---Project Top ---plan ---member ---publication ---
：：：　Publication　：：：


(A) Replication System (construction of artificial life, universal properties of reaction networkd dynamics with recursive production, ...)
(B) Adaptation (in relationship with fluctuations and network)
(C) Cell differentiation, Development, Multicellularity
(D) Evolution
(E) Diversity and Symbiosis
(F) Basic Expereminetal Methods in Complex Systems Biology
(G) Basic Theory for Biological System
(H) General



(A) Replication System (construction of artificial life, universal properties of reaction networkd dynamics with recursive production, ...)

Awazu A. and Kaneko K.
"Glassy" Relaxation in Catalytic Reaction Networks"
Phys Rev. E, 80, 041931 (2009)

Awazu A. and Kaneko K.
"Self-organized criticality of a catalytic reaction network under flow"
Phys. Rev. E .80, 010902(R) 2009a (Rapid Communication).

Matsuura, T., Kazuta, Y., Aita, T., Adachi, J., and Yomo, T.
"Quantifying epistatic interactions among the components constituting the protein translation system."
Molecular Systems Biology, 5: 297. (2009)

Nishimura, K., Hosoi, T., Sunami, T., Toyota, T., Fujinami, M., Oguma, K., Matsuura, T., Suzuki, H., Yomo, T.
"Population analysis of structural properties of giant liposomes by flow cytometry"
Langmuir, 25, 10439-10443, 2009.

Hosoda, K., Sunami, T., Kazuta, Y., Matsuura, T., Suzuki, H., Yomo, T.,
"Quantitative Study of the Structure of Multilamellar Giant Liposomes As a Container of Protein Synthesis Reaction, "
Langmuir, 24, 13540-13548, 2008.

Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T.
"Importance of translation-replication balance for efficient replication by the self-encoded replicase"
ChemBioChem, 9, 3023-8 (2008)

Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T.
"Replication of genetic information with self-encoded replicase in liposomes"
ChemBioChem, 9,2403-10 (2008)

Toyota T., Takakura K., Kageyama Y., Kurihara K., Maru N., Ohnuma K., Kaneko K., and Sugawara T.
" Flow Cytometric Investigation of Self-Reproducing Giant Multilamellar Vesicles "
Langmuir,24 (2008) 3037-3044

Awazu A. and Kaneko K.
"Discretenss-induced Transition in Catalytic Reaction Networks",
Phys Rev. E 76, 041915 (2007)

Furusawa, C., and Kaneko, K.
"Universal Statistics for Chemical Abundances in Reprducing Cell."
Journal of Korean Physical Scoiety, 50: 142-9.(2007)

Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., and Yomo, T.
"Kinetic analysis of the entire RNA amplification process by Qbeta replicase."
J. Biol. Chem. 282(21), 15516-15527 (2007)

Kaneko, K.
"From a set of chemical reactions to reproducing cells"
Origin of Life and Evolution of Biosphere, 37: 449-53. (2007)

Kaneko, K.
"Minority control and Genetic Takeover."
Origin of Life and Evolution of Biosphere, 37: 465-8.(2007)

Togashi, Y. and Kaneko, K.
"Switching Dynamics in reaction Networks Induced by Molecular Discreteness."
J Phys. Condens. Matt. 19. (2007)

Kazuta, Y., Adachi, J., Matsuura, T., Ono, N., Mori, H., and Yomo, T.
"Comprehensive analysis of the effects of Escherichia coli ORFs on protein translation reaction."
Molecular & Cellular Proteomics, 7 (8): 1530-1540.

Kita, H., J. Cho, Matsuura, T., Nakaishi, T., Taniguchi, I., Ichikawa, T., Shima, Y., Urabe, I., Yomo, T.
"Functional Qbeta replicase genetically fusing essential subunits EF-Ts and EF-Tu with beta-subunit."
J Biosci Bioeng 101(5): 421-6. (2006)

Sato, K., Obinata, K., Sugawara, T., Urabe, I. and Yomo, T.
"Quantification of structural properties of cell-sized individual liposomes by flow cytometry."
J. Biosci. Bioeng. 102, 171-178 (2006).

Sunami, T., Sato, K., Matsuura, T., Tsukada, K., Urabe, I., and Yomo, T.
"Femtoliter compartment in liposomes for in vitro selection of proteins."
Anal. Biochem. 357, 128-136 (2006).

