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Edward R. Dougherty
Robert M. Kennedy ’26 Chair Professor
Director, Genomic Signal Processing Laboratory
Office: 216L Zachry

Education:

• Rutgers University, New Brunswick, NJ. Ph.D. 1974, Mathematics
• Stevens Institute of Technology, Hoboken, NJ. M.S. 1986, Computer Science
• Fairleigh Dickinson University, Teaneck, NJ. M.S. 1969, Mathematics
• Fairleigh Dickinson University, Teaneck, NJ. B.S. 1967, Mathematics

Related Links:

• Genomic Signal Processing Laboratory
• Translational Genomics Research Institute (TGen)
• Biomedical Imaging Program
• Dr.Dougherty's Lectures

Interest Areas:

Genomic Signal Processing:

• Gene-Expression-Based Cancer Classification
• Genetic Regulatory Networks
• Microarray Analysis
• Small-Sample Classification and Error Estimation

Image Analysis:

• Mathematical Morphology
• Nonlinear Signal Processing
• Statistical Filter Design
• Granulometries and Image Texture

Honors and Awards:

• University Distinguished Lecture, Texas A&M University, 2008
• Robert M. Kennedy '26 Chair, 2007.
• Doctor Honoris Causa, Tampere University of Technology, 2007.
• Association of Former Students Distinguished Achievement Award in Research, 2005.
• SPIE President?s Award, 2004.
  
• Fellow, Texas Engineering Experiment Station, 2002.
  
• Halliburton Professor, Dwight Look College of Engineering, 2001.
  
• Fellow, International Society of Optical Engineering, 2000.

Professional Activities:

• Editor:
  
  • SPIE/IS&T Journal of Electronic Imaging
    
  • SPIE/IEEE Series on Imaging Science and Technology
    
• Editorial Board:
  
  • Journal of Environmental Health Perspectives
    
  • EURASIP Journal of Signal Processing and Bioinformatics
    
  • Journal of Cancer Informatics
    
  • Journal of Mathematical Imaging and Vision
    
  • Journal of Pattern Recognition
    
  • Journal of Real-Time Imaging
    
  • Journal of Image Analysis and Stereology
    
  • Journal of Biological System
    
• Special-issue editor:
  
  • Journal of Mathematical Imaging and Vision (with J. Astola on nonlinear image processing)
    
  • Journal of Visual Communication and Image Representation (with J. Serra on mathematical morphology)
    
  • Journal of Pattern Recognition (with I. Molchanov on random sets)
    
  • Journal of Mathematical Imaging and Vision (with J. Astola), Special issue on Nonlinear Image Processing and Pattern Recognition, 2002.
    
  • EURASIP Journal of Signal Processing (with J. Astola, I. Tabus, I. Shmulevich), Special issue on Genomic Signal Processing, 2003.
    
  • EURASIP Journal on Applied Signal Processing (with X. Wang, Y. Chen, C. Perterson), Special issue on Genomic Signal Processing, 2003.
    
  • IEEE Transactions on Signal Processing (with J. Astola, J. Goutsias, I. Shmulevich), Special issue on Genomic Signal Processing, 2006.
    
  • IEEE Signal Processing Magazine (with G. Stolovitzky, I. Tabus, and X. Wang), Special issue on Signal Processing in Genomics, 2007.
    
  • Current Genomics (with X. Cai, R. Yamaguci, Y. Huang, and S. Kim), Special issue on Genomic Signal Processing, 2009.
    
• Chair for 32 SPIE Conferences

Publication Statistics:

Journal papers: 246, Conference papers: 266, Book chapters: 31, Patents: 6, Books (authored): 15, Books (edited): 5.

