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Qian, X. and E. R. Dougherty, “On the Long-Run Sensitivity of Probabilistic Boolean Networks,” Journal of theoretical biology, Vol. 257, No. 4, 560-577, 2009. [pdf]
Dougherty, E.R., Brun, M., Trent, J. M., and M. L. Bittner, “Conditioning-Based Modeling of Contextual Genomic Regulation,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 2, 310-320, 2009. [pdf]
Xiao, Y., and E. R. Dougherty, “The Impact of Function Perturbations in Boolean Networks,” Bioinformatics, Vol. 23, No. 10, 1265-1273, 2007. [pdf]
Brun, M., Kim, S., Choi, W., and E. R. Dougherty, “Comparison of Gene Regulatory Networks via Steady-State Trajectories,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2007, No. 1, 1-11, 2007. [pdf]
Ivanov, I., Pal, R., and E. R. Dougherty, “Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks,” IEEE Transactions on Signal Processing, Vol. 55, No. 5, 2310-2322, 2007. [pdf]
Ivanov, I., and E. R. Dougherty, “Modeling genetic regulatory networks: continuous or discrete?,” Journal of Biological Systems, Vol. 14, No. 02, 219-229, 2006. [pdf]
Brun, M., Dougherty, E. R., and I. Shmulevich, “Steady-state probabilities for Attractors in Probabilistic Boolean Networks,” Signal Processing, Vol. 85, No. 10, 1993-2013, 2005.[pdf]
Ivanov, I., and E. R. Dougherty, “Reduction Mappings Between Probabilistic Boolean Networks,” EURASIP Journal on Applied Signal Processing, Vol. 2004, 125-131, 2004. [pdf]
Shmulevich, I., Gluhovsky, I., Hashimoto, R. F., Dougherty, E. R., and W. Zhang, “Steady‐State Analysis of Genetic Regulatory Networks Modelled by Probabilistic Boolean Networks,” Comparative and functional genomics, Vol. 4, No. 6, 601-608, 2003. [pdf]
Shmulevich, I., Lähdesmäki, H., Dougherty, E. R., Astola, J., and W. Zhang, “The Role of Certain Post Classes in Boolean Network Models of Genetic Networks,” Proceedings of the National Academy of Sciences, Vol. 100, No. 19, 10734-10739, 2003. [pdf]
Dougherty, E. R., and I. Shmulevich, “Mappings Between Probabilistic Boolean Networks,” Signal Processing, Vol. 83, No. 4, 799-809, 2003. [pdf]
Kim, S., Li, H., Dougherty, E. R., Cao, N., Chen, Y., Bittner, M., and E. B. Suh, “Can Markov Chain Models Mimic Biological Regulation?,” Journal of Biological Systems, Vol. 12, No. 6, 1304-1321, 2002. [pdf]
Shmulevich, I., Dougherty, E. R., and W. Zhang,”From Boolean to Probabilistic Boolean Networks as Models of Genetic Regulatory Networks,” Proceedings of IEEE, Vol. 90, No. 11, 1778-1792, 2002. [pdf]
Shmulevich, I., Dougherty, E. R., Kim, S., and W. Zhang,”Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks,” Bioinformatics, Vol. 18, No. 2, 261-274, 2002. [pdf]
Su, J., Yoon, B.J. and Dougherty, E.R., “Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity,” PloS One, Vol. 4, No. 12, e8161, 2009. [pdf]
Vahedi, G., Ivanov, I., and E. R. Dougherty, “Inference of Boolean Networks Under Constraint on Bidirectional Gene Relationships,” IET systems biology, Vol. 3, No. 3, 191-202, 2009. [pdf]
Liu, W., Harri, L. Ã., Dougherty, E. R., and I. Shmulevich, “Inference of Boolean Networks Using Sensitivity Regularization,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, No. 1, 1, 2008. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Inferring Connectivity of Genetic Networks Using Information Theoretic Criteria,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, 262-274, 2008. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Recovering Genetic Regulatory Networks From Chromatin Immunoprecipitation (ChIP) and Steady State Microarray Data,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, No. 1, 1, 2008. [pdf]
Dougherty, E. R., “Validation of Inference Procedures for Gene Regulatory Networks,” Current Genomics, Vol. 8, No. 6, 351-359, September, 2007. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, 262-274, 2008. [pdf]
