Journal Publications

In this page, all journal publications from GSP Lab are listed. They have been ordered in reverse chronological order, starting with the most recent:

You can also browse papers by,

Author

Edward R. Dougherty
Aniruddha Datta
Ulisses Braga-Neto
Byung-Jun Yoon
Erichin Serpedin
Jean-Francois Chamberland

Topic

2011

Zhao, C., Ivanov, I., Bittner, M. L., and Dougherty, E. R., "Pathway Regulatory Analysis in the Context of Bayesian Networks Using the Coefficient of Determination" in Biological Systems, Vol. 19, No. 4, 651-682. [More Details] [PDF]

Dougherty, E. R., Zollanvari, A., and Braga-Neto, U. M., "The Illusion of Distribution-Free Small-Sample Classification in Genomics" in Current Genomics, Vol. 12, No. 5, 333-341. [More Details] [PDF]

Sima, C., Braga-Neto, U. M., and Dougherty, E. R., "High-Dimensional Bolstered Error Estimation" in Bioinformatics, Vol. 27, No. 21, 3056-3064. [More Details] [PDF]

Zollanvari, A., Braga-Neto, U. M., and Dougherty E. R., "Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis" in IEEE Transactions on Signal Processing, Vol. 59, No. 9, 4238-4255. [More Details] [PDF]

Esfahani, M. S., Yoon, B-J., and Dougherty, E. R., "Probabilistic Reconstruction of the Tumor Progression Process in Gene Regulatory Networks in the Presence of Uncertainty" in BMC Bioinformatics, 12(Suppl 10):S9, October, 2011. [More Details] [PDF]

Ghaffari, N., Ivanov, I., Qian, X., and Dougherty, E. R., "A CoD-Based Stationary Control Policy for Intervening in Large Gene Regulatory Networks" in BMC Bioinformatics 2011, 12(Suppl 10):S10doi:10.1186/1471-2105-12-S10-S10. [More Details] [PDF]

Dalton, L. A., and Dougherty, E. R., "Bayesian Minimum Mean-Square Error Estimation for Classification Error—Part II: Linear Classification of Gaussian Models" in IEEE Transactions on Signal Processing, Vol. 59, No. 1, 130-144. [More Details] [PDF]

Dalton, L. A., and Dougherty, E. R., "Bayesian Minimum Mean-Square Error Estimation for Classification Error—Part I: Definition and the Bayesian MMSE Error Estimator for Discrete Classification" in IEEE Transactions on Signal Processing, Vol. 59, No. 1, 115-129. [More Details] [PDF]

Dalton, L. A., and Dougherty, E. R., "Application of the Bayesian MMSE Error Estimator for Classification Error to Gene-Expression Microarray Data" in Bioinformatics, Vol. 27, No. 13, 1822-1831. [More Details] [PDF]

Yousefi, M. R., Hua, J., and Dougherty, E. R., "Multiple-Rule Bias in the Comparison of Classification Rules" in Bioinformatics, Vol. 27, No. 12, 1675-1683. [More Details] [PDF]

Meskin, N., Nounou, H., Nounou, M., Datta, A., and Dougherty, E. R., "Intervention in Biological Phenomena Modeled by S-Systems" in IEEE Transactions on Biomedical Engineering, Vol. 58, No. 5, 1260-1267. [More Details] [PDF]

Dougherty, E. R., "Validation of Gene Regulatory Networks: Scientific and Inferential" in Briefings in Bioinformatics, Vol. 12, No. 3, 245-252. [More Details] [PDF]

Li, X., Qian, L., Bittner, M. L., and Dougherty, E. R., "Characterization of Drug Efficacy Regions Based on Dosage and Frequency Schedules" in IEEE Transactions on Biomedical Engineering, Vol. 58, No. 3, 488-498. [More Details] [PDF]

Layek, R., Datta, A., and Dougherty, E. R., "From Biological Pathways to Networks" in Molecular BioSystems, Vol. 7, No. 3, 843-851. [More Details] [PDF]

Layek, R., Datta, A., Bittner, M. L., and Dougherty, E. R., "Cancer Therapy Design Based on Pathway Logic" in Bioinformatics, Vol. 27, No. 4, 548-555. [More Details] [PDF]

2010

Qian, X., Ghaffari, N., Ivanov, I., and Dougherty, E. R., "State Reduction for Network Intervention in Probabilistic Boolean Networks" in Bioinformatics, Vol. 26, No. 24, 3098-3104. [More Details] [PDF]

Ivanov, I., Simeonov, P., Ghaffari, N., Qian, X., and Dougherty, E. R., "Selection Policy-Induced Reduction Mappings for Boolean Networks" in IEEE Transactions on Signal Processing, Vol. 58, No. 9, 4871-4882. [More Details] [PDF]

Sun, Y., Zhang, J., Braga-Neto, U. M., and Dougherty, E. R., "BPDA - A Bayesian Peptide Detection Algorithm for Mass Spectrometry" in BMC Bioinformatics, Vol. 11, September 2010, p. 490, doi:10.1186/1471-2105-11-490. [More Details] [PDF]

Dougherty, E. R., and Bittner, M. L., "Causality, Randomness, Intelligibility, and the Epistemology of the Cell" in Current Genomics, Vol. 11, No. 4, 221-237. [More Details] [PDF]

Chapkin, R. S., Zhao, C., Ivanov, I., Davidson, L. A., Goldsby, J. S., Lupton, J. R., Mathai, R. A., Segel, M., Donovan, S. M., and Dougherty, E. R., "Non-invasive Stool-based Detection of Infant Gastrointestinal Development using Gene Expression Profiles Derived from Exfoliated Epithelial Cells" in American Journal of Physiology – Gastrointestinal and Liver Physiology, Vol. 298, 582-589. [More Details] [PDF]