Journal Papers (2004-2008):

• Choudhary, A., Hua, J., Bittner, M. L., and E. R. Dougherty, “The Effect of Population Contexts on Classifier Performance,” Biological Systems, Vol. 16, No. 4, 495-517, December, 2008.
• Qian, X., and E. R. Dougherty, “Effect of Function Perturbation on the Steady-State Distribution of Genetic Regulatory Networks: Optimal Structural Intervention,” IEEE Transactions on Signal Processing, doi: 10.1109/TSP.2008.928089, Vol. 56, No. 10, Part 1, 4966-4975, October, 2008.
• 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 on Biomedical Engineering, Vol. 15, No. 10, 2319-2331, October, 2008.
• Hanczar, B., and E. R. Dougherty, “Classification with Reject Option in Gene Expression Data, Bioinformatics, Vol. 24, 1889-1895, doi: 10.1093/bioinformatics/btn349, September, 2008.
• Qian, L., Wang, H., and E. R. Dougherty, “Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks using Genetic Programming and Kalman Filtering,” IEEE Transactions on Signal Processing, Vol. 56, No. 7, 3327-3339, July, 2008.
• Liu, W., Lähdesmäki, H., Dougherty, E. R,. and I. Shmulevich, “Inference of Boolean Networks using Sensitivity Regularization, EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, doi:10.1155/2008/780541, June, 2008.
• 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 Signal Processing, Vol. 2, No. 3, 412-423, June, 2008.
• 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, June, 2008.
• Sima, C., and E. R. Dougherty, “The Peaking Phenomenon in the Presence of Feature Selection,” Pattern Recognition Letters, Vol. 29, 1667-1674, June, 2008.
• Zhao, W., Agyepong, K., Serpedin, E., and E. R. Dougherty, “Detecting Periodic Genes from Irregularly Sampled Gene Expressions for Drosophila Melanogaster, EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 769293, 8 pages, doi:10.1155/2008/769293, June, 2008.
• 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, Article ID 248747, 12 pages, doi:10.1155/2008/248747, June, 2008.
• Faryabi, B., Vahedi, G., Chamberland, J-F., Datta, A., and E. R. Dougherty, “Optimal Constrained Intervention in Genetic Regulatory Networks,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 620767, 10 pages, doi:10.1155/2008/620767, May, 2008.
• 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, April, 2008.
• 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, Article ID 297945, 8 pages, doi:10.1155/2008/297945, April, 2008.
• Dougherty, E. R., “On the Epistemological Crisis in Genomics,” Current Genomics, Vol. 9, No. 2, 69-79, April, 2008.
• 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, March, 2008.
• Chakraborty, S., Mallick, B. K., Ghosh, D., Ghosh, M., and E. R. Dougherty, “Gene Expression-Based Glioma Classification Using Hierarchical Bayesian Vector Machines,” Indian Journal of Statistics, Vol. 69, Part 3, 514-547, December, 2007.
• 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, November, 2007.
• 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, Article ID 38473, 12 pages, doi:10.1155/2007/38473, October, 2007.
• Dougherty, E. R., “Validation of Inference Procedures for Gene Regulatory Networks,” Current Genomics, Vol. 8, No. 6, 351-359, September, 2007.
• 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, May, 2007.
• Xiao, Y., and E. R. Dougherty, “The Impact of Function Perturbations in Boolean Networks,” Bioinformatics, Vol. 23, No. 10, 1265-1273, May, 2007.
• Brun, M., Kim, S., Choi, W., and E. R. Dougherty, “Comparison of Network Models via Steady- State Trajectories,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2007, Article ID 82702, 11 pages, doi:10.1155/2007/82702, May, 2007.
• 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, Article ID 32454, 15 pages, doi:10.1155/2007/32454, May, 2007.