Marshall, S., Yu, L., Xiao, Y., and E. R. Dougherty, “Inference of Probabilistic Boolean Networks from a Single Observed Temporal Sequence,” EURASIP Journal on Bioinformatics and Systems Biology., Vol. 2007, No. 1, 1-15, 2007. [pdf]
Xiao Y., and E. R. Dougherty, “Optimizing Consistency-Based Design of Context- Sensitive Gene Regulatory Networks,” IEEE Transactions on Circuits and Systems I, Vol. 53, No. 11, 2431-2437, 2006. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Inferring Gene Regulatory Networks from Time Series Data Using the Minimum Description Length Principle,” Bioinformatics, Vol. 22, No. 17, 2129-2135, 2006. [pdf]
Dougherty, E. R., and Y. Xiao, “Design of Probabilistic Boolean Networks under the Requirement of Contextual Data
Consistency,” IEEE Transactions on Signal Processing, Vol. 54, No. 9, 3603-3613, 2006. [pdf]
Pal, R. Ivanov, I., Datta, A., and E. R. Dougherty, “Generating Boolean Networks with a Prescribed Attractor Structure,” Bioinformatics, Vol. 21, No. 21, 4021-4025, 2005. [pdf]
Zhou, X., Wang, X., Pal, R., Ivanov, I., Bittner, M. L., and E. R. Dougherty, “A Bayesian Connectivity-Based Approach to Constructing Probabilistic Gene Regulatory Networks,” Bioinformatics, Vol. 20. No. 17, 2918-2927, 2004. [pdf]
Hashimoto, R., Kim, S., Shmulevich, I., Zhang, W., Bittner, M. L., and E. R. Dougherty, “A Directed-Graph Algorithm to Grow Genetic Regulatory Subnetworks from Seed Genes Based on Strength of Connection,” Bioinformatics, Vol. 20, No. 8, 1241-1247, 2004. [pdf]
Zhou, X., Wang, X., 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, 745-761, 2003. [pdf]
Martins, D., Braga-Neto, U., Hashimoto, R., Bittner, M. L., and E. R. Dougherty, “Intrinsically Multivariate Predictive Genes,” IEEE Journal of Selected Topics in Signal Processing, Vol. 2, No. 3, 424-439, 2008. [pdf]
Pal, R., Datta, A., Fornace, A. J., Bittner, M. L., and E. R. Dougherty, “Boolean Relationships Among Genes Responsive to Ionizing Radiation in the NCI 60 ACDS,” Bioinformatics, 21, No. 8, 1542-1549, 2005. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Gene prediction Using Multinomial Probit Regression with Bayesian Gene Selection,” Applied Signal Processing, Vol. 4, No. 1, 115-124, 2004. [pdf]
Kim, S., Dougherty, E. R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., and M. Bittner, “Multivariate Measurement of Gene Expression Relationships,” Genomics, Vol. 67, No. 2, 201-209, 2000. [pdf]
Kim, S., Dougherty, E. R., Bittner, M. L., Chen, Y., Sivakumar, K., Meltzer, P., 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, 411–424, 2000 . [pdf]
Dougherty, E. R., Kim, S., and Y. Chen, “Coeffcient of Determination in Nonlinear Signal Processing,” Signal Processing Vol. 80, No. 10, 2219-2235, 2000. [pdf]
Dougherty, E. R., Bittner, M., L., Chen, Y., Kim, S., Sivakumar, K., Barrera, J., Meltzer, P., and J. Trent, “Nonlinear Filters in Genomic Control,” Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing, Antalya, Turkey, June, 1999. [pdf]
Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., and E. R. Dougherty, “Sampling-Rate-Dependent Probabilistic Boolean Networks,” Journal of Theoretical Biology, Vol. 261, No. 4, 540-547, 2009. [pdf]
Faryabi, B., Vahedi, G., Datta, A., Chamberland, J. F., and E. R. Dougherty, “Recent Advances in Intervention in Markovian Regulatory Networks,” Current Genomics, Vol.10, No. 7, 463-477, 2009. [pdf]
Pal, R., Datta, A., and E. R. Dougherty, “Bayesian Robustness in the Control of Gene Regulatory Networks,” IEEE Transactions on Signal Processing, Vol. 57, No. 9, 3667-3678, 2009. [pdf]
Layek, R., Datta, A., Pal, R., and E. R. Dougherty, “Adaptive Intervention in Probabilistic Boolean Networks,” Bioinformatics, Vol. 25, No. 16, 2042-2048, 2009. [pdf]
