Andre S Ribeiro

Summary

Affiliation: University of Calgary
Country: Canada

Publications

  1. ncbi request reprint A general modeling strategy for gene regulatory networks with stochastic dynamics
    Andre Ribeiro
    Institute for Biocomplexity and Informatics, Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
    J Comput Biol 13:1630-9. 2006
  2. ncbi request reprint SGN Sim, a stochastic genetic networks simulator
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    Bioinformatics 23:777-9. 2007
  3. ncbi request reprint Noisy attractors and ergodic sets in models of gene regulatory networks
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    J Theor Biol 247:743-55. 2007
  4. ncbi request reprint Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, Department of Physics and Astronomy, University of Calgary, Canada
    Phys Rev E Stat Nonlin Soft Matter Phys 75:061903. 2007
  5. ncbi request reprint CellLine, a stochastic cell lineage simulator
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    Bioinformatics 23:3409-11. 2007
  6. ncbi request reprint Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models
    Rui Zhu
    Department of Chemistry, University of Calgary, Canada
    J Theor Biol 246:725-45. 2007
  7. ncbi request reprint Mutual information in random Boolean models of regulatory networks
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
    Phys Rev E Stat Nonlin Soft Matter Phys 77:011901. 2008
  8. ncbi request reprint Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
    Andre S Ribeiro
    Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
    Phys Rev E Stat Nonlin Soft Matter Phys 76:051915. 2007

Detail Information

Publications8

  1. ncbi request reprint A general modeling strategy for gene regulatory networks with stochastic dynamics
    Andre Ribeiro
    Institute for Biocomplexity and Informatics, Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
    J Comput Biol 13:1630-9. 2006
    ..Therefore, the general strategy here proposed may be used to simulate real genetic networks...
  2. ncbi request reprint SGN Sim, a stochastic genetic networks simulator
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    Bioinformatics 23:777-9. 2007
    ....
  3. ncbi request reprint Noisy attractors and ergodic sets in models of gene regulatory networks
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    J Theor Biol 247:743-55. 2007
    ..We show that, in this case, two distinct ergodic sets exist and are stable within a wide range of parameters variations and, to some extent, to external perturbations...
  4. ncbi request reprint Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, Department of Physics and Astronomy, University of Calgary, Canada
    Phys Rev E Stat Nonlin Soft Matter Phys 75:061903. 2007
    ....
  5. ncbi request reprint CellLine, a stochastic cell lineage simulator
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Canada
    Bioinformatics 23:3409-11. 2007
    ....
  6. ncbi request reprint Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models
    Rui Zhu
    Department of Chemistry, University of Calgary, Canada
    J Theor Biol 246:725-45. 2007
    ..The binary code can be described by the corresponding Boolean network models in certain conditions. We discuss these conditions, suggesting a method to connect Boolean models, mean-field models, and stochastic chemical models...
  7. ncbi request reprint Mutual information in random Boolean models of regulatory networks
    Andre S Ribeiro
    Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
    Phys Rev E Stat Nonlin Soft Matter Phys 77:011901. 2008
    ..The contribution from pairs that are directly linked approaches zero for critical networks and peaks deep in the disordered regime...
  8. ncbi request reprint Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
    Andre S Ribeiro
    Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
    Phys Rev E Stat Nonlin Soft Matter Phys 76:051915. 2007
    ..The results provide an explanation of how cells with bistable GRNs, inherently stochastic, can synchronize or uniformly differentiate into stable states, by interacting with nearest neighbors...