• Johnson, C. D., Balagurunathan, Y., Dougherty, E. R., Afshari, C. A., He, Q., and K. S. Ramos, “Insight Into Redox-regulatory Gene Networks in Vascular Cells,” Bioinformation, Vol. 1, No. 10, 379-383, April, 2007.
• Dougherty, E. R., Hua, J., and M. L. Bittner, “Validation of Computational Methods in Genomics,” Current Genomics, Vol. 8, No. 1, 1-19, March, 2007.
• 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, March, 2007.
• 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, Article ID 16354, 11 pages, doi:10.1155/2007/16354, February, 2007.
• 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 January, 2007.
• 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, 57-63, January, 2007.
• 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, December, 2006.
• 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, November, 2006.
• Sima, C., and E. R. Dougherty, “What Should Be Expected from Feature Selection in Small-Sample Settings,” Bioinformatics, Vol. 22, No. 19, 2430-2436, October, 2006.
• Dougherty, E. R., and M. Brun, “On the Number of Close-to-Optimal Feature Sets,” Cancer Informatics, Vol. 2, 189-196, September, 2006.
• 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, September, 2006.
• 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, September, 2006.
• Sima, C., and E. R. Dougherty, “Optimal Convex Error Estimators for Classification,” Vol. 39, No. 6, 1763-1780, Pattern Recognition, September, 2006.
• 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, Part 2, 2375-2387, June, 2006.
• Ivanov, I., and E. R. Dougherty, “Modeling Genetic Regulatory Networks: Continuous or Discrete?” Biological Systems, Vol. 14, No. 2, 219-229, June, 2006.
• 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, Article ID 43056, 13 pages, May, 2006.
• 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, 7:274, May, 2006.
• Datta, A., Pal, R., and E. R. Dougherty, “Intervention in Probabilistic Gene Regulatory Networks,” Current Bioinformatics, Vol. 1, No. 2, 167-184, May, 2006.
• 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, April, 2006.
• Zhou, X., Wang, X., and E. R. Dougherty, “Multi-class Cancer Classification Using Multinomial Probit Regression with Bayesian Variable Selection,” IEE Proceedings on Systems Biology, Vol. 153, No. 2, 70-78, March, 2006.
• Dougherty, E. R., and U. Braga-Neto, “Epistemology of Computational Biology: Mathematical Models and Experimental Prediction as the Basis of Their Validity,” Biological Systems, Vol. 14, No. 1, 65-90, March, 2006.
• 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, January, 2006.
• Dougherty, E. R., “Feature-Selection Overfitting with Small-Sample Classifier Design,” IEEE Intelligent Systems Magazine, 64-66, December, 2005.
• Dougherty, E. R., “The Fundamental Role of Pattern Recognition for Gene Expression/Microarray Data in Bioinformatics, Pattern Recognition, Vol. 38, No. 12, 2226-2228, December, 2005.
• 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, December, 2005.
• Dougherty, E. R., Datta, A., and C. Sima, “Research Issues in Genomic Signal Processing,” IEEE Signal Processing Magazine, Vol. 22, No. 6, 46-68, November, 2005.
• 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, November, 2005.
• Braga-Neto, U., and E. R. Dougherty, “Exact Performance of Error Estimators for Discrete Classifiers,” Pattern Recognition, Vol. 38, No. 11, 1799-1814, November, 2005.
• Brun, M., Dougherty, E. R., and I. Shmulevich, “Steady-State Probabilities for Attractors in Probabilistic Boolean Networks,” EURASIP Journal on Signal Processing, Vol. 85, No. 10, 1993-2013, October, 2005.
• Dougherty, E. R., Hua, J., Xiong, Z., and Y. Chen, “Optimal Robust Classifiers,” Pattern Recognition, Vol. 38, No. 10, 1520-1532, October, 2005.