Ghaffari, N., Ivanov, I., Qian, X., and Dougherty, E. R., "A CoD-Based Reduction Algorithm Preserving the Effects of Stationary Control Policies" in Bioinformatics, Vol. 26, No. 12, 1556-1563. [More Details] [PDF]

Braga-Neto, U. M., and Dougherty, E. R., "Exact Correlation between Actual and Estimated Errors in Discrete Classification" in Pattern Recognition Letters, Vol. 31, 407–413. [More Details] [PDF]

Wang, H., Qian, L., and Dougherty, E. R., "Inference of Gene Regulatory Networks Using S-System: A Unified Approach" in IET Systems Biology, Vol. 4, No. 2, 145-156. [More Details] [PDF]

Zhao, C., Bittner, M. L. Chapkin, R., and Dougherty, E. R., "Characterization of the Effectiveness of Reporting Lists of Small Feature Sets Relative to the Accuracy of the Prior Biological Knowledge" in Cancer Informatics, Vol. 9, 49-60. [More Details] [PDF]

Hanczar, B., Hua, J., Sima, C., Weinstein, J., Bittner. M. L., and Dougherty, E. R., "Small- Sample Precision of ROC-related Estimates" in Bioinformatics, Vol. 26, No. 6, 822-830. [More Details] [PDF]

Hanczar, B., and Dougherty, E. R., "On the Comparison of Classification Algorithms for Microarray Data" in Current Bioinformatics, Vol. 5, No. 1, 29-39. [More Details] [PDF]

Dougherty, E. R., Sima, C., Hua, J., Hanczar, B., and Braga-Neto, U. M., "Performance of Error Estimators for Classification" in Current Bioinformatics, Vol. 5, No. 1, 53-67. [More Details] [PDF]

Zollanvari, A., Braga-Neto, U. M., and Dougherty, E. R., "On the Joint Sampling Distribution Between the Actual Classification Error and the Resubstitution and Leave-One-Out Error Estimators for Linear Classifiers" in IEEE Transactions on Information Theory, Vol. 56, No. 2, 784-804. [More Details] [PDF]

Dougherty, E. R., Pal, R., Qian, X., Bittner, M. L., and Datta, A., "Stationary and Structural Control in Gene Regulatory Networks: Basic Concepts" in International Journal of Systems Science, Vol. 41, No. 1, 5-16. [More Details] [PDF]

Yousefi, M. R., Hua, J., Sima, C., and Dougherty, E. R., "Reporting Bias When Using Real Data Sets to Analyze Classification Performance" in Bioinformatics, Vol. 26, No. 1, 68-76. [More Details] [PDF]

2009

Dougherty, E. R., "Translational Science: Epistemology and the Investigative Process" in Current Genomics, Vol. 10, No. 2, 102-109. [More Details] [PDF]

Dougherty, E. R., "Epistemology and the Role of Mathematics in Translational Science" in 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. [More Details] [PDF]

Vahedi, G., Faryabi, B., Chamberland, J-F., Datta, A., and Dougherty, E. R., "Sampling-Rate-Dependent Probabilistic Boolean Networks" in Theoretical Biology, Vol. 261, 540-547. [More Details] [PDF]

Faryabi, B., Vahedi, G., Datta, A., Chamberland, J-F., and Dougherty, E. R., "Recent Advances in the External Control of Markovian Gene Regulatory Networks" in Current Genomics, Vol. 10, No. 7, 463-477. [More Details] [PDF]

Zollanvari, A., Braga-Neto, U. M., and Dougherty, E. R., "On the Sampling Distribution of Resubstitution and Leave-one-out Error Estimators for Linear Classifiers" in Pattern Recognition, Vol. 42, No. 11, 2705-2723. [More Details] [PDF]

Zollanvari, A., Cunningham, M. J., Braga-Neto, U. M., and Dougherty, E. R., "Analysis and Modeling of Time-Course Gene-Expression Profiles from Nanomaterial-Exposed  Primary Human Epidermal Keratinocytes" in BMC Bioinformatics, 10(Suppl 11):S10, doi:10.1186/1471-2105-10-S11-S10. [More Details] [PDF]

Pal, R., Datta, A., and Dougherty, E. R., "Bayesian Robustness in the Control of Gene Regulatory Networks" in IEEE Transactions on Signal Processing, Vol. 57, No. 9, 3667-3678. [More Details] [PDF]

Dougherty, E. R., Hua, J., and Sima, C., "Performance of Feature Selection Methods" in Current Genomics, Vol. 10, No. 6, 365-374. [More Details] [PDF]

Su, J., Yoon, B-J., and Dougherty, E. R., "Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity" in PLoS ONE, Vol. 4, No. 12. [More Details] [PDF]

Vahedi, G., Ivanov, I., and Dougherty, E. R., "Inference of Boolean Networks under Constraint on Bidirectional Gene Relationships" in IET Systems Biology Journal, Vol. 3, Iss. 3, 191–202. [More Details] [PDF]

Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., and Dougherty, E. R., "Optimal Intervention Strategies for Cyclic Therapeutic Methods" in IEEE Transactions of Biomedical Engineering, Vol. 56, No. 2, 281-291. [More Details] [PDF]

Faryabi, B., Vahedi, G., Chamberland, J-F., Datta, A., and Dougherty, E. R., "Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited" in EURASIP Journal of Bioinformatics and Systems Biology, Vol. 2009 (2009), Article ID 360864, 13 pages, doi:10.1155/2009/360864. [More Details] [PDF]

Zhao, W., Serpedin, E., and Dougherty, E. R., "Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge" in EURASIP Journal of Bioinformatics and Systems Biology, Vol. 2009, Article ID 683463, 9 pages, doi:10.1155/2009/683463. [More Details] [PDF]

Zhao, W., Serpedin, E., and Dougherty, E. R., "Spectral Preprocessing for Clustering Time Series Gene Expressions" in EURASIP Journal of Bioinformatics and Systems Biology, Vol. 2009, Article ID 713248, 10 pages, doi:10.1155/2009/713248. [More Details] [PDF]

