Inference

A Bayesian Connectivity-Based Approach to Constructing Probabilistic Gene Regulatory Networks

Zhou, X., Wang, X., Pal, R., Ivanov, I., Bittner, M. L., and Dougherty, E. R., Bioinformatics, Vol. 20. No. 17, 2918-2927, November, 2004

Construction of Genomic Networks Using Mutual-Information Clustering and Reversible-Jump Markov-Chain-Monte-Carlo Predictor Design

Zhou, X., Wang, X., and Dougherty, E. R., Signal Processing, Vol. 83, No. 4, 745-761, 2003

Design of Probabilistic Boolean Networks under the Requirement of Contextual Data Consistency

Dougherty, E. R., and Xiao, Y., IEEE Transactions on Signal Processing, Vol. 54, No. 9, 3603- 3613, 2006

Generating Boolean Networks with a Prescribed Attractor Structure

Pal, R., Ivanov, I., Datta, A., and Dougherty, E. R., Bioinformatics, Vol. 21, No. 21, 4021-4025, November, 2005

Growing Genetic Regulatory Networks from Seed Genes

Hashimoto, R., Kim, S., Shmulevich, I., Zhang, W., Bittner, M. L., and Dougherty, E. R., Bioinformatics, Vol. 20, No. 8, 1241-1247, 2004

Inference of Boolean Networks using Sensitivity Regularization

Liu, W., Lhdesmki, H., Dougherty, E. R., and Shmulevich, I., EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, doi:10.1155/2008/780541, June, 2008

Inference of Boolean Networks under Constraint on Bidirectional Gene Relationships

Vahedi, G., Ivanov, I., and Dougherty, E. R., IET Systems Biology Journal, Vol. 3, Iss. 3, 191–202, 2009

Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks using Genetic Programming and Kalman Filtering

Qian, L., Wang, H., and Dougherty, E. R., IEEE Transactions on Signal Processing, Vol. 56, No. 7, 3327-3339, July, 2008

Inference of Probabilistic Boolean Networks from a Single Observed Temporal SequenceInference of Probabilistic Boolean Networks from a Single Observed Temporal Sequence

Marshall, S., Yu, L., Xiao, Y., and Dougherty, E. R., EURASIP Journal on Bioinformatics and Systems Biology., Vol. 2007, Article ID 32454, 15 pages, May, 2007

Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria

Zhao, W., Serpedin, E., and Dougherty, E. R., IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, 262-274, April, 2008

Inferring Gene Regulatory Networks from Time Series Data Using the Minimum Description Length Principle

Zhao, W., Serpedin, E., and Dougherty, E. R., Bioinformatics, Vol. 22, No. 17, 2129-2135, 2006

Optimizing Consistency-Based Design of Context-Sensitive Gene Regulatory Networks

Xiao, Y., and Dougherty, E. R., IEEE Transactions on Circuits and Systems I, Vol. 53, No. 11, 2431-2437, November, 2006

Recovering Genetic Regulatory Networks From Chromatin Immunoprecipitation (ChIP) and Steady State Microarray Data

Zhao, W., Serpedin, E., and Dougherty, E. R., EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 248747, 12 pages, doi:10.1155/2008/248747, June, 2008

Validation of Inference Procedures for Gene Regulatory Networks

Dougherty, E. R., Current Genomics, Vol. 8, No. 6, 351-359, September, 2007