Qian, X., Ivanov, I., Ghaffari, N., and E. R. Dougherty, “Intervention in Gene Regulatory Networks via Greedy Control Policies Based on Long-Run Behavior,” BMC systems biology, Vol. 3, No. 1, 1, 2009. [pdf]
Faryabi, B., Vahedi, G., Chamberland, J. F., Datta, A., and E. Dougherty, “Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2009, No. 1, 1, 2009. [pdf]
Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., and E. R. Dougherty, “Optimal Intervention Strategies for Cyclic Therapeutic Methods,” IEEE Transactions of Biomedical Engineering, Vol. 56, No. 2, 281-291, 2009. [pdf]
Faryabi, B., Vahedi, G., Chamberland, J. F., Datta, A., and E. R. Dougherty, “Optimal Constrained Stationary Intervention in Gene Regulatory Networks,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, No. 1, 1, 2008. [pdf]
Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., and E. R. Dougherty, “Intervention in Gene Regulatory Networks via a Stationary Mean-First-Passage-Time Control Policy,” IEEE Transactions of Biomedical Engineering, Vol. 55, No. 10, 2319-2331, 2008. [pdf]
Faryabi, B., Chamberland, J. F., Vahedi, G., Datta, A., and E. R. Dougherty, “Optimal Intervention in Asynchronous Genetic Regulatory Networks,” IEEE Journal of Selected Topics in SignalProcessing, Vol. 2, No. 3, 412-423, 2008. [pdf]
Pal, R., Datta, A., and E. R. Dougherty, “Robust Intervention in Probabilistic Boolean Networks,” IEEE Transactions on Signal Processing, Vol. 56, No. 3, 1280-1294, 2008. [pdf]
Faryabi, B., Datta, A., and E. R. Dougherty, “On Approximate Stochastic Control in Genetic Regulatory Networks,” IET Systems Biology, Vol. 1, No. 6, 361-368, 2007. [pdf]
Datta, A., Pal, R., Choudhary, A., and E. R. Dougherty, “Control Approaches for Probabilistic Gene Regulatory Networks,” IEEE Signal Processing Magazine, Vol. 24, No. 1, 54-63, 2007. [pdf]
Pal, R., Datta, A., and E. R. Dougherty, “Optimal Infinite Horizon Control for Probabilistic Boolean Networks,” IEEE Transactions on Signal Processing, Vol. 54, No. 6, 2375-2387, 2006. [pdf]
Choudhary, A., Datta, A., Bittner, M. L., and E. R. Dougherty, “Intervention in a Family of Boolean Networks,”Bioinformatics, Vol. 22, No. 2, 226-232, 2006. [pdf]
Pal, R., Datta, A., Bittner, M. L., and E. R. Dougherty, “Intervention in Context-Sensitive Probabilistic Boolean Networks,” Bioinformatics, Vol. 21, No. 7, 1211-1218, 2005. [pdf]
Datta, A., Choudhary, A., Bittner, M. L., and Dougherty, E. R., “External Control in Markovian Genetic Regulatory Networks: The Imperfect Information Case,” Bioinformatics, Vol. 20, No. 6, 924-930, 2004. [pdf]
Datta, A., Choudhary, A., Bittner, M. L., and E. R. Dougherty, “External Control in Markovian Genetic Regulatory Networks,” Machine Learning, Vol. 52, No. 1-2, 169-181, 2003. [pdf]
Shmulevich, I., Dougherty, E. R., and W. Zhang, “Gene Perturbation and Intervention in Probabilistic Boolean Networks,” Bioinformatics, Vol. 18, No. 10, 1319-1331, 2002. [pdf]
Shmulevich, I., Dougherty, E. R., and W. Zhang, “Control of stationary behavior in Probabilistic Boolean Networks by means of structural intervention,” Biological Systems, Vol. 10, No. 4, 431-446, 2002. [pdf]
Performance Analysis and Error Estimation [back to TOC]
Zollanvari, A., Braga-Neto, U. M., and E. R. Dougherty, “On the Sampling Distribution of Resubstitution and Leave-One-Out Error Estimators for Linear Classifiers,” Pattern Recognition, Vol. 42, No. (11), 2705-2723, 2009. [pdf]
Hanczar, B., Hua, J., and E. R. Dougherty, “Decorrelation of the True and Estimated Classifier Errors in High-Dimensional Settings,” EURASIP journal on Bioinformatics and Systems Biology, Vol. 2007, 2, 2007. [pdf]
Xiao, Y., Hua, J., and E. R. Dougherty, “Quantification of the Impact of Feature Selection on Cross-Validation Error Estimation Precision,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2007, 1-1, 2007. [pdf]
