@article{UllnerAresMorellietal.2012,
  author    = {Ullner, E. and Ares, S. and Morelli, L. G. and Oates, A. C. and J{\"u}licher, F. and Nicola, E. and Heussen, R. and Whitmore, D. and Blyuss, K. and Fryett, M. and Zakharova, A. and Koseska, A. and Nene, N. R. and Zaikin, Alexei},
  title     = {Noise and oscillations in biological sysems multidisciplinary approach between experimental biology, theoretical modelling and synthetic biology},
  series = {International journal of modern physics : B, Condensed matter physics, statistical physics, applied physics},
  volume    = {26},
  journal   = {International journal of modern physics : B, Condensed matter physics, statistical physics, applied physics},
  number    = {25},
  publisher = {World Scientific},
  address   = {Singapore},
  issn      = {0217-9792},
  doi       = {10.1142/S0217979212460095},
  pages     = {12},
  year      = {2012},
  abstract  = {Rapid progress of experimental biology has provided a huge flow of quantitative data, which can be analyzed and understood only through the application of advanced techniques recently developed in theoretical sciences. On the other hand, synthetic biology enabled us to engineer biological models with reduced complexity. In this review we discuss that a multidisciplinary approach between this sciences can lead to deeper understanding of the underlying mechanisms behind complex processes in biology. Following the mini symposia "Noise and oscillations in biological systems" on Physcon 2011 we have collected different research examples from theoretical modeling, experimental and synthetic biology.},
  language  = {en}
}
@article{ZakharovaNikoloskiKoseska2013,
  author    = {Zakharova, A. and Nikoloski, Zoran and Koseska, Aneta},
  title     = {Dimensionality reduction of bistable biological systems},
  series = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology},
  volume    = {75},
  journal   = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology},
  number    = {3},
  publisher = {Springer},
  address   = {New York},
  issn      = {0092-8240},
  doi       = {10.1007/s11538-013-9807-8},
  pages     = {373 -- 392},
  year      = {2013},
  abstract  = {Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.},
  language  = {en}
}