• 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, July, 2005.
• Chen, J., Dougherty, E. R., Demir, S., Friedman, C., Sheng Li, C., and S. Wong, “Grand Challenges for Multimodal Bio-Medical Systems,” IEEE Circuits and Systems Magazine, Spring Quarter, 46-52, May, 2005.
• 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, May, 2005.
• 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, 21, No. 8, 1509-1515, April, 2005.
• 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, April, 2005.
• 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, April, 2005.
• 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, April, 2005.
• 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, March, 2005.
• 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, March, 2005.
• 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, March, 2005.
• Dougherty, E. R., and A. Datta, “Genomic Signal Processing: Diagnosis and Therapy,” IEEE Signal Processing Magazine, 107-112, Vol. 22 No. 1, January, 2005.
• 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, January, 2005.
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,” , Vol. 20. No. 17, 2918-2927 November, 2004.
• 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, November, 2004.
• Zhou, X., Wang, X., and E. R. Dougherty, “Nonlinear-Probit Gene Classification Using Mutual-Information and Wavelet Based Feature Selection,” , Vol. 12, No. 3, 371-386, September, 2004.
• 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, 6797-6804, September, 2004.
• Attoor, S. N., and E. R. Dougherty, “Classifier Performance as a Function of Distributional Complexity,” Pattern Recognition, Vol. 37, No. 8, 1629-1640, August, 2004.
• Dougherty, E. R., “Automatic Design of Morphological Operators,” Electronic Imaging, Vol. 13, No. 3, 486-491, July, 2004.
• 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, July, 2004.
• 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, July, 2004.
• 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, July, 2004.
• Braga-Neto, U. M., and E. R. Dougherty, “Bolstered Error Estimation,” Pattern Recognition, Vol. 37, No. 6, 1267-1281, June, 2004.
• 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, May, 2004.
• Dougherty, E. R., and M. Brun, “A Probabilistic Theory of Clustering,” Pattern Recognition, Vol. 37, No. 5, 917-925, May, 2004.
• 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, May, 2004.
• Datta, A., Choudhary, A., Bittner, M. L., and E. R. Dougherty, “External Control in Markovian Genetic Regulatory Networks: The Imperfect Information Case,” Bioinformatics, Vol. 20, 924-930, April, 2004.
• 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, March, 2004.
• Zhou, X., Wang, X., Dougherty, E. R., Russ, D., and E. Suh, “Gene Clustering Based on Clusterwide Mutual Information,” Computational Biology, Vol. 11, No. 1, 147-162, February, 2004.
• Braga-Neto, U. M., and E. R. Dougherty, “Is Cross-Validation Valid for Small-Sample Microarray Classification, Bioinformatics, Vol. 20, No. 3, 374-380, February, 2004.
• 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, January, 2004.
• Dougherty, E. R., Shmulevich, I., and M. L. Bittner, “Genomic Signal Processing: The Salient Issues,” EURASIP Journal on Applied Signal Processing, Vol. 4, No. 1, 146-153, January, 2004.
• Ivanov, I., and E. R. Dougherty, “Reduction Mappings Between Probabilistic Boolean Networks,” EURASIP Journal on Applied Signal Processing, Vol. 4, No. 1, 125-131, January, 2004.
• Zhou, X., Wang, X., and E. R. Dougherty, “Gene Prediction Using Multinomial Probit Regression with Bayesian Gene Selection,” EURASIP Journal on Applied Signal Processing, Vol. 4, No. 1, 115-124, January, 2004.
• 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, January, 2004.

