This page aims to be a comprehensive source of information about research work on Probabilistic Boolean Networks and related topics. The page will primarily house publications related to PBN research, with frequent updates as they become available. Other materials, such as presentation slides and posters, workshop announcements, software, and other information will also be available.
To contribute an update, please e-mail Ilya Shmulevich (
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 | BN/PBN MATLAB Toolbox (.zip file) This toolbox is written in MATLAB and can be used to work with Boolean Networks and Probabilistic Boolean Networks. It includes functions for simulating the network dynamics, computing network statistics (numbers and sizes of attractors, basins, transient lengths, Derrida curves, percolation on 2-D lattices, influence matrices), computing state transition matrices and obtaining stationary distributions, inferring networks from data, generating random networks and functions, visualization and printing, intervention, and membership testing of Boolean functions. |
| See the file Contents.m for a listing of included functions. In MATLAB, type help Contents |
| This toolbox is maintained by Harri Lähdesmäki and Ilya Shmulevich. |
| Slides: Computational and Experimental Approaches to the Study of Genetic Networks [.pdf format] |
| Slides: Probabilistic Boolean Networks [.pdf format] |
| Poster: Probabilistic Boolean Networks (overview) [.gif format] |
| Poster: Context-sensitive probabilistic Boolean networks to mimic biological regulation, Oncogenomics 2003, Phoenix, AZ, January 29-February 2, 2003. (S. Kim, H. Li, D. Russ, J. Whitmore, Y. Chen, E. R. Dougherty, E. Suh, and M. L. Bittner) [.pdf format] |
I. Shmulevich, E.R. Dougherty, and W. Zhang, "From Boolean to probabilistic Boolean networks as models of genetic regulatory networks,'' Proceedings of the IEEE, Vol. 90, No. 11, pp. 1778-1792, 2002.
I. Shmulevich, E. R. Dougherty, S. Kim, W. Zhang, "Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks," Bioinformatics, Vol. 18, No. 2, pp. 261-274, 2002
I. Shmulevich, E. R. Dougherty, W. Zhang, "Gene Perturbation and Intervention in Probabilistic Boolean Networks," Bioinformatics, Vol. 18, No. 10, pp. 1319-1331, 2002.
I. Shmulevich, E.R. Dougherty, and W. Zhang, "Control of stationary behavior in Probabilistic Boolean Networks by means of structural intervention," Journal of Biological Systems, Vol. 10, No. 4, pp. 431-445, 2002.
S. Kim, H. Li, E. R. Dougherty, N. Cao, Y. Chen, M. Bittner, and E. B. Suh, "Can Markov Chain Models Mimic Biological Regulation?," Journal of Biological Systems, Vol. 10, No. 4, pp. 431-445, 2002.
E. R. Dougherty and I. Shmulevich, "Mappings Between Probabilistic Boolean Networks," Signal Processing, Vol. 83, No. 4, pp. 799-809, 2003.
A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External Control in Markovian Genetic Regulatory Networks," Machine Learning, Vol. 52, no. 1-2, pp. 169-191, 2003.
I. Shmulevich, I. Gluhovsky, R. Hashimoto, E. R. Dougherty, and W. Zhang, "Steady-State Analysis of Genetic Regulatory Networks Modeled by Probabilistic Boolean Networks," Comparative and Functional Genomics, Vol. 4, No. 6, pp. 601-608, 2003. [Supplementary material available here]
R. F. Hashimoto, S. Kim, I. Shmulevich, W. Zhang, M. L. Bittner, E. R. Dougherty, "Growing genetic regulatory networks from seed genes," Bioinformatics, Vol. 20, No. 8, pp. 1241-1247, 2004.
I. Ivanov, E. R. Dougherty, "Reduction Mappings Between Probabilistic Boolean Networks," Journal of Applied Signal Processing, Vol. 2004, No. 1, pp. 125-131, 2004.
A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External control in Markovian genetic regulatory networks: the imperfect information case," Bioinformatics, Vol. 20, No. 6, pp. 924-930, 2004.
X. Zhou, X. Wang, R. Pal, I. Ivanov, M. Bittner, E. R. Dougherty, "A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks," Bioinformatics, Vol. 20, No. 17, pp. 2918-2927, 2004.
