kaneko, Physical Review E, 73(1), 011912 (2006)

  61. Precise Metabolic flux analysis of coryneform bacteria by gas chromatgraphy-mass spectrometry and verification by nuclear magnetic resonance, T. Shirai, K. Matsuzaki, M. Kuzumoto, K. Nagahisa, C. Furusawa, S.Shioya, and H Shimizu, J. Biosci. Bioeng., 102(5), 413-24 (2006)

  62. Morphogenesis, plasticity, and irreversibility, C. Furusawa and K. Kaneko, Int. Jour. Dev. Biol,, 50(2), 223 (2006)

  63. An evolutionary relationship between genetic variation and phenotypic fluctuation, K. Kaneko and C. Furusawa, Jour. Theor. Biol., 240(1),78 (2006)

  64. Comparative analysis of transcriptional responses to saline stress in the laboratory and brewing strains of Saccharomyces cerevisiae with DNA microarray, T. Hirasawa, Y. Nakakura, K. Yoshikawa, K. Ashitani, K. Nagahisa, C. Furusawa, Y. Katakura, H. Shimizu and S. Shioya, Appl. MicroBio. Beotech., 70(3) 346 (2006)

    65. 2005


  65. Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture, S. Tada, T. Era, C. Furusawa, H. Sakurai, S. Nishikawa, M. Kinoshita, K. Nakao, T. Chiba, and S-I. Nishikawa, Development 132(19), 4363 (2005)

  66. DNA microarray analysis on Saccharomyces cerevisiae under high carbon dioxide concentration in fermentation process, K. Nagahisa, T. Nakajima, K. Yoshikawa, T. Hirasawa, Y. Katakura, C. Furusawa, S. Shioya, and H. Shimizu, Biotechnol. Bioprocess Eng, 10, 451-461 (2005)

  67. Universal statistics of cells with recursive production, K. Kaneko and C. Furusawa, Lecture notes in complex systems vol. 3: Networks of Interacting Machines (edited by D. Armbruster, K. Kaneko, and A.S. Mikhailov), World Scientific (2005)

  68. Ubiquity of log-normal distribution in intra-cellular reaction dynamics, C. Furusawa, T. Suzuki, A. Kashiwagi, T. Yomo, and K. Kaneko, Biophysics, 1, 25 (2005)

    69. 2004


  69. Selection of initial conditions for recursive production of multicellular organisms, Hiroshi Yoshida, C. Furusawa, and K. Kaneko, Jour. Theor. Biol. 233(4), 501 (2004)

  70. Global change in Escherichia coli gene expression in initial stage of symbiosis with Dictyostelium cells, S-I. Matsuyama* C. Furusawa*, M. Todoriki, I. Urabe, T. Yomo, Biosystems. 73(3):163-71 (2004) *equally contributed

    71. 2003


  71. Robust development as a consequence of generated positional information, C. Furusawa and K. Kaneko, Jour. Thoer. Biol., 224(4), 413-35(2003)

  72. Zipf's law in gene expression, C. Furusawa and K. Kaneko, Physical Review Letters, 90, 088102(2003)

    73. 2002


  73. Origin of multicellular organisms as an inevitable consequence of dynamical systems, C. Furusawa and K. Kaneko, Anatomical Record, 268 327-342(2002)

    74. 2001


  74. Theory of robustness of irreversible differentiation in a stem cell system: chaos hypothesis, C. Furusawa and K. Kaneko, J. Theor. Biol. 209, 395-416 (2001)

    75. 2000


  75. Complex organization in multicellularity as a necessity in evolution, C. Furusawa and K. Kaneko, Artificial Life 6 265-281 (2000)

  76. Robust and irreversible development in cell society as a general consequence of intra-inter dynamics, K. Kaneko and C. Furusawa, Physica A, 280, 22-33 (2000)

  77. Origin of complexity in multicellular organisms, C. Furusawa and K. Kaneko, Physical Review Letters, 84, 6130-6134(2000)

    78. 1998


  78. Emergence of rules in cell society: differentiation, hierarchy, and stability, C. Furusawa and K. Kaneko, Bull. Math. Biol., 60, 659-687 (1998)

  79. Emergence of multicellular organisms with dynamic differentiation and spatial pattern, C. Furusawa and K. Kaneko, Artificial Life, 4 , 79-93 (1998)


Proceedings


  1. "On Attractor Perturbation through System-inherent Fluctuations and its Response", K. Leibnitz, C. Furusawa and M Murata, International Symposium on Nonlinear Theory and its Applications (NOLTA), Special Session on Applications of Nonlinear Theory to Ambient Networks (2009)