Books or Authoritative References

Authored:

• Shmulevich, I., and E. R. Dougherty, Probabilistic Boolean Networks: A Model for Gene Regulatory Networks, SIAM Press, New York, in press, 2009.
• Shmulevich, I., and E. R. Dougherty, Genomic Signal Processing, Princeton University Press, Princeton, 2007.
• Datta, A., and E. R. Dougherty, Introduction to Genomic Signal Processing with Control, CRC Press, New York, 2007.
• Dougherty, E. R., and R. A. Lotufo, Hands-On Morphological Image Processing, SPIE Press, Bellingham, 2003.
• Dougherty, E. R., Random Processes for Image and Signal Processing, Series on Imaging Science and Engineering, SPIE Press and IEEE Presses, Bellingham, 1999.
• Sinha, D., and E. R. Dougherty, Introduction to Computer-Based Imaging Systems, SPIE Press, Bellingham, 1998.
• Loce, R. P., and E. R. Dougherty, Enhancement and Restoration of Digital Documents: Statistical Design of Nonlinear Algorithms, SPIE Press, Bellingham, 1997.
• Dougherty, E. R., and P. Laplante, Introduction to Real-Time Imaging, SPIE Press and IEEE Press, Bellingham, 1995.
• Dougherty, E.R., and J. Astola, An Introduction to Nonlinear Image Processing, SPIE Press, Bellingham, 1994.
• Dougherty, E. R., An Introduction to Morphological Image Processing, SPIE Press, Bellingham, 1992.
• Dougherty, E. R., Probability and Statistics for the Engineering, Computing, and Physical Sciences, Prentice-Hall, Englewood Cliffs, 1990.
• Dougherty, E. R., and Giardina, C. R., Mathematical Methods for Artificial Intelligence and Autonomous Systems, Prentice-Hall, Englewood Cliffs, January, 1988.
• Giardina, C. R., and Dougherty, E. R., Morphological Methods in Image and Signal Processing, Prentice-Hall, Englewood Cliffs, 1988.
• Dougherty, E. R., and Giardina, C. R., Image Processing - Continuous to Discrete, Prentice-Hall, Englewood Cliffs, 1987.
• Dougherty, E. R., and Giardina, C. R., Matrix Structured Image Processing, Prentice-Hall, Englewood Cliffs, 1987.

Edited:

• Dougherty, E. R., Shmulevich, I., Chen, J., and Z. J. Wang, editors, Genomic Signal Processing and Statistics, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, New York, 2005.
• Dougherty, E. R., and J. Astola, editors, Nonlinear Filters for Image Processing, Series on Imaging Science and Engineering, SPIE Press and IEEE Presses, Bellingham, 1999.
• Dougherty, E. R., editor, Electronic Imaging Technology, SPIE Press, Bellingham, 1999.
• Dougherty, E.R., editor, Digital Image Processing Methods, Marcel Dekker, New York, 1994.
• Dougherty, E. R., editor, Mathematical Morphology in Image Processing, Marcel Dekker, New York, 1993.

Book Chapters (1999 through 2009):