W.-K. Ching, E. S. Fung, M. K. Ng, "Building Genetic Networks for Gene Expression Patterns," in Lecture Notes in Computer Science, Vol. 3177, pp. 17 - 24, Jan 2004.
U. M. Braga-Neto, R. Hashimoto, E. R. Dougherty, D. V. Nguyen, R. J. Carroll, “Is Cross-validation Better than Resubstitution for Ranking Genes?” Bioinformatics, Vol. 20, No. 2, 253-258, 2004.
R. Pal, A. Datta, M. L. Bittner, E. R. Dougherty, "Intervention in context-sensitive probabilistic Boolean networks," Bioinformatics, Vol. 21, No. 7, pp. 1211-1218, 2005.
M. Brun, E. R. Dougherty, I. Shmulevich, “Steady-State Probabilities for Attractors in Probabilistic Boolean Networks,” Signal Processing, Vol. 85, No. 4, pp. 1993-2013, 2005.
W.-K. Ching, E. S. Fung, M. K. Ng, T. Akutsu, "On construction of stochastic genetic networks based on gene expression sequences," International Journal of Neural Systems, Vol. 15, No. 4, pp. 297–310, 2005.
R. Pal, I. Ivanov, A. Datta, M. L. Bittner, E. R. Dougherty, "Generating Boolean networks with a prescribed attractor structure," Bioinformatics, Vol. 21, No. 21, pp. 4021-4025, 2005.
H. Li, M. Zhan, "Systematic intervention of transcription for identifying network response to disease and cellular phenotypes," Bioinformatics, Vol. 22, No. 1, pp. 96-102, 2006.
A. Choudhary, A. Datta, M. L. Bittner, E. R. Dougherty, "Intervention in a family of Boolean networks," Bioinformatics, Vol. 22, No. 2, pp. 226-232, 2006.
H. Lähdesmäki, S. Hautaniemi, I. Shmulevich, O. Yli-Harja, "Relationships Between Probabilistic Boolean Networks and Dynamic Bayesian Networks as Models of Gene Regulatory Networks" Signal Processing, Vol. 86, No. 4, pp. 814-834, 2006.
E. R. Dougherty, Y. Xiao, "Design of Probabilistic Boolean Networks Under the Requirement of Contextual Data Consistency," IEEE Transactions on Signal Processing, Vol. 54, No. 9, pp. 3603-3613, Sept. 2006.
Y. Xiao, E. R. Dougherty, “Optimizing Consistency-based Design of Context-sensitive Gene Regulatory Networks,” IEEE Transactions on Circuits and Systems I, Vol. 53, No. 11, pp. 2431-2437, 2006.
R. Pal, A. Datta, E. R. Dougherty, “Optimal Infinite Horizon Control for Probabilistic Boolean Networks,” IEEE Transactions on Signal Processing, Vol. 54, no. 6, pp. 2375-2387, 2006.
P. C. Y. Chen, J. W. Chen, "A Markovian Approach to the Control of Genetic Regulatory Networks," Biosystems, Vol. 90, No. 2, pp. 535-545, 2006.
S-Q. Zhang, W.-K. Ching, M. K. Ng , T. Akutsu, "Simulation study in Probabilistic Boolean Network models for genetic regulatory networks," International Journal on Data Mining and Bioinformatics, Vol. 1, No. 3, 2007.
W.-K. Ching, S. Zhang , M. K. Ng , T. Akutsu, "An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks," Bioinformatics Vol. 23, pp. 1511-1518, 2007.
Y. Xiao, E. R. Dougherty, “The Impact of Function Perturbations in Boolean Networks,” Bioinformatics Vol. 23, No. 10, 1265-1273, 2007.
S. Marshall, L. Yu, Y. Xiao, E. R. Dougherty, "Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence," EURASIP Journal on Bioinformatics and Systems Biology., Vol. 2007, Article ID 32454, 15 pages, May, 2007.
A. Datta, R. Pal, A. Choudhary, E. R. Dougherty, “Control Approaches for Probabilistic Gene Regulatory Networks”, IEEE Signal Processing Magazine, Vol. 24, No. 1, 54-63, 2007.
P. Li, C. Zhang, E. J. Perkins, P. Gong, Y. Deng, "Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks," BMC Bioinformatics, Vol. 8(Suppl 7):S13, 2007.