  2. "Systems Biology Approach for Irreversible Differentiation in a Stem Cell System: Chaos Hypothesis", C. Furusawa and K. Kaneko, The Tenth International Conference on Systems Biology, CD-ROM (2009)

  3. "Flux balance analysis of Corynebacterium glutamicum using a genome-scale metabolic model", C. Furusawa, Y. Shinfuku, N. Sorpitiporn, M. Sono, T. Hirasawa, and H. Shimizu, Asia Pacific Biochemical Engineering Conference (APBioChEC), CD-ROM (2009)

  4. "A model-based analysis method for detection of single-base substitution using resequencing microarrays", N. Ono, S. Suzuki, C. Furusawa, H. Shimizu and T. Yomo, Asia Pacific Biochemical Engineering Conference (APBioChEC), CD-ROM (2009)

  5. "A noise-driven mechanism for adaptive growth rate regulation", C. Furusawa and K. Kaneko, 1st International Workshop on Technologies for Ambient Information Society (TAIS), CD-ROM (2008)

  6. "Metabolic flux balance analysis of an industrially useful microorganism Corynebacerium glutamicum by a genome-scale reconstructed model", The 3rd International Conference on Bio-Inspired Models of Network, Information, and Computing Systems (BIONETICS), CD-ROM (2008)

  7. "Quantitative expression analysis using oligonucleotide microarrays based on a physico-chemical model", N. Ono, S. Suzuki, C. Furusawa, H. Shimizu and T. Yomo, The 3rd International Conference on Bio-Inspired Models of Network, Information, and Computing Systems (BIONETICS), CD-ROM (2008)

  8. "Integration analysis of phenome and transctiptome in yeast under stress conditions", K. Yoshikawa, T. Tanaka, K. Nagahisa, C. Furusawa, and H. Shimizu, 23rd International Conference on Yeast Genetics and Molecular Biology, Vol.24, Issue S1, p.S140, 13-34 (2007)

  9. "Analysis of the relationship between noise in gene expression and regulatory structure in amino acid biosynthesis pathways", T. Yamada, C. Furusawa, T. Yomo and H. Shimizu, The Eighth International Conference on Systems Biology, CD-ROM (2007)

  10. "Universal statistics for chemical abundances in reproducing cell", C. Furusawa and K. Kaneko, Journal of Korean Physical Society, 50, 142-149 (2007)

  11. "Inverse metabolic engineering by integration of multiple omics analyses", H. Shimizu, T. Hirasawa, K. Yoshikawa, Y. Nakakura, K. Nagahisa, C. Furusawa, Y. Katakura, and S. Shioya, Proceedings of 10th Computer Applications in Biotechnology, vol.1, 15-20 (2007)

  12. "Analysis of fluctuation in gene expression based on continuous culture system", T. Yamada, M. Sadamitsu, K. Nagahisa, A. Kashiwagi, C. Furusawa, T. Yomo, and H. Shimizu, Proceedings of Biologically Inspired Approaches to Advanced Information Technology (BioADIT2006), 113-127 (2006)

  13. "Emergence of two power-laws in evolution of biochemical network; embedding abundance distribution into topology", C. Furusawa and K. Kaneko, Proceedings of Biologically Inspired Approaches to Advanced Information Technology (BioADIT2006), 80-92 (2006)

  14. "Molecular breeding of osmotic stress tolerant yeast strains based on clustering analysis of gene expression", K. Yoshikawa, G. Pandey, T. Hirasawa, Y. Katakura, K. Nagahisa, C. Furusawa, S. Shioya, and H. Shimizu, Proceedings of Asia pacific biochemical engineering conference, P3-081 4 pages (2005)

  15. "Analysis of DNA microarray data using self-organizing map and hierarchical clustering", K. Yoshikawa, G. Pandey, T. Hirasawa, Y. Katakura, K. Nagahisa, C. Furusawa, S. Shioya, and H. Shimizu, Proceedings of Asia Pacific Confederation of Chemical Engineering Conference (APCChE04), (3P-01-055), 10 pages (2004)

  16. "Analysis of Cell Population Dynamics in Continuous Culture of Escherichia coli", T. Yamada, K. Maeoka, A. Kashiwagi, K. Nagahisa, C. Furusawa, S. Shioya,T. Yomo, and H. Shimizu, Proceedings of Asia Pacific Confederation of Chemical Engineering Conference (APCChE04), (3P-01-064), 10 pages (2004)