Xu, Q., Hua, J., Braga-Neto, U. M. Xiong, Z., Suh, E., and E. R. Dougherty, “Confidence Intervals for the True Classification Error Conditioned on the Estimated Error,” Technology in Cancer Research and Treatment, Vol. 5, No. 6, 579-590, 2006. [pdf]
Sima, C., and E. R. Dougherty, “Optimal Convex Error Estimators for Classification,” Pattern Recognition, Vol. 39, No. 6, 1763-1780, 2006. [pdf]
Sima, C., Attoor, S., Braga-Neto, U., Lowey, J., Suh, E., and E. R. Dougherty, “Impact of Error Estimation on Feature-Selection Algorithms,” Pattern Recognition, Vol. 38, No. 12, 2472-2482, 2005. [pdf]
Braga-Neto, U., and E. R. Dougherty, “Exact Performance Measures and Distributions of Error Estimators for Discrete Classifiers,” Pattern Recognition, Vol. 38, No. 11, 1799-1814, 2005. [pdf]
Sima, C., Braga-Neto, U., and E. R. Dougherty, “Superior Feature-Set Ranking For Small Samples Using Bolstered Error Estimation,” Bioinformatics, Vol. 21, No. 7, 1046-1054, 2005. [pdf]
Attoor, S. N., and E. R. Dougherty, “Classifier Performance as a Function of Distributional Complexity,” Pattern Recognition, Vol. 37, No. 8, 1629-1640, 2004. [pdf]
Braga-Neto, U. M., and E. R. Dougherty, “Bolstered Error Estimation,” Pattern Recognition, Vol. 37, No. 6, 1267-1281, 2004. [pdf]
Braga-Neto, U. M., and E. R. Dougherty, “Is Cross-Validation Valid for Small-Sample Microarray Classification,” Bioinformatics, Vol. 20, No. 3, 374-380, 2004. [pdf]
Braga-Neto, U. M., Hashimoto, R., Dougherty, E. R., Nguyen, D. V., and R. J. Carroll, “Is Cross-validation Better than Resubstitution for Ranking Genes,” Bioinformatics, Vol. 20, No. 2, 253-258, 2004. [pdf]
Brun, M., Sabbagh, D., Kim, S., and E. R. Dougherty, “Corrected Small-Sample Estimation for the Error of the Optimal Binary Filter,” Bioinformatics, Vol. 19, No. 8, 944-951, 2003. [pdf]
Hsing, T., Attoor, S., and E. R. Dougherty, “Relation Between Permutation-test P Values and Classifier Error Estimates,” Machine Learning, Vol. 52, No. 1-2, 11-30, 2003. [pdf]
Brun, M., Xu, Q., and E. R. Dougherty, “Which is Better: Hold-out or Full-sample Classifier Design,” EURASIP Journal on Bioinformatics and Systems Biology,, Vol. 2008, No. 1, 1, 2008. [pdf]
Hua, J., Lowey, J., Xiong, Z., and E. R. Dougherty, “Noise-Injected Neural Networks Show Promise for Use on Small-Sample Expression Data,” BMC Bioinformatics, Vol. 7, No. 1, 1, 2006. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Multi-class Cancer Classification Using Multinomial Probit Regression with Bayesian Variable Selection,” IEE Proceedings System Biology, Vol. 153, No. 2, 70-78, 2006. [pdf]
Dougherty, E. R., Hua, J., Xiong, Z., and Y. Chen, “Optimal Robust Classifiers,” Pattern Recognition, Vol. 38, No. 10, 1520-1532, 2005. [pdf]
Fu, W. J., Dougherty, E. R., Mallick, B., and R. J. Carroll, “How Many Samples Are Needed to Build a Classifier: A General Sequential Approach,” Bioinformatics, Vol. 21, No. 1, 63-70, 2005. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Nonlinear-Probit Gene Classification Using Mutual-Information and Wavelet Based Feature Selection,” Biological Systems, Vol. 12, No. 3, 371-386, 2004. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “A Bayesian Approach to Nonlinear Probit Gene Selection and Classification,” Franklin Institute, Vol. 341, No. 1, 2, 137-156, 2004. [pdf]
Dougherty, E. R., and J. Barrera, “Pattern Recognition Theory in Nonlinear Signal Processing,” Mathematical Imaging and Vision, Vol. 16, No. 3, 181-197, 2002. [pdf]
Hua, J., Tembe, W. D., and E. R. Dougherty, “Performance of Feature-Selection Methods in the Classification of High-Dimension Data,” Pattern Recognition, Vol. 42, No. 3, 409-424, 2009. [pdf]
Sima, C., and E. R. Dougherty, “The Peaking Phenomenon in the Presence of Feature Selection,” Pattern Recognition Letters, Vol. 29, No. 11, 1667-1674, 2008. [pdf]