S. Q. Zhang, W. K. Ching, M. K. Ng, T. Akutsu, "Simulation Study in Probabilistic Boolean Network Models for Genetic Regulatory Networks," International Journal of Data Mining and Bioinformatics, Vol. 1, No. 3, pp. 217-240, 2007.
B. Faryabi, A. Datta, E.R. Dougherty, "On Approximate Stochastic Control in Genetic Regulatory Networks," IET Systems Biology, Vol. 1, No. 6, pp. 361-368, 2007.
B. Faryabi, G. Vahedi, J.F. Chamberland, A. Datta, E.R. Dougherty, "Optimal constrained stationary intervention in gene regulatory networks," EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 620767, 2008.
S. Kim, E. R. Dougherty, Y. Chen, K. Sivakumar, P. Meltzer, J. M. Trent, and M. Bittner, "Multivariate Measurement of Gene Expression Relationships," Genomics, Vol. 67, pp. 201-209, 2000.
S. Kim, E. R. Dougherty, M. L. Bittner, Y. Chen, K. Sivakumar, P. Meltzer, and J. M. Trent, "General Nonlinear Framework for the Analysis of Gene Interaction via Multivariate Expression Arrays," Journal of Biomedical Optics, Vol. 5, No. 4, pp. 411-424, 2000.
E. R. Dougherty, S. Kim, and Y. Chen, "Coefficient of Determination in Nonlinear Signal Processing," Signal Processing, Vol. 80, pp. 2219-2235, 2000.
I. Tabus and J. Astola, "On the Use of MDL Principle in Gene Expression Prediction," Journal of Applied Signal Processing, Vol. 2001, No. 4, pp. 297-303, December 2001.
I. Shmulevich, A. Saarinen, O. Yli-Harja, J. Astola, "Inference of genetic regulatory networks under the Best-Fit Extension paradigm," in Computational And Statistical Approaches To Genomics, W. Zhang and I. Shmulevich, Eds., Kluwer Academic Publishers, Boston, 2002.
I. Tabus, J. Rissanen, and J. Astola, "Normalized maximum likelihood models for Boolean regression with application to prediction and classification in genomics," in Computational And Statistical Approaches To Genomics, W. Zhang and I. Shmulevich, Eds., Kluwer Academic Publishers, Boston, 2002.
H. Lähdesmäki, I. Shmulevich, and O. Yli-Harja, "On Learning Gene Regulatory Networks Under the Boolean Network Model," Machine Learning, Vol. 52, pp. 147-167, 2003.
R. F. Hashimoto, E. R. Dougherty, M. Brun, Z-Z. Zhou, M. L. Bittner, and J. M. Trent, "Efficient selection of feature sets possessing high coefficients of determination based on incremental determinations," Signal Processing, Vol. 83, No. 4, pp. 695-712, 2003.
X. Zhou, X. Wang, and E. R. Dougherty, "Construction of genomic networks using mutual-information clustering and reversible-jump Markov-chain-Monte-Carlo predictor design," Signal Processing, Vol. 83, No. 4, pp. 745-761, 2003.
X. Zhou, X. Wang, E. R. Dougherty, "Gene prediction Using Multinomial Probit Regression with Bayesian Gene Selection,” Journal of Applied Signal Processing, Vol. 4, No. 1, pp. 115-124, 2004.
W. Zhao, E. Serpedin, E. R. Dougherty, "Inferring gene regulatory networks from time series data using the minimum description length principle," Bioinformatics, Vo. 22, No. 17, pp. 2129-2135, 2006.
W. Liu, H. Lähdesmäki, E. R. Dougherty, I. Shmulevich, "Inference of Boolean Networks using Sensitivity Regularization," EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, 2008.
J. Dougherty, I. Tabus, J. Astola, "Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length," EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 482090, 2008.
| Workshop on Discrete Models for Genetic Regulatory Networks, College Station, TX, November 7-8, 2005. |
| Workshop on Discrete Models for Genetic Regulatory Networks, College Station, Texas, November 5-6, 2003. |
| First Workshop on Probabilistic Boolean Networks in Genomic Signal Processing, Bethesda, Maryland, February 20-21, 2002. |
This page is maintained by Ilya Shmulevich