Qian, X., and Dougherty, E. R., "On the Long-run Sensitivity of Probabilistic Boolean Networks" in Theoretical Biology, doi:10.1016/j.jtbi.2008.12.023, Vol. 257, No. 4, 560-577. [More Details] [PDF]

Hua, J., Waibhav, T., and Dougherty, E. R., "Performance of Feature Selection Methods in the Classification of High-Dimensional Data" in Pattern Recognition, doi:10.1016/j.patcog.2008.08.001, Vol. 42, No. 3, 409-424. [More Details] [PDF]

2008

Choudhary, A., Hua, J., Bittner, M. L., and Dougherty, E. R., "The Effect of Population Contexts on Classifier Performance" in Biological Systems, Vol. 16, No. 4, 495-517. [More Details] [PDF]

Byung-Jun Yoon, "Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints" in EURASIP Journal on Bioinformatics and Systems Biology, accepted. [More Details] [PDF]

Martins, D., Braga-Neto, U., Hashimoto, R., Bittner, M. L., and Dougherty, E. R., "Intrinsically Multivariate Predictive Genes" in IEEE Journal of Selected Topics in Signal Processing, Vol. 2, No. 3, 424-439. [More Details] [PDF]

Sima, C., and Dougherty, E. R., "The Peaking Phenomenon in the Presence of Feature Selection" in Pattern Recognition Letters, Vol. 29, 1667-1674. [More Details] [PDF]

Liu, W., Lhdesmki, H., Dougherty, E. R., and Shmulevich, I., "Inference of Boolean Networks using Sensitivity Regularization" in EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, doi:10.1155/2008/780541. [More Details] [PDF]

Faryabi, B., Vahedi, G., Chamberland, J. F., Datta, A., and Dougherty, E. R., "Optimal Constrained Stationary Intervention in Gene Regulatory Networks" in EURASIP Journal on Bioinformatics and Systems Biology, vol. 2008, Article ID 620767, 10 pages, doi: 10.1155/2008/620767. [More Details] [PDF]

Brun, M., Xu, Q., and Dougherty, E. R., "Which is Better: Hold-out or Full-sample Classifier Design" in EURASIP Journal on Bioinformatics and Systems Biology,, Vol. 2008, Article ID 297945, 8 pages, doi:10.1155/2008/297945. [More Details] [PDF]

Zhao, W., Serpedin, E., and Dougherty, E. R., "Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria" in IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, 262-274. [More Details] [PDF]

Vahedi, G., Faryabi, B., Chamberland, J. F., Datta, A., and Dougherty, E. R., "Intervention in Gene Regulatory Networks via a Stationary Mean-First-Passage-Time Control Policy" in IEEE Transactions of Biomedical Engineering, Vol. 55, No. 10, 2319-2331. [More Details] [PDF]

Qian, X., and Dougherty, E. R., "Effect of Function Perturbation on the Steady-State Distribution of Genetic Regulatory Networks: Optimal Structural Intervention" in IEEE Transactions on Signal Processing, doi: 10.1109/TSP.2008.928089, Vol. 56, No. 10, Part 1, 4966-4975. [More Details] [PDF]

Hanczar, B., and Dougherty, E. R., "Classification with Reject Option in Gene Expression Data" in Bioinformatics, Vol. 24, 1889-1895, doi: 10.1093/bioinformatics/btn349. [More Details] [PDF]

Qian, L., Wang, H., and Dougherty, E. R., "Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks using Genetic Programming and Kalman Filtering" in IEEE Transactions on Signal Processing, Vol. 56, No. 7, 3327-3339. [More Details] [PDF]

Zhao, W., Serpedin, E., and Dougherty,  E. R., "Recovering Genetic Regulatory Networks From Chromatin Immunoprecipitation (ChIP) and Steady State Microarray Data" in EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 248747, 12 pages, doi:10.1155/2008/248747. [More Details] [PDF]

Faryabi, B., Chamberland, J. F., Vahedi, G., Datta, A., and Dougherty, E. R., "Optimal Intervention in Asynchronous Genetic Regulatory Networks" in IEEE Journal of Selected Topics in Signal Processing, Vol. 2, No. 3, 412-423. [More Details] [PDF]

Byung-Jun Yoon, and Vaidyanathan, P. P., "Fast Structural Alignment of RNAs by Optimizing the Adjoining Order of Profile-csHMMs" in IEEE Journal of Selected Topics in Signal Processing, vol. 2, pp. 400-411. [More Details] [PDF]

Xu, Q., Hua, J., Xiong, Z., Bittner, M. L., and Dougherty, E. R., "The Effect of Microarray Image Compression on Expression-Based Classification" in Signal, Image and Video Processing, doi: 10.1007/s11760-008-0059-2. [More Details] [PDF]

Zhao, W, Agyepong, K., Serpedin, E., and Dougherty, E. R., "Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study" in EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 769293, 8 pages, doi: 10.1155/2008/769293. [More Details] [PDF]

Pal, R., Datta, A. and Dougherty, E. R., "Robust Intervention in Probabilistic Boolean Networks" in IEEE Transactions on Signal Processing, Vol. 56, No. 3, 1280-1294. [More Details] [PDF]

Byung-Jun Yoon, and Vaidyanathan, P. P., "Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results" in IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology with IEEE Transactions on Circuits and Systems: Part-I), Vol. 53, 10-25. [More Details] [PDF]

Qian, X., Sing-Hoi Sze, and Byung-Jun Yoon, "Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models" in Journal of Computational Biology, accepted. [More Details] [PDF]

Dougherty, E. R., "On the Epistemological Crisis in Genomics" in Current Genomics, Vol. 9, No. 2, 69-79. [More Details] [PDF]