• Dougherty, E. R., “Epistemology and the Role of Mathematics in Translational Science,” Festschrift in Honor of Jaakko Astola on the Occasion of his 60th Birthday, eds. I. Tabus, K. Egiazarian and M. Gabbouj, Tampere International Center for Signal Processing, TICSP Series #47, 60-78, 2009.
• Zhou, X., Wang, X., and E. R. Dougherty, “Genomic Networks: Statistical Inference from Microarray Data,” Wiley Encyclopedia of Biomedical Engineering, ed. M. Akay, John Wiley & Sons, Hoboken, 2006.
• Hirata, R., Brun, M., Barrera, J., and E. R. Dougherty, “Aperture Filters: Theory, Application, and Multivariate Analysis,” Advances in Nonlinear Signal and Image Processing, eds. S. Marshall and G. L. Sicuranza, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, New York, 2006.
• Barrera, J., Banon, G. J. F., and E. R. Dougherty, “Automatic Design of Morphological Operators,” Space, Structure, and Randomness, eds. M. Bilodeau, F. Meyer, and M. Schmitt, Lecture Notes in Statistics, Springer, New York, 2005.
• Dougherty, E. R., Shmulevich, I., Chen, J., and Z. J. Wang, “Genomic Signal Processing: Perspectives,” Genomic Signal Processing and Statistics, eds. E. R. Dougherty, I. Shmulevich, J. Chen, and Z. J. Wang, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, New York, 2005.
• Braga-Neto, U., and E. R. Dougherty, “Classification,” Genomic Signal Processing and Statistics, eds. E. R. Dougherty, I. Shmulevich, J. Chen, and Z. J. Wang, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, New York, 2005.
• Shmulevich, I., and E. R. Dougherty, “Modeling Genetic Regulatory Networks with Probabilistic Boolean Networks,” Genomic Signal Processing and Statistics, eds. E. R. Dougherty, I. Shmulevich, J. Chen, and Z. J. Wang, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, New York, 2005.
• Suh, E. B., Russ, D. E., Dougherty, E. R., Kim, S., Bittner, M. L., Chen, Y., and R. L. Martino, “Parallel Computation for Coefficients of Determination in the Context of Multivariate Gene-Expression Analysis,” Biocomputing, ed. P. Laplante, Nova Science, 2003.
• Shmulevich, I., and E. R. Dougherty, “Genetic Regulatory Networks: A Nonlinear Signal Processing Perspective,” Nonlinear Signal and Image Processing: Theory, Methods, and Applications, eds. G. Arce and K. Barner, CRC Press, 2003.
• Dougherty, E. R., and Attoor, S. N., "Design Issues and Comparison of Methods for Microarray-Based Classification," Computational And Statistical Approaches To Genomics, eds. W. Zhang and I. Shmulevich, Kluwer Academic Publishers, New York, 2002.
• Chen, Y., Dougherty, E. R., Bittner, M. L., Meltzer, P., and J. M. Trent, "Microarray Image Analysis and Gene Expression Ratio Statistics," Computational And Statistical Approaches To Genomics, eds. W. Zhang and I. Shmulevich, Kluwer Academic Publishers, New York, 2002.
• Suh, E. B., Dougherty, E. R., Kim, S., Bittner, M. L., Chen, Y., Russ, D. E., and R. R. Martino, "Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene-Expression Relations," Computational And Statistical Approaches To Genomics, eds. W. Zhang and I. Shmulevich, Kluwer Academic Publishers, New York, 2002.
• Dougherty, E. R., "Foundations of Morphological Image Processing," Encyclopedia of Imaging Science and Technology, ed. J. P. Hornak, John Wiley, New York, 2002.
• Dougherty, E. R., and Y. Chen, "Optimal and Adaptive Design of Logical Granulometric Filters," Advances in Imaging and Electron Physics, Vol. 117, ed. P. Hawkes, Academic Press, 1-71, New York, 2001.
• Mousses, S., Bittner, M. L., Chen, Y., Dougherty, E. R., Baxevanis, A. Meltzer, P. S., and J. M. Trent, "Gene Expression Analysis by cDNA Microarrays," Functional Genomics, eds., S. P. Hunt and F. J. Livesey, Oxford University Press, New York, 2000.
• Dougherty, E. R., and A. T. Popov, "Fuzzy Mathematical Morphology Based on Fuzzy Inclusion," Fuzzy Techniques in Image Processing, eds. E. Kerre and M. Nachtegael, Physica-Verlag, Berlin, 2000.
• Dougherty, E. R., and J. Barrera, "Logical Image Operators," Nonlinear Filters for Image Processing, eds. E. Dougherty, and J. Astola, 1-60, SPIE and IEEE Presses, Bellingham, 1999.
• Dougherty, E. R., and J. Barrera, "Computational Gray-Scale Image Operators," Nonlinear Filters for Image Processing, eds. E. Dougherty, and J. Astola, 61-98, SPIE and IEEE Presses, Bellingham, 1999.
• Dougherty, E. R., "Translation-Invariant Set Operators," Nonlinear Filters for Image Processing, eds. E. Dougherty, and J. Astola, 99-120, SPIE and IEEE Presses, Bellingham, 1999.
• Dougherty, E. R., and Y. Chen, "Granulometric Filters," Nonlinear Filters for Image Processing, eds. E. Dougherty, and J. Astola, 121-162, SPIE and IEEE Presses, Bellingham, 1999.
• Sinha, D. and E. R. Dougherty, "Hardware Architecture for Image Processing," Electronic Imaging Technology, ed. E. Dougherty, 387-426, SPIE Press, Bellingham, 1999.
• Loce, R. P., and E. R. Dougherty, "Enhancement of Digital Documents," Electronic Imaging Technology, ed. E. Dougherty, 167-223, SPIE Press, Bellingham, 1999.