C.Furusawa and K. Kaneko
"Evolutionary origin of power-laws in Biochemical Reaction Network; embedding abundance distribution into topology"
Physical Review E, 73, 011912PDF

C. Furusawa, T. Suzuki, A. Kashiwagi, T. Yomo, and K. Kaneko
" Ubiquity of Log-normal Distributions in Intra-cellular Reaction Dynamics "
BIOPHYSICS, 1(2005) 25 PDF

(B) Adaptation (in relationship with fluctuations and network)

Kashiwagi, A., Sakurai, T., Tsuru, S., Ying, B.W., Mori K., Yomo, T.
"Construction of Escherichia coli Gene Expression Level Perturbation Collection."
Metabolic Engineering 11(1): 56-63 (2009)

Pfeuty B. and K. Kaneko
"The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches"
Physical Biology, 6 (2009) 046013

Tsuru, S., Ichinose, J., Kashiwagi, A., Ying, B.W., Kaneko, K.., and Yomo, T.
"Noisy cell growth rate leads to fluctuating protein concentration in bacteria"
Physical Biology. 6: 1-9(2009)

Furusawa, C. and Kaneko, K.
"A generic mechanisms for adaptive growth rate regulation."
PLoS Computational Biology, 4(2008) e3

Pfeuty B., T. David-Pfeuty, and K. Kaneko
"Underlying Principles of cell fate determination during G1 phase of the mammalian cell cycle"
Cell Cycle 7 (2008) 1-13

Pfeuty B. and K. Kaneko
"Minimal requirements for a robust cell size control in eukaryotic cells"
Physical Biology, 4 (2007) 194-204

Miki Matsuo, Koichi Fujimoto and Tatsuo Shibata
"Relation between Adaptation and Irreversible Circulation in Bacteria Chemotaxis"
Progress of Theoretical Physics Supplement No.161 (2006) 251-254

Tatsuo Shibata and Koichi Fujimoto
"Noisy signal amplification in ultrasensitive signal transduction"
Proc. Natl. Acad. Sci. USA. 102(2005), 331-336 PDF

Kashiwagi, A., Urabe, I., Kaneko, K., and Yomo, T.
"Adaptive response of a gene network to environmental changes by fitness-induced attractor selection."
PLoS One 1(1): e49.(2006)

M. Inoue and K. Kaneko,
"Condition for Intra-cellular Adaptive Dynamics for Chemotaxis"
Phys. Rev. E. 74, (2006), 011903PDF

(C) Cell differentiation, Development, Multicellularity

Gregor, T., Fujimoto, K, .Masaki N., and Sawai, S.
"The onset of collective behavior in social amoebae"
(Sciene, in press)

Furusawa, C. and Kaneko, K.
"Chaotic expression dynamics implies pluripotency: when theory and experiment meet"
Biology Direct, 15(4), 17 (2009)

Yoshida H. and Kaneko K.
"Unified description of regeneration by coupled dynamical systems theory: Intercalary/segmented regeneration in insect legs"
Developmental Dynamics 238 (2009) 1974-1983

Fujimoto, K., Ishihara, S., and Kaneko, K.
"Network evolution of body plans."
PLoS ONE, 3, e2772. (2008)

Kaneko K., Sato K., Michiue T., Okabayashi K., Ohnuma K.,. Danno H., and Asashima M.
"Developmental Potential Describing Morphogenesis in vivo and in vitro"
J Experimental Zoology B 310 (2008) 492-503

Sawai, S., Guan, X. J., Kuspa, A., and Cox, E. C.
"High-throughput analysis of spatio-temporal dynamics in Dictyostelium."
Genome Biol 8(7): R144(2007)

S. Ishihara and K. Kaneko
"Turing pattern with proportion preservation"
J. Theo. Biol. 238 (2006) 683-693 PDF

C.Furusawa and K. Kaneko
"Morphogenesis, Plasticity, and Irreversibility"
International Journal of Developmental Biology, 50(2006), 223-232PDF

Ishihara S, Fujimoto K, Shibata T.
"Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes"
Genes to Cells. 10, (2005), 1025-38

(D) Evolution

K.Kaneko
"Relationship of genetic and epigenetic fluctuations of phenotypes"
in preparation (submitted)

Ito, Y., Toyota, H., Kaneko, K., and Yomo, T.
"How selection effects phenotypic fluctuation."
Mol Syst Biol 5: 264. (2009)

K. Kaneko
"Relationship among Phenotypic Plasticity, Genetic and Epigenetic Fluctuations, Robustness, and Evolovability; Waddington's Legacy revisited under the Spirit of Einstein"
J Biological Science, 34 (2009) 529-542

Sakata, A., Hukushima K,, and Kaneko K.
"Funnel landscape and mutational robustness as a result of evolution under thermal noise"
Phys. Rev. Lett., 102 (2009a) 148101

Sakata, A., Hukushima K,, and Kaneko K.
"A statistical-mechanical study of evolution of robustness in noisy environment"
Phys. Rev. E., in press.(2009b)