2007

Hanczar, B., Hua, J., Dougherty, E. R.,"Decorrelation of the True and Estimated Classifier Errors in High-dimensional Settings" in EURASIP Journal on Bioinformatics and Systems Biology, Article ID 38473, 12 pages. [More Details] [PDF]

Dougherty, E. R., Brun, M., Trent, J., and Bittner, M. L., "Conditioning-Based Model of Contextual Regulation" in IEEE/ACM Transactions on Computational Biology and Bioinformatics preprint, doi:10.1109/TCBB.2007.7024. [More Details] [PDF]

Xiao, Y., and Dougherty, E. R., "The Impact of Function Perturbations in Boolean Networks" in Bioinformatics, Vol. 23, No. 10, 1265-1273. [More Details] [PDF]

Brun, M., Kim, S., Choi, W., and Dougherty, E. R., "Comparison of Gene Regulatory Networks via Steady-State Trajectories" in EURASIP Journal on Bioinformatics and Systems Biology Vol. 2007, Article ID 82702, 11 pages. [More Details] [PDF]

Ivanov,I., Pal, R., and Dougherty, E. R., "Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks" in IEEE Transactions on Signal Processing, Vol. 55, No. 5, 2310-2322. [More Details] [PDF]

Dougherty, E. R., "Validation of Inference Procedures for Gene Regulatory Networks" in Current Genomics, Vol. 8, No. 6, 351-359. [More Details] [PDF]

Marshall, S., Yu, L., Xiao, Y., and Dougherty, E. R., "Inference of Probabilistic Boolean Networks from a Single Observed Temporal Sequence" in EURASIP Journal on Bioinformatics and Systems Biology., Vol. 2007, Article ID 32454, 15 pages. [More Details] [PDF]

Johnson, C. D., Balagurunathan, Y., Dougherty, E. R., Afshari, C. A., He, Q., and Ramos, K. S., "Insight Into Redox-regulatory Gene Networks in Vascular Cells" in Bioinformation, Vol. 1, No. 10, 379-383. [More Details] [PDF]

Brun, M., Sima, C., Hua, J., Lowey, J., Carroll, B., Suh, E., and Dougherty, E. R., "Model-Based Evaluation of Clustering Validation Measures" in Pattern Recognition, Vol. 40, No. 3, 807-824. [More Details] [PDF]

Xiao, Y., Hua, J., and Dougherty, E. R., "Quantification of the Impact of Feature Selection on Cross-Validation Error Estimation Precision" in EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2007, Article ID 16354, 11 pages. [More Details] [PDF]

Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Tembe, W., Joshipura, K., Huentelman, M. J., Dougherty, E. R., and Stephan, D. A., "SNiPer-HD: Improved Genotype Calling Accuracy by an Expectation-Maximization Algorithm for High-Density SNP Arrays" in Bioinformatics, Vol. 23, 57-63. [More Details] [PDF]

Byung-Jun Yoon, and Vaidyanathan, P. P., "Computational Identification and Analysis of Noncoding RNAs - Unearthing the Buried Treasures in the Genome" in IEEE Signal Processing Magazine, Special Issue on Signal Processing Methods in Genomics and Proteomics, Vol. 24, No. 1, 64-74. [More Details] [PDF]

Faryabi, B., Datta, A., and Dougherty, E. R., "On Approximate Stochastic Control in Genetic Regulatory Networks" in IET Systems Biology, Vol. 1, No. 6, 361-368. [More Details] [PDF]

Datta, A., Pal, R., Choudhary, A. and Dougherty, E. R., "Control Approaches for Probabilistic Gene Regulatory Networks" in IEEE Signal Processing Magazine, Vol. 24, No. 1, 54-63. [More Details] [PDF]

Dougherty, E. R., Hua, J., and Bittner, M. L., "Validation of Computational Methods in Genomics" in Current Genomics, Vol. 8, No. 1, 1-19. [More Details] [PDF]

2006

Ivanov, I., and Dougherty, E. R., "Modeling Genetic Regulatory Networks: Continuous or Discrete?" in Biological Systems, Vol. 14, No. 2, 219-229. [More Details] [PDF]

Xu, Q., Hua, J., Braga-Neto, U. M. Xiong, Z., Suh, E., and Dougherty, E. R., "Confidence Intervals for the True Classification Error Conditioned on the Estimated Error" in Technology in Cancer Research and Treatment, Vol. 5, No. 6, 579-590. [More Details] [PDF]

Xiao, Y., and Dougherty, E. R., "Optimizing Consistency-Based Design of Context-Sensitive Gene Regulatory Networks" in IEEE Transactions on Circuits and Systems I, Vol. 53, No. 11, 2431-2437. [More Details] [PDF]

Byung-Jun Yoon, and Vaidyanathan, P. P., "Context-sensitive Hidden Markov Models for Modeling Long-range Dependencies in Symbol Sequences" in IEEE Transactions on Signal Processing, Vol. 54, 4169-4184. [More Details] [PDF]

Sima, C., and Dougherty, E. R., "What Should Be Expected from Feature Selection in Small-Sample Settings" in Bioinformatics, Vol. 22, No. 19, 2430-2436. [More Details] [PDF]

Sima, C., and Dougherty, E. R., "Optimal Convex Error Estimators for Classification" in Pattern Recognition, Vol. 39, No. 6, 1763-1780. [More Details] [PDF]

Byung-Jun Yoon, and Malvar, H. S., "A Practical Approach for the Design of Nonuniform Lapped Transforms" in IEEE Signal Processing Letters, Vol. 13, 469-452. [More Details] [PDF]

Hua, J., Lowey, J., Xiong, Z., and Dougherty, E. R., "Noise-Injected Neural Networks Show Promise for Use on Small-Sample Expression Data" in BMC Bioinformatics, 7:274. [More Details] [PDF]