  17. "Metabolic flux analysis in two kinds of coryneform bacteria with GC-MS and NMR", T. Shirai, M. Kuzumoto, K. Matsuzaki, Y. Satou, K. Nagahisa, C. Furusawa, H. Shimizu, and S. Shioya , Proceedings of Asia Pacific Confederation of Chemical Engineering Conference (APCChE04), (3P-01-52), 10 pages (2004)

  18. "Metabolic pathway recruiting through modeling of Saccharomyces cerevisiae based on genomics for industrial application", S. Shioya, H. Shimizu, T. Hirasawa, K. Nagahisa, K. Katakura, and C. Furusawa, Proceeding of Asia Pacific Confederation of Chemical Engineering Conference (APCChE04), (2L-03), 10 pages (2004)

  19. "Zipf's Law in Gene Expression", C. Furusawa and K. Kaneko, Proceedings of 3rd International Conference on Systems Biology, 101-104 (2002)

  20. "Complex Organization in muticellularity as a necessity in evolution", C. Furusawa and K. Kaneko, Proceedings of Seventh International Conference on Artificial Life, 103-112 (2000)

  21. "Emergence of Multicellular Organisms with Dynamic Differentiation and Spatial Pattern", C. Furusawa and K. Kaneko, Proceedings of Sixth International Conference on Artificial Life 49-59 (1998)

  22. "Emergence of Differentiation Rules leading to Hierarchy and Diversity", C. Furusawa and K. Kaneko, Proceedings of Fourth European Conference on Artificial Life, 172-181 (1997)


Reviews


  1. 「複製細胞の反応ネットワークダイナミクス」, 金子邦彦, 古澤力, ネットワーク科学への招待, サイエンス社 (2008)

  2. 「メタボロームデータを用いた代謝フラックス解析」, 清水浩, 古澤力, 白井智量, メタボロミクスの先端技術と応用（福崎英一郎　編）, シーエムシー出版 (2008)

  3. 「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, Vol. 66, No. 8, pp.426-432 (2008)

  4. 「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, vol.86, No.1, p.14 (2008)

  5. 「複製細胞の反応ネットワークダイナミクス」, 金子邦彦, 古澤力, 数理科学７月号 (2007)

  6. 「多細胞生物の再帰的増殖と細胞タイプ多様性の両立条件」, 吉田寛, 古澤力, 金子邦彦, 生物物理 47(10), 29-35 (2007)

  7. 「情報科学を基盤とする有用生物創製へむけて」, 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)

  8. 「遺伝子発現のZipf則」, 古澤力, 生産と技術　57(1), 56-59 (2005)

  9. 「複雑系としての生命システムの論理 --細胞状態の普遍統計則を中心にして--」, 古澤力, 金子邦彦、細胞工学 2(4), 452-458 (2004)

  10. 「生分解性高分子生産プロセスにおけるモデル予測制御」, 清水浩, 増田康之, 永久圭介, 古澤力, 塩谷捨明, 計測自動制御学会誌，43(9) 691-695 (2004)

  11. 「複雑系細胞生物学ことはじめ」、金子邦彦、古澤力、バイオサイエンスの新世紀 第１４巻 「生命工学：新しい生命へのアプローチ」(山村 新一、浅島 誠 編)、共立出版 (2002)

  12. 「細胞分化の動的モデル 〜 細胞社会の現象論的理解を目指して 〜」、古澤力、シリーズ・ニューバイオフィジックス II 第８巻、「複雑系のバイオフィジックス」(金子邦彦 編)、共立出版 (2001)


Patent/Awards


  1. Best Presentation Award, "Flux balance analysis of Corynebacterium glutamicum using a genome-scale metabolic model", Chikara Furusawa, Asia Pacific Biochemical Engineering Conference (APBioChEC 2009)

  2. Poster Award, "Theory of Irreversible Differentiation in a Stem Cell System: Chaos Hypothesis", Chikara Furusawa and Kunihiko Kaneko, The 23rd Naito Conference on Molecular Basis for Maintenance and Differentiation of Stem Cells[III]

  3. 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 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 日本生物工学会平成１９年度論文賞

  4. 事業推進担当者名：古澤 力, 縣 朋治, 小野直亮, 鈴木真吾, 柏木明子, 四方哲也, 清水浩, 金子邦彦
    発明の名称：マイクロアレイデータの解析方法及び解析装置
    出願日：平成18年8月2日
    出願番号：特許出願2006-211110



furusawa

Chikara Furusawa, Ph.D

Team Leader
Laboratory for Multiscale Biosystem Dynamics,
Quantitative Biology Center,
RIKEN

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

Tel: +81-70-6800-3908

e-mail:
chikara.furusawa _at_
riken.jp