K. Kaneko
"Shaping Robust System Through Evolution"
Chaos, 18 (2008) 026112

K. Kaneko and C. Furusawa
"Consistency Principle in Biological Dynamical Systems"
Theory in Biosciences, 127 (2008) 195-204

Kaneko, K.
"Evolution of robustness to noise and mutation in gene expression dynamics."
PLoS ONE 2(5): e434. (2007)

Sato, K. and K. Kaneko
"Evolution equation of phenotype distribution: general formulation and application to error catastrophe."
Phys Rev E Stat Nonlin Soft Matter Phys 75(6 Pt 1): 061909.(2007)

Chioko Nagao, Tomoki P. Terada, Tetsuya Yomo, and Masaki Sasai
"Correlation between evolutionary structural development and protein folding"
Proc. Natl. Acad. Sci. USA, 102(2005), 18950-18955 PDF

Tetsuya Yomo, Yoichiro Ito, Katsuhiko Sato and Kunihiko Kaneko
"Phenotypic fluctuation rendered by a single genotype and evolutionary rate"
Physica A, 350(2005)1-5 PDF

K. Sato and K. Kaneko
"On the Distribution of State Values of Reproducing Cells: the General Evolution Equation and its Applications"
Physical Biology, 3, 74-82 PDF

K. Kaneko and C. Furusawa
"An Evolutionary Relationship between Genetic Variation and Phenotypic Fluctuation"
Jour. Theore. Biol, 240 (2006), 78-86 PDF

(E) Diversity and Symbiosis

Kihara, K., Mori, K., Suzuki, S., Ono, N., Furusawa, C., and Yomo, T.
"Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum."
Biosystems, 96: 141-164 (2009)

Tachikawa, M.
"Fluctuation induces evolutionary branching in a mathematical model of ecosystems."
PLoS ONE, 12, e3925 Dec. (2008)

Yamada, A., Matsuyama, S., Todoriki, M., Kashiwagi, A., Urabe, I., and Yomo, T.
"Phenotypic plasticity of Escherichia coli at initial stage of symbiosis with Dictyostelium discoideum."
BioSsystems, 92(1): 1-9. (2008)

Lawson D., Jensen H.J., and Kaneko K.
"Diversity as a product of interspecial interactions"
J theor. Biol. 243(2006) 299-307

(F) Basic Expereminetal Methods in Complex Systems Biology

Ono, N., Suzuki, S., Furusawa, C., Agata, T, Kashiwagi, A., Shimizu, H., and Yomo, T.
"An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays"
submitted to Bioinformatics

Furusawa, C., Ono, N., Suzuki, S., Agata, T., Shimizu, H., and Yomo, T.
"Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays"
Bioinformatics, 25:36?41. ,(2009)

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

Suzuki, S, Ono, N., Furusawa, C., Kashiwagi, A., and Yomo, T.
"Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarray."
BMC genomics, 8(1): 373(2007)

(G) Basic Theory for Biological System

Tachikawa, M.
"Regular and irregular modulation of frequencies in limit cycle oscillator networks."
Submitted. (http://arxiv.org/abs/0902.0218).

Nakajima、A. and Kaneko K.
"Regulative Differentiation as Bifurcation of Interacting Cell Population"
J. Theor Biol. 253 (2008) 779-787

Tachikawa, M. and Fujimoto, K.
"Emergence of multiple-time scales in coupled oscillators with plastic frequencies."
Europhysics Letters, 78, 20004. (2007)

Watanabe, Y. and Kaneko, K.
"State Generation by Transient Truncation in Coupled Threshold Dynamics."
Phys. Rev. E., 75, 016206 (2007)

Masashi Tachikawa
" Specific locking in populations dynamics: Symmetry analysis for coupled heteroclinic cycles "
Journal of Computational and Applied Mathematics, 201, Issue 2 , 15 April 2007, 374-380 (proceeding)

Masashi Tachikawa
"Convective Stabilization of Saddle Fixed Points in an Open Flow System"
Progress of Theoretical PhysicsSupplement No.161 (2006), 352-355

Frederick H. Willeboordse and Kunihiko Kaneko
"Externally controlled attractor selection in a high-dimensional system"
Physical Review E, 72 (2005), 026207 PDF

K. Kaneko
"Inter-Intra Molecular Dynamics as an Iterated Function System"
J. Phys. Soc. Japan 74 (2005), 2386-2390 PDF

S. Ishihara and K. Kaneko
"Magic number 7 ± 2 in networks of threshold dynamics",
Phys. Rev. Lett., 94(2005) 058102 PDF

H. Morita and K. Kaneko
"Collective oscillation in a Hamiltonian dynamical system"
Phys. Rev. Lett., 94(2005) 087203 PDF

(H) General