Choudhary, A., Brun, M., Hua, J., Lowey, J., Suh, E., and Dougherty, E. R., "Genetic Test Bed for Feature Selection" in Bioinformatics, Vol. 22, No. 7, 837-842. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Multi-class Cancer Classification Using Multinomial Probit Regression with Bayesian Variable Selection" in IEE Proceedings System Biology, Vol. 153, No. 2, 70-78. [More Details] [PDF]

Choudhary, A., Datta, A., Bittner, M. L., and Dougherty, E. R., "Intervention in a Family of Boolean Networks" in Bioinformatics, Vol. 22, No. 2, 226-232. [More Details] [PDF]

Zhao, W., Serpedin, E., and Dougherty, E. R., "Inferring Gene Regulatory Networks from Time Series Data Using the Minimum Description Length Principle" in Bioinformatics, Vol. 22, No. 17, 2129-2135. [More Details] [PDF]

Dougherty, E. R., and Xiao, Y., "Design of Probabilistic Boolean Networks under the Requirement of Contextual Data Consistency" in IEEE Transactions on Signal Processing, Vol. 54, No. 9, 3603- 3613, 2006. [More Details] [PDF]

Pal, R., Datta, A. and Dougherty, E. R., "Optimal Infinite Horizon Control for Probabilistic Boolean Networks" in IEEE Transactions on Signal Processing, Vol. 54, No. 6, 2375-2387. [More Details] [PDF]

Dougherty, E. R., and Brun, M., "On the Number of Close-to-Optimal Feature Sets" in Cancer Informatics, Vol. 2, 189-196. [More Details] [PDF]

Hua, J., Balagurunathan, Y. Chen, Y., Lowey, J., Bittner, M., Xiong, Z., Suh, E., and Dougherty, E. R., "Normalization Benefits Microarray-Based Classification" in EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2006. [More Details] [PDF]

Dougherty, E. R., and Braga-Neto, U., "Epistemology of Computational Biology: Mathematical Models and Experimental Prediction as the Basis of Their Validity" in Journal of Biological Systems, Vol. 14, No. 1, 65-90. [More Details] [PDF]

2005

Sima, C., Attoor, S., Braga-Neto, U., Lowey, J., Suh, E., and Dougherty, E. R., "Impact of Error Estimation on Feature Selection" in Pattern Recognition, Vol. 38, No. 12, 2472-2482. [More Details] [PDF]

Dougherty, E. R., "Feature-Selection Overfitting with Small-Sample Classifier Design" in IEEE Intelligent Systems Magazine, 64-66. [More Details] [PDF]

Pal, R., Ivanov, I., Datta, A., and Dougherty, E. R., "Generating Boolean Networks with a Prescribed Attractor Structure" in Bioinformatics, Vol. 21, No. 21, 4021-4025. [More Details] [PDF]

Braga-Neto, U., and Dougherty, E. R., "Exact Performance Measures and Distributions of Error Estimators for Discrete Classifiers" in Pattern Recognition, Vol. 38, No. 11, 1799-1814. [More Details] [PDF]

Brun, M., Dougherty, E. R., and Shmulevich, I., "Steady-State Probabilities for Attractors in Probabilistic Boolean Networks" in Signal Processing, Vol. 85, No. 10, 1993-2013. [More Details] [PDF]

Dougherty, E. R., Hua, J., Xiong, Z., and Chen, Y., "Optimal Robust Classifiers" in Pattern Recognition, Vol. 38, No. 10, 1520-1532. [More Details] [PDF]

Silva, P. J. S., Hashimoto, R. F., Kim, S., Barrera, J., Brandao, L. O., Suh, E., and Dougherty, E. R., "Feature Selection Algorithms to Find Strong Genes" in Pattern Recognition Letters, Vol. 26, No. 10, 1444-1453. [More Details] [PDF]

Hsing, T., Liu, L-Y., Brun, M., and Dougherty, E. R., "The Coefficient of Intrinsic Dependence (Feature Selection Using el CID)" in Pattern Recognition, Vol. 38, No. 5, 623-636. [More Details] [PDF]

Pal, R., Datta, A., Bittner, M. L., and Dougherty, E. R., "Intervention in Context-Sensitive Probabilistic Boolean Networks" in Bioinformatics, Vol. 21, No. 7, 1211-1218. [More Details] [PDF]

Sima, C., Braga-Neto, U., and Dougherty, E. R., "Superior Feature-Set Ranking For Small Samples Using Bolstered Error Estimation" in Bioinformatics, Vol. 21, No. 7, 1046-1054. [More Details] [PDF]

Choudhary, A., Datta, A., Bittner, M. L., and Dougherty, E. R., "Gene Selection Using Logistic Regressions Based on AIC, BIC, and MDL Criteria" in New Mathematics and Natural Computation, Vol. 1, No. 1, 129-145. [More Details] [PDF]

Hua, J., Xiong, Z., and Dougherty, E. R., "Determination of the Optimal Number of Features for Quadratic Discriminant Analysis Via the Normal Approximation to the Discriminant Distribution" in Pattern Recognition, Vol. 38, No. 3, 403-421. [More Details] [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 Carroll, R. J., "Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis" in Statistical Applications in Genetics and Molecular Biology, Vol. 4, No. 1. [More Details] [PDF]

Fu, W. J., Dougherty, E. R., Mallick, B., and Carroll, R. J., "How Many Samples Are Needed to Build a Classifier: A General Sequential Approach" in Bioinformatics, Vol. 21, No. 1, 63-70. [More Details] [PDF]

Byung-Jun Yoon and Vaidyanathan, P. P., "A Multirate DSP Model for Estimation of Discrete Probability Density Functions" in IEEE Transactions on Signal Processing, Vol. 53, 252-264. [More Details] [PDF]

Pal, R., Datta, A., Fornace, A. J., Bittner, M. L., and Dougherty, E. R., "Boolean Relationships Among Genes Responsive to Ionizing Radiation in the NCI 60 ACDS" in Bioinformatics, 21, No. 8, 1542-1549. [More Details] [PDF]

Hua, J., Xiong, Z., Lowey, J., Suh, E., and Dougherty, E. R., "Optimal Number of Features as a Function of Sample Size for Various Classification Rules" in Bioinformatics, 21, No. 8, 1509-1515. [More Details] [PDF]

2004

Zhou, X., Wang, X., Pal, R., Ivanov, I., Bittner, M. L., and Dougherty, E. R., "A Bayesian Connectivity-Based Approach to Constructing Probabilistic Gene Regulatory Networks" in Bioinformatics, Vol. 20. No. 17, 2918-2927. [More Details] [PDF]

Attoor, S., Dougherty, E. R., Chen, Y., Bittner, M. L., and Trent, J. M., "Which is Better for cDNA-Microarray-Based Classification: Ratios or Direct Intensities" in Bioinformatics, Vol. 20, No. 16, 2513-2520. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Nonlinear-Probit Gene Classification Using Mutual-Information and Wavelet Based Feature Selection" in Biological Systems, Vol. 12, No. 3, 371-386. [More Details] [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 Chapkin, R. S., "Chemopreventive n-3 Polyunsaturated Fatty Acids Reprogram Genetic Signatures During Colon Cancer Initiation and Progression in the Rat" in Cancer Research, Vol. 64, 6797-6804. [More Details] [PDF]

Attoor, S. N., and Dougherty, E. R., "Classifier Performance as a Function of Distributional Complexity" in Pattern Recognition, Vol. 37, No. 8, 1629-1640. [More Details] [PDF]

Dougherty, E. R., "Automatic Design of Morphological Operators" in Electronic Imaging, Vol. 13, No. 3, 486-491.

Brun, M., Hirata, R., Barrera, J., and Dougherty, E. R., "Nonlinear Filter Design Using Envelopes" in Mathematical Imaging and Vision, Vol. 21, No. 1, 81-97.

Dougherty, E.R., "A Lattice-Based Minimal Gray-Scale Switching Algorithm for Obtaining the Optimal Increasing Filter from the Optimal Filter" in Mathematical Imaging and Vision, Vol. 21, No. 1, 43-52.

Braga-Neto, U. M., and Dougherty, E. R., "Bolstered Error Estimation" in Pattern Recognition, Vol. 37, No. 6, 1267-1281. [More Details] [PDF]

Dougherty, E. R., and Brun, M., "A Probabilistic Theory of Clustering" in Pattern Recognition, Vol. 37, No. 5, 917-925. [More Details] [PDF]

Green, A., Dougherty, E. R., Marshall, S., and Greenhalgh, D., "Optimal Filters with Multiresolution Apertures" in Mathematical Imaging and Vision, Vol. 20, No. 3, 237-250.

Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpisheh, Marcel Brun, M. H., Walker, M. K., Dougherty, E. R., and Ramos, K. S., "Unraveling Gene-Gene Interactions Regulated by Ligands of the Aril Hydrocarbon Receptor" in Environmental Health Perspectives, Vol. 112, No. 4, 403-412. [More Details] [PDF]

Ivanov, I., and Dougherty, E. R., "Reduction Mappings Between Probabilistic Boolean Networks" in Applied Signal Processing, Vol. 4, No. 1, 125-131. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Gene Prediction Using Multinomial Probit Regression with Bayesian Gene Selection" in Applied Signal Processing, Vol. 4, No. 1, 115-124. [More Details] [PDF]

Braga-Neto, U. M., Hashimoto, R., Dougherty, E. R., Nguyen, D. V., and Carroll, R. J., "Is Cross-validation Better than Resubstitution for Ranking Genes" in Bioinformatics, Vol. 20, No. 2, 253-258. [More Details] [PDF]

Hashimoto, R., Kim, S., Shmulevich, I., Zhang, W., Bittner, M. L., and Dougherty, E. R., "A Directed-Graph Algorithm to Grow Genetic Regulatory Subnetworks from Seed Genes Based on Strength of Connection" in Bioinformatics, Vol. 20, No. 8, 1241-1247. [More Details] [PDF]

Datta, A., Choudhary, A., Bittner, M. L., and Dougherty, E. R., "External Control in Markovian Genetic Regulatory Networks: The Imperfect Information Case" in Bioinformatics, Vol. 20, No. 6, 924-930. [More Details] [PDF]

Braga-Neto, U. M., and Dougherty, E. R., "Is Cross-Validation Valid for Small-Sample Microarray Classification" in Bioinformatics, Vol. 20, No. 3, 374-380. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "A Bayesian Approach to Nonlinear Probit Gene Selection and Classification" in Franklin Institute, Vol. 341, No. 1, 2, 137-156. [More Details] [PDF]

Zhou, X., Wang, X., Dougherty, E. R., Russ, D., and Su, E., "Gene Clustering Based on Clusterwide Mutual Information" in Journal of Computational Biology, Vol. 11, No. 1, 147-161. [More Details] [PDF]

Balagurunathan, Y., Wang, N., Dougherty, E. R., Nguyen, D. V., Chen, Y., Bittner, M. L., Trent, J. M., and Carroll, R. J., "Noise Factor Analysis for cDNA Microarrays" in Biomedical Optics, Vol. 9, No. 4, 663-845. [More Details] [PDF]

Vaidyanathan. P. P., and Byung-Jun Yoon, "The Role of Signal-processing Concepts in Genomics and Proteomics" in Journal of the Franklin Institute (invited paper), Special Issue on Genomics, Vol. 341, 111-135. [More Details] [PDF]

2003

Shmulevich, I., Gluhovsky, I., Hashimoto, R., Dougherty, E. R., and Zhang, W., "Steady-State Analysis of Genetic Regulatory Networks Modeled by Probabilistic Boolean Networks" in Comparative Functional Genomics, Vol. 4, 601-608. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Missing Value Estimation using Linear and Nonlinear Regression with Bayesian Gene Selection" in Bioinformatics, Vol. 19, No. 17, 2302-2307. [More Details] [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 Kallioniemi, O., "RNAi Microarray Analysis in Cultured Mammalian Cells" in Genome Research, Vol. 13, 2341-2347. [More Details] [PDF]

Franciškovic-Bilinski, S., Bilinski, H., Vdovic, N., Balagurunathan, Y., and Dougherty, E. R., "Application of Image-based Granulometry to Siliceous and Calcareous Estuarine and Marine Sediments" in Estuarine, Coastal, and Shelf Science, Vol. 58, No. 2, 227-239.

Green, A., Marshall, S., Greenhalgh, D., and Dougherty, E. R., "Design of Multi-mask Apertures" in Signal Processing, Vol. 83, No. 9, 1961-1971.

Balagurunathan, Y., and Dougherty, E. R., "Morphological Quantification of Surface Roughness" in Optical Engineering, Vol. 42, No. 6, 1795-1804.

Brun, M., Dougherty, E. R., Hirata, R., and Barrera, J., "Design of Optimal Binary Filters Under Joint Multiresolution-Envelope Constraint" in Pattern Recognition Letters, Vol. 24, No. 7, 937-945.

McKenzie, J., Marshall, S., Gray, A. J., and Dougherty, E. R., "Morphological Texture Analysis Using the Texture Evolution Function" in International Journal of Pattern Recognition and Artificial Intelligence, Vol. 17, No. 2, 167-185.

Hashimoto, R., Dougherty, E. R., Brun, M., Zhou, Z., Bittner, M. L., and Trent, J. M., "Efficient Selection of Feature Sets Possessing High Coefficients of Determination Based on Incremental Determinations" in Signal Processing, Vol. 83, No. 4, 695-712. [More Details] [PDF]

Balagurunathan, Y. and Dougherty, E. R., "Granulometric Parametric Estimation for the Random Boolean Model Using Optimal Linear Filters and Optimal Structuring Elements" in Pattern Recognition Letters, Vol. 24, No. 2, 283-293.

Shmulevich, I., Lahdesmaki, H., Dougherty, E. R., Astola, J., and Zhang, W., "The Role of Certain Post Classes in Boolean Network Models of Genetic Networks" in Proceedings of the National Academy of Science, Vol. 100, No. 19, 10734-10739. [More Details] [PDF]

Dougherty, E. R., and Shmulevich, I., "Mappings Between Probabilistic Boolean Networks" in Signal Processing, Vol. 83, No. 4, 799-809. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Construction of Genomic Networks Using Mutual-Information Clustering and Reversible-Jump Markov-Chain-Monte-Carlo Predictor Design" in Signal Processing, Vol. 83, No. 4, 745-761. [More Details] [PDF]

Datta, A., Choudhary, A., Bittner, M. L., and Dougherty, E. R., "External Control in Markovian Genetic Regulatory Networks" in Machine Learning, Vol. 52, No. 1-2, 169-181. [More Details] [PDF]

Brun, M., Sabbagh, D., Kim, S., and Dougherty, E. R., "Corrected Small-Sample Estimation for the Error of the Optimal Binary Filter" in Bioinformatics, Vol. 19, No. 8, 944-951. [More Details] [PDF]

Hsing, T., Attoor, S., and Dougherty, E. R., "Relation Between Permutation-test P Values and Classifier Error Estimates" in Machine Learning, Vol. 52, No. 1-2, 11-30. [More Details] [PDF]

Lee, K. E., Sha, N., Dougherty, E. R., Vannucci, M., and Mallick, B. K., "Gene Selection: A Bayesian Variable Selection Approach" in Bioinformatics, Vol. 19, 90-97. [More Details] [PDF]

Zhou, X., Wang, X., and Dougherty, E. R., "Binarization of Microarray Data Based on a Mixture Model" in Molecular Cancer Therapeutics, Vol. 2, No. 7, 679-684. [More Details] [PDF]

Morikawa, J., Li, H., Kim, S., Nishii, K., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., Zhang, W., and Kobayashi, T., "Identification of Signature Genes by Microarray for Acute Myeloid Leukemia Without Maturation (FAB-M1) and AML with t(15;17)(q22;q12)(PML/RARa)" in International Journal of Oncology, Vol. 23, No. 3, 617- 625. [More Details] [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 Ramos, K. S., "Genomic Profiles and Predictive Biological Networks in Oxidant-Induced Atherogenesis" in Physiological Genomics, Vol. 13, 263-275. [More Details] [PDF]

Kobayashi, T., Yamaguchi, M., Kim, S., Morikawa, J., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., and Zhang, W., "Gene Expression Profiling Identifies Strong Feature Genes that Classify de novo CD5+ and CD5 Diffuse Large B-cell Lymphoma and Mantle Cell Lymphoma" in Cancer Research, Vol. 63, 60-66. [More Details] [PDF]

2002

Dougherty, E. R., "Granulometric Size Density for Segmented Random-Disk Models" in Mathematical Imaging and Vision, Vol. 17, No. 3, 267-276.

Balagurunathan, Y., and Dougherty, E. R., "Optimal Linear Granulometric Estimation for Random Sets" in Pattern Recognition, Vol. 35, No. 6, 1315-1325.

Hirata, R., Brun, M., Barrera, J., and Dougherty, E. R., "Multiresolution Design of Aperture Filters" in Mathematical Imaging and Vision, Vol. 16, No. 3, 199-222, May, 2002.

Kim, S., Dougherty, E. R., Barrera, J., Chen, Y., Bittner, M. L., Trent, J. M., "Strong Feature Sets from Small Samples" in Journal of Computational Biology, Vol.9, No.1, 127-146. [More Details] [PDF]

Grigoryan, A. M., Hostetter, G., Kallioniemi, O., and Dougherty, E. R., "Simulation Toolbox for 3D-FISH Spot Counting Algorithms" in Real-Time Imaging, Vol. 8, No. 3, 203-212.

