We are studying complex dynamical systems for gaining insights into fundamental principles governing living systems at various scales of organization. We have focused on: the relationships between the structure of such systems and their dynamics; the ability to balance robustness with adaptability in an uncertain and variable environment while making decisions in response to information in the environment; and the coordination of complex behaviors and memory. We are currently exploring information-theoretic approaches to tackle these questions, using mathematical and statistical modeling, computer simulations, and large-scale biological measurements.
A. Sadot, S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, I. Shmulevich, "Information-Theoretic Analysis of the Dynamics of an Executable Biological Model," PLoS ONE, Vol. 8, No. 3, e59303, 2013.
A. V. Ratushny, I. Shmulevich, J. D. Aitchison, "Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues," PLoS Computational Biology, Vol. 7, No. 6, e1002091, 2011.
D. J. Galas, M. Nykter, G. W. Carter, N. D. Price, I. Shmulevich, "Biological information as set-based complexity," IEEE Transactions on Information Theory, Vol. 56, No. 2, pp. 667-677, 2010.
M. Nykter, J. Kesseli, and I. Shmulevich, Dynamical systems analysis of stack filters, In I. Tabus, K. Egiazarian, and M. Gabbouj, editors, Festschrift in honor of Jaakko Astola on the occasion of his 60th Birthday, pages 169-181, Tampere International Center of Signal Processing, 2009.
E. Balleza, E. Alvarez-Buylla, A. Chaos, S. A. Kauffman, I. Shmulevich, M. Aldana, "Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms," PLoS ONE, Vol. 3, No. 6, e2456, 2008.
M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, I. Shmulevich, "Critical networks exhibit maximal information diversity in structure-dynamics relationships," Physical Review Letters, Vol. 100, 058702, 2008.
M. Nykter, N. D. Price , M. Aldana, S. A. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, I. Shmulevich, "Gene Expression Dynamics in the Macrophage Exhibit Criticality," Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 6, pp. 1897-1900, 2008.
S. A. Kauffman, R. K. Logan, R. Este, R. Goebel, D. Hobill, I. Shmulevich, "Propagating Organization: An Enquiry," Biology and Philosophy, Vol. 23, No. 1, pp. 27-45, 2007.
P. Krawitz, I. Shmulevich, "Entropy of complex relevant components in Boolean networks," Physical Review E, Vol. 76, 036115, 2007.
P. Krawitz, I. Shmulevich, "Basin Entropy in Boolean Network Ensembles," Physical Review Letters, Vol. 98, No. 15, pp. 158701, 2007.
T. Toulouse, P. Ao, I. Shmulevich, S. A. Kauffman, “Noise in a Small Genetic Circuit that Undergoes Bifurcation,” Complexity, Vol. 11, No. 1, pp. 45-51, 2005.
I. Shmulevich, S. A. Kauffman, M. Aldana, "Eukaryotic cells are dynamically ordered or critical but not chaotic" Proceedings of the National Academy of Sciences of the USA, Vol. 102, No. 38, pp. 13439-13444, 2005.
I. Shmulevich, H. Lähdesmäki, E. R. Dougherty, J. Astola, W. Zhang, "The role of certain Post classes in Boolean network models of genetic networks," Proceedings of the National Academy of Sciences of the USA, Vol. 100, No. 19, pp. 10734-10739, 2003.
I. Shmulevich, S. A. Kauffman, "Activities and Sensitivities in Boolean Network Models," Physical Review Letters, Vol. 93, No. 4, pp. 048701(1-4), 2004.