Structure

Can Markov Chain Models Mimic Biological Regulation

Kim, S., Li, H., Dougherty, E. R., Chao, N., Chen, Y., Bittner, M. L., and Suh, E. B., Biological Systems, Vol. 10, No. 4, 447-458, 2002

Comparison of Gene Regulatory Networks via Steady-State Trajectories

Brun, M., Kim, S., Choi, W., and Dougherty, E. R., EURASIP Journal on Bioinformatics and Systems Biology Vol. 2007, Article ID 82702, 11 pages, May, 2007

Conditioning-Based Model of Contextual Regulation

Dougherty, E. R., Brun, M., Trent, J., and Bittner, M. L., IEEE/ACM Transactions on Computational Biology and Bioinformatics preprint, 29 Aug. 2007, doi:10.1109/TCBB.2007.70247.

Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks

Ivanov,I., Pal, R., and Dougherty, E. R., IEEE Transactions on Signal Processing, Vol. 55, No. 5, 2310-2322, May, 2007

Effect of Function Perturbation on the Steady-State Distribution of Genetic Regulatory Networks: Optimal Structural Intervention

Qian, X., and Dougherty, E. R., IEEE Transactions on Signal Processing, doi: 10.1109/TSP.2008.928089, Vol. 56, No. 10, Part 1, 4966-4975, October, 2008

From Boolean to Probabilistic Boolean Networks as Models of Genetic Regulatory Networks

Shmulevich, I., Dougherty, E. R., Zhang, W., Proceedings of IEEE, Vol. 90, No. 11, 1778-1792, 2002

Mappings Between Probabilistic Boolean Networks

Dougherty, E. R., and Shmulevich, I., Signal Processing, Vol. 83, No. 4, 799-809, 2003

Modeling Genetic Regulatory Networks: Continuous or Discrete?

Ivanov, I., and Dougherty, E. R., Biological Systems, Vol. 14, No. 2, 219-229, June, 2006

On the Long-run Sensitivity of Probabilistic Boolean Networks

Qian, X., and Dougherty, E. R., Theoretical Biology, doi:10.1016/j.jtbi.2008.12.023, Vol. 257, No. 4, 560-577, 2009

Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks

Shmulevich, I, Dougherty, E. R. , Kim, S, Zhang, W., Bioinformatics, Vol. 18, No. 2, pp. 261-274, 2002

Reduction Mappings Between Probabilistic Boolean Networks

Ivanov, I., and Dougherty, E. R., Applied Signal Processing, Vol. 4, No. 1, 125-131, January, 2004

Steady-State Analysis of Genetic Regulatory Networks Modeled by Probabilistic Boolean Networks

Shmulevich, I., Gluhovsky, I., Hashimoto, R., Dougherty, E. R., and Zhang, W., Comparative Functional Genomics, Vol. 4, 601-608, December, 2003

Steady-State Probabilities for Attractors in Probabilistic Boolean Networks

Brun, M., Dougherty, E. R., and Shmulevich, I., Signal Processing, Vol. 85, No. 10, 1993-2013, October, 2005

The Impact of Function Perturbations in Boolean Networks

Xiao, Y., and Dougherty, E. R., Bioinformatics, Vol. 23, No. 10, 1265-1273, May, 2007

The Role of Certain Post Classes in Boolean Network Models of Genetic Networks

Shmulevich, I., Lahdesmaki, H., Dougherty, E. R., Astola, J., and Zhang, W., Proceedings of the National Academy of Science, Vol. 100, No. 19, 10734-10739, 2003