Sima, C., and E. R. Dougherty, “What Should Be Expected from Feature Selection in Small-Sample Settings,” Bioinformatics, Vol. 22, No. 19, 2430-2436, 2006. [pdf]
Dougherty, E. R., and M. Brun, “On the Number of Close-to-Optimal Feature Sets,” Cancer Informatics, Vol. 2, 189-196, 2006. [pdf]
Choudhary, A., Brun, M., Hua, J., Lowey, J., Suh, E., and E. R. Dougherty, “Genetic Test Bed for Feature Selection,” Bioinformatics, Vol. 22, No. 7, 837-842, 2006. [pdf]
Dougherty, E. R., “Feature-Selection Overfitting with Small-Sample Classifier Design,” IEEE Intelligent Systems Magazine, Vol. 20, No. 6, 64-66, December, 2005. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Gene Selection Using Logistic Regressions Based on AIC, BIC, and MDL Criteria,” New Mathematics and Natural Computation, Vol. 1, No. 1, 129-145, 2005. [pdf]
Hua, J., Xiong, Z., Lowey, J., Suh, E., and E. R. Dougherty, “Optimal Number of Features as a Function of Sample Size for Various Classification Rules,” Bioinformatics, Vol. 21, No. 8, 1509-1515, 2005. [pdf]
Silva, P. J. S., Hashimoto, R. F., Kim, S., Barrera, J., Brandao, L. O., Suh, E., and E. R. Dougherty, “Feature Selection Algorithms to Find Strong Genes,” Pattern Recognition Letters, Vol. 26, No. 10, 1444-1453, 2005. [pdf]
Hsing, T., Liu, L-Y., Brun, M., and E. R. Dougherty, “The Coefficient of Intrinsic Dependence (Feature Selection Using el CID),”Pattern Recognition, Vol. 38, No. 5, 623- 636, 2005. [pdf]
Hua, J., Xiong, Z., and E. R. Dougherty, “Determination of the Optimal Number of Features for Quadratic Discriminant Analysis Via the Normal Approximation to the Discriminant Distribution,” Pattern Recognition, Vol. 38, No. 3, 403-421, 2005. [pdf]
Hashimoto, R., Dougherty, E. R., Brun, M., Zhou, Z., Bittner, M. L., and J. M. Trent,” Efficient Selection of Feature Sets Possessing High Coefficients of Determination Based on Incremental Determinations,” Signal Processing, Vol. 83, No. 4, 695-712, 2003. [pdf]
Lee, K. E., Sha, N., Dougherty, E. R., Vannucci, M., and B. K. Mallick, “Gene Selection: A Bayesian Variable Selection Approach,” Bioinformatics, Vol. 19, No. 1, 90-97, 2003. [pdf]
S. Kim, Dougherty, E. R., Barrera, J., Chen, Y., Bittner, M. L., and J. M. Trent, “Strong Feature Sets from Small Samples,” Journal of Computational Biology, Vol.9, No. 1, 127-146, 2002. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Spectral Preprocessing for Clustering Time-Series Gene Expressions,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2009, No. 1, 1, 2009. [pdf]
Brun, M., Sima, C., Hua, J., Lowey, J., Carroll, B., Suh, E., and E. R. Dougherty, “Model-Based Evaluation of Clustering Validation Measures,” Pattern Recognition, Vol. 40, No. 3, 807-824, 2007. [pdf]
Zhou, X., Wang, X., Dougherty, E. R., Russ, D., and E. Su, “Gene Clustering Based on Clusterwide Mutual Information,” Journal of Computational Biology, Vol. 11, No. 1, 147-161, 2004. [pdf]
Dougherty, E. R., and M. Brun, “A Probabilistic Theory of Clustering,” Pattern Recognition, Vol. 37, No. 5, 917-925, 2004. [pdf]
Dougherty, E. R., Barrera, J., Brun, M., Kim, S., Cesar, R. M., Chen, Y., Bittner, M., and J. M. Trent, “Inference from Clustering with Application to Gene-Expression Microarrays,” Journal of Computational Biology, Vol. 9, No. 1, 105-126, 2002. [pdf]
Xu, Q., Hua, J., Xiong, Z., Bittner, M. L., and E. R. Dougherty,”The Effect of Microarray Image Compression on Expression-Based Classification,” Signal, Image and Video Processing, Vol. 3, No. 1, 53-61, 2009. [pdf]
Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Tembe, W., Joshipura, K., Huentelman, M. J., Dougherty, E. R., and D. A. Stephan, “SNiPer-HD: Improved Genotype Calling Accuracy by an Expectation-Maximization Algorithm for High-Density SNP Arrays,” Bioinformatics, Vol. 23, No. 1, 57-63, 2007. [pdf]
Hua, J., Balagurunathan, Y. Chen, Y., Lowey, J., Bittner, M., Xiong, Z., Suh, E., and E. R. Dougherty, “Normalization Benefits Microarray-Based Classification,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2006, 2006. [pdf]
Attoor, S., Dougherty, E. R., Chen, Y., Bittner, M. L., and J. M. Trent, “Which is Better for cDNA-Microarray-Based Classification: Ratios or Direct Intensities,” Bioinformatics, Vol. 20, No. 16, 2513-2520, 2004. [pdf]
Balagurunathan, Y., Wang, N., Dougherty, E. R., Nguyen, D. V., Chen, Y., Bittner, M. L., Trent, J. M., and R. J. Carroll, “Noise Factor Analysis for cDNA Microarrays,”Biomedical Optics, Vol. 9, No. 4, 663-845, 2004. [pdf]
Mousses, S., Caplen, N. J., Cornelison, R., Weaver, D., Basik, M., Hautaniemi, S., Elkahloun, A. G., Lotufo, R. A., Choudary, A., Dougherty, E. R., Suh, E., and O. Kallioniemi, “RNAi Microarray Analysis in Cultured Mammalian Cells,” Genome Research, Vol. 13, No. 10, 2341-2347, 2003. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Binarization of Microarray Data Based on a Mixture Model,” Molecular Cancer Therapeutics, Vol. 2, No. 7, 679-684, 2003. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Missing Value Estimation using Linear and Nonlinear Regression with Bayesian Gene Selection,” Bioinformatics, Vol. 19, No. 17, 2302-2307, 2003. [pdf]
Chen, Y., Kamat, V., Dougherty, E. R., Bittner, M. L., Meltzer, P. S., and J. M. Trent, “Ratio Statistics of Gene Expression Levels and Applications to Microarray Data Analysis,” Bioinformatics, Vol. 18, No. 9, 1207-1215, 2002. [pdf]
Balagurunathan, Y., Dougherty, E. R., Chen, Y., Bittner, M. L., and J. M. Trent, “Simulation of cDNA Microarrays via a Parameterized Random Signal Model,” Biomedical Optics, Vol. 7, No. 3, 507-523, 2002. [pdf]
Chen, Y., Dougherty, E. R., and M. L. Bittner, “ Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images,” Journal Of Biomedical Optics, Vol. 2, No. 4, 364–374, 1997. [pdf]
Zollanvari, A., Cunningham, M. J., Braga-Neto, U., and E. R. Dougherty, “Analysis and Modeling of Time-Course Gene-Expression Profiles from Nanomaterial-Exposed Primary Human Epidermal Keratinocytes,” BMC bioinformatics, Vol.10, No. 11, 1, 2009. [pdf]
Zhao, C., Ivanov, I., Dougherty, E. R., Hartman, T. J., Lanza, E., Bobe, G., Colburn, N. H., Lupton, J. R., Davidson, L. A., and R. S. Chapkin, “Noninvasive Detection of Candidate Molecular Biomarkers in Subjects with a History of Insulin Resistance and Colorectal Adenomas,” Cancer Prevention Research, 2(6), pp.590-597, 2009. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2009 No. 1, 1, 2009. [pdf]
Zhao, W., Agyepong, K., Serpedin, E. and E. R., Dougherty, “Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, No. 1, 1, 2008. [pdf]
Johnson, C. D., Balagurunathan, Y., Dougherty, E.R., Afshari, C.A., He, Q. and K. S. Ramos, “Insight into Redox-Regulated Gene Networks in Vascular Cells,” Bioinformation, Vol. 1, No. 10, 379-383, 2007. [pdf]
Davidson, L. A., Nguyen, D. V., Hokanson, R. M., Callaway, E. S., Isett, R., Turner, N. D., Dougherty, E. R., Lupton, J. R., Carroll, R. J., and R. S. Chapkin, “Chemopreventive n-3 Polyunsaturated Fatty Acids Reprogram Genetic Signatures During Colon Cancer Initiation and Progression in the Rat,” Cancer Research, Vol. 64, No. 18, 6797-6804, 2004. [pdf]
Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpishch, Marcel Brun, M. H., Walker, M. K., Dougherty, E. R., and K. S. Ramos, “Unraveling Gene-Gene Interactions Regulated by Ligands of the Aril Hydrocarbon Receptor,” Environmental Health Perspectives, Vol. 112, No. 4, 403-412, 2004. [pdf]
Morikawa, J., Li, H., Kim, S., Nishii, K., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., Zhang, W., and T. Kobayashi., “Identification of Signature Genes by Microarray for Acute Myeloid Leukemia Without Maturation (FAB-M1) and AML with t(15;17)(q22;q12)(PML/RARa),” International Journal of Oncology, Vol. 23, No. 3, 617-625, 2003. [pdf]
Johnson, C. D., Balagurunathan, Y., Lu, K. P., Tadesse, M., Falahatpisheh, M. H., Balagurunathan, Y., Carroll, R. A., Dougherty, E. R., Afshari, C. A., and K. S. Ramos, “Genomic Profiles and Predictive Biological Networks in Oxidant-Induced Atherogenesis,” Physiological Genomics, Vol. 13, No. 3, 263-275, 2003. [pdf]
Kobayashi, T., Yamaguchi, M., Kim, S., Morikawa, J., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., and W. Zhang, “Gene Expression Profiling Identifies Strong Feature Genes that Classify de novo CD5+ and CD5 Diffuse Large B-cell Lymphoma and Mantle Cell Lymphoma,” Cancer Research, Vol. 63, No. 1, 60-66, 2003. [pdf]
Kim, S., Dougherty, E. R., Shmulevich, I., Hess, K. R., Hamilton, S. R., Trent, J. M., Fuller, G. N., and W. Zhang, “Identification of Combination Gene Sets for Glioma Classification,” Molecular Cancer Therapeutics, Vol. 1, No. 13, 1229-1236, 2002. [pdf]
Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M. L., Simon, R., Meltzer, P., Usterson, B., Esteller, M., Raffeld, M., Yakhini, Z., Ben-Dor, A., Dougherty, E. R., Kononen, J. A., Bubendorf, L., Fehrle, W., Pittaluga, S., Gruvberger, S., Loman, N., Johannsson, O., Olsson, H., Wilfond, B., Sauter, G., Kallioniemi, O.-P., Borg Å., and J. Trent, “Gene Expression Profiles in Hereditary Breast Cancer,“New England Journal of Medicine, Vol. 344, No. 8, 539-548, 2001. [pdf]
Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., Dougherty, E., Wang, E., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C., Berens, M., Alberts, D., Sondak, V., Hayward, N., and J. Trent, “Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling,” Nature, Vol. 406, No. 6795, 536-540, 2000. [pdf]
Leyk, M., Nguyen, D. V., Attoor, S. N., Dougherty, E. R., Turner, N. D., Bancroft, L. K., Chapkin, R. S., Lupton, J. R., and R. J. Carroll, “Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis,” Statistical Applications in Genetics and Molecular Biology, Vol. 4, No. 1, 2005. [pdf]
Grigoryan, A. M., Hostetter, G., Kallioniemi, O., and E. R. Dougherty, “Simulation Toolbox for 3D-FISH Spot Counting Algorithms,” Real-Time Imaging, Vol. 8, No. 3, 203-212, 2002. [pdf]
Grigoryan, A., Dougherty, E. R., Kononen, J., Bubendorf, L., Hostetter, G., and O. Kallioniemi, “Morphological Spot Counting from Stacked Images for Automated Analysis of Gene Copy Numbers by Fluorescence In Situ Hybridization,” Biomedical Optics, Vol. 7, No. 1, 109-122, 2002. [pdf]
Morphological Granulometric Analysis [back to TOC]
Franciškovic-Bilinski, S., Bilinski, H., Vdovic, N., Balagurunathan, Y., and E. R. Dougherty, “Application of Image-based Granulometry to Siliceous and Calcareous Estuarine and Marine Sediments,” Estuarine, Coastal, and Shelf Science, Vol. 58, No. 2, 227-239, 2003. [pdf]
Balagurunathan, Y., and E. R. Dougherty, “Morphological Quantification of Surface Roughness,” Optical Engineering, Vol. 42, No. 6, 1795-1804, 2003. [pdf]
McKenzie, J., Marshall, S., Gray, A. J., and E. R. Dougherty, “Morphological Texture Analysis Using the Texture Evolution Function,” International Journal of Pattern Recognition and Artificial Intelligence, Vol. 17, No. 2, 167-185, 2003. [pdf]
Balagurunathan, Y., and E. R. Dougherty, “Granulometric Parametric Estimation for the Random Boolean Model Using Optimal Linear Filters and Optimal Structuring Elements,” Pattern Recognition Letters, Vol. 24, No. 2, 283-293, 2003. [pdf]
Dougherty, E. R., “Granulometric Size Density for Segmented Random-Disk Models,” Mathematical Imaging and Vision, Vol. 17, No. 3, 267-276, 2002. [pdf]
Balagurunathan, Y., and E. R. Dougherty, “Optimal Linear Granulometric Estimation for Random Sets,” Pattern Recognition, Vol. 35, No. 6, 1315-1325, 2002. [pdf]
Sivakumar, K., Balagurunathan, Y., and E. R. Dougherty, “Asymptotic Joint Normality of the Granulometric Moments,” Pattern Recognition Letters, Vol. 22, No. 14, 1537-1543, 2001. [pdf]
Theera-Umpon, N., Dougherty, E. R., and P. Gader, “Non-Homothetic Granulometric Mixing Theory,” Pattern Recognition, Vol. 34, No. 12, 2547-2560, 2001. [pdf]
Dougherty, E. R., and Y. Chen, “Robust Optimal Granulometric Bandpass Filters,” Signal Processing, Vol. 81, 1357-1372, 2001. [pdf]
Balagurunathan, Y., Dougherty, E. R., Franciskovic-Bilinski, S., Bilinski, H., and N. Vdovi, “Morphological Granulometric Analysis of Sediment Images,” Image Analysis and Stereology, Vol. 20, No. 2, 87-99, 2001. [pdf]
Batman, S., and E. R. Dougherty, “Morphological Granulometric Estimation of Random Patterns in the Context of Parameterized Random Sets,” Pattern Recognition, Vol. 34, No. 6, 2001. [pdf]
Dougherty, E. R., “Optimal Conjunctive Granulometric Bandpass Filters,” Mathematical Imaging and Vision, Vol. 14, No. 1, 39-51, 2001. [pdf]
Sivakumar, K., Patel, M. J., Kehtarnavaz, N., Balagurunathan, Y., and E. R. Dougherty, “A Constant-time Algorithm for Erosions/Dilations with Applications to Morphological Texture Feature Computation,” Real-Time Imaging, Vol. 6, 223-239, 2000. [pdf]
Batman, S., Dougherty, E. R., and F. Sand “Heterogeneous Morphological Granulometries,” Pattern Recognition, Vol. 33, No. 6, 1047-1057, 2000. [pdf]
Dougherty, E. R., “Automatic Design of Morphological Operators,” Electronic Imaging, Vol. 13, No. 3, 486-491, 2004. [pdf]
Brun, M., Hirata, R., Barrera, J., and E. R. Dougherty, “Nonlinear Filter Design Using Envelopes,” Mathematical Imaging and Vision, Vol. 21, No. 1, 81-97, 2004. [pdf]
Dougherty, E. R., “A Lattice-Based Minimal Gray-Scale Switching Algorithm for Obtaining the Optimal Increasing Filter from the Optimal Filter,” Mathematical Imaging and Vision, Vol. 21, No. 1, 43-52, 2004. [pdf]
Green, A., Dougherty, E. R., Marshall, S., and D. Greenhalgh, “Optimal Filters with Multiresolution Apertures,” Mathematical Imaging and Vision, Vol. 20, No. 3, 237-250, 2004.
Green, A., Marshall, S., Greenhalgh, D., and E. R. Dougherty, “Design of Multi-mask Apertures,” Signal Processing, Vol. 83, No. 9, 1961-1971, 2003. [pdf]
Brun, M., Dougherty, E. R., Hirata, R., and J. Barrera, “Design of Optimal Binary Filters Under Joint Multiresolution-Envelope Constraint,” Pattern Recognition Letters, Vol. 24, No. 7, 937-945, 2003. [pdf]
Hirata, R., Brun, M., Barrera, J., and E. R. Dougherty, “Multiresolution Design of Aperture Filters,” Mathematical Imaging and Vision, Vol. 16, No. 3, 199-222, 2002. [pdf]
Grigoryan, A. M., and E. R. Dougherty, “Bayesian Robust Optimal Linear Filters,” Signal Processing, Vol. 81, No. 12, 2503-2521, 2001. [pdf]
Grigoryan, A. M., and E. R. Dougherty, “Optimization of Linear Filters under Power-Spectral-Density Stabilization,” IEEE Trans. on Signal Processing, Vol. 49, No. 10, 1-8, 2001. [pdf]
Dougherty, E. R., Barrera, J., Mozelle, G., Kim, S., and M. Brun, “Multiresolution Analysis for Optimal Binary Filters,” Mathematical and Imaging and Vision, Vol. 14, No. 1, 53-72, 2001. [pdf]
Hirata, N. T., Dougherty, E. R., and J. Barrera, “Iterative Design of Morphological Binary Image Operators,” Optical Engineering, Vol. 39, No. 12, 3106-3123, 2000. [pdf]
Barrera, J., Dougherty, E. R., and M. Brun, “Hybrid Human-Machine Binary Morphological Operator Design: An Independent Constraint Approach,” Signal Processing, Vol. 80, No. 8, 1469-1487, 2000. [pdf]
Kamat, V. G., Dougherty, E. R., and J. Barrera, “Multiresolution Bayesian Design of Binary Filters,” Electronic Imaging, Vol. 9, No., 3, 283-295, 2000. [pdf]
Hirata, N., Dougherty, E. R., and J. Barrera, “A Switching Algorithm for Design of Optimal Increasing Binary Filters over Large Windows,” Pattern Recognition, Vol. 33, No. 6, 1059-1081, 2000. [pdf]
Hirata, R., Dougherty, E. R., and J. Barrera, “Aperture Filters,” Signal Processing, Vol. 80, No. 4, 697-721, 2000. [pdf]