Balagurunathan, Y., Dougherty, E. R., Chen, Y., Bittner, M. L., and Trent, J. M., "Simulation of cDNA Microarrays via a Parameterized Random Signal Model" in Biomedical Optics, Vol. 7, No. 3, 507-523. [More Details] [PDF]

Chen, Y., Kamat, V., Dougherty, E. R., Bittner, M. L., Meltzer, P. S., and Trent, J. M., "Ratio Statistics of Gene Expression Levels and Applications to Microarray Data Analysis" in Bioinformatics, Vol.18, No.9, 1207-1215. [More Details] [PDF]

Shmulevich, I, Dougherty, E. R. , Kim, S, Zhang, W., "Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks" in Bioinformatics, Vol. 18, No. 2, pp. 261-274. [More Details] [PDF]

Dougherty, E. R., and Barrera, J., "Pattern Recognition Theory in Nonlinear Signal Processing" in Mathematical Imaging and Vision, Vol. 16, No. 3, 181-197.

Grigoryan, A., Dougherty, E. R., Kononen, J., Bubendorf, L., Hostetter, G., and Kallioniemi, O., "Morphological Spot Counting from Stacked Images for Automated Analysis of Gene Copy Numbers by Fluorescence in Situ Hybridization" in Biomedical Optics, Vol. 7, No. 1, 109-122.

Dougherty, E. R., Barrera, J., Brun, M., Kim, S., Cesar, R. M., Chen, Y., Bittner, M., Trent, J. M., "Inference from Clustering with Application to Gene-Expression Microarrays" in Journal of Computational Biology, Vol. 9 No. 1, 105-126. [More Details] [PDF]

Kim, S., Dougherty, E. R., Shmulevich, I., Hess, K. R., Hamilton, S. R., Trent, J. M., Fuller, G. N., and Zhang, W., "Identification of Combination Gene Sets for Glioma Classification" in Molecular Cancer Therapeutics, Vol. 1, No. 13, 1229-1236. [More Details] [PDF]

Shmulevich, I., Dougherty, E. R., Zhang, W., "Gene Perturbation and Intervention in Probabilistic Boolean Networks" in Bioinformatics, Vol. 18, 1319-1331. [More Details] [PDF]

Shmulevich, I., Dougherty, E. R., Zhang, W., "From Boolean to Probabilistic Boolean Networks as Models of Genetic Regulatory Networks" in Proceedings of IEEE, Vol. 90, No. 11, 1778-1792. [More Details] [PDF]

Shmulevich, I., Dougherty, E. R., Zhang, W., "Control of Stationary Behavior in Probabilistic Boolean Networks by Means of Structural Intervention" in Biological Systems, Vol. 10, No. 4, 431-446. [More Details] [PDF]

Kim, S., Li, H., Dougherty, E. R., Chao, N., Chen, Y., Bittner, M. L., and Suh, E. B., "Can Markov Chain Models Mimic Biological Regulation" in Biological Systems, Vol. 10, No. 4, 447-458. [More Details] [PDF]

2001

Sivakumar, K., Balagurunathan, Y., and Dougherty, E. R., "Asymptotic Joint Normality of the Granulometric Moments" in Pattern Recognition Letters, Vol. 22, No. 14, 1537-1543.

Theera-Umpon, N., Dougherty, E. R., and Gader, P., "Non-Homothetic Granulometric Mixing Theory" in Pattern Recognition, Vol. 34, No. 12, 2547-2560.

Grigoryan, A. M., and Dougherty, E. R., "Bayesian Robust Optimal Linear Filters" in Signal Processing, Vol. 81, No. 12, 2503-2521.

Grigoryan, A. M., and Dougherty, E. R., "Optimization of Linear Filters under Power-Spectral-Density Stabilization" in IEEE Trans. on Signal Processing, Vol. 49, No. 10, 1-8.

Dougherty, E. R., and Chen, Y., "Robust Optimal Granulometric Bandpass Filters" in Signal Processing, Vol. 81, 1357-1372.

Balagurunathan, Y., Dougherty, E. R., Franciskovic-Bilinski, S., Bilinski, H., and Vdovi, N., "Morphological Granulometric Analysis of Sediment Images" in Image Analysis and Stereology, Vol. 20, No. 2, 87-99.

Batman, S., and Dougherty, E. R., "Morphological Granulometric Estimation of Random Patterns in the Context of Parameterized Random Sets" in Pattern Recognition, Vol. 34, No. 6.

Dougherty, E. R., "Optimal Conjunctive Granulometric Bandpass Filters" in Mathematical Imaging and Vision, Vol. 14, No. 1, 39-51.

Hirata, R., Brun, M., Barrera, J., and Dougherty, E. R., "Multiresolution Design of Aperture Filters" in Mathematical Imaging and Vision, Vol. 16, No. 3, 199-222.

Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O. P., Wilfond, B., Borg, A., Trent, J., Raffeld, M., Yakhini, Z., Ben-Dor, A., Dougherty, E. R., Kononen, J., Bubendorf, L., Fehrle, W., Pittaluga, S., Gruvberger, S., Loman, N., Johannsson, O., Olsson, H., Sauter, G., "Gene Expression Profiles in Hereditary Breast Cancer" in New England Journal of Medicine, Vol. 344, No. 8, 539-548. [More Details] [PDF]

2000

Hirata, N. T., Dougherty, E. R., and Barrera, J., "Iterative Design of Morphological Binary Image Operators" in Optical Engineering, Vol. 39, No. 12, 3106-3123.

Barrera, J., Dougherty, E. R., and Brun, M., "Hybrid Human-Machine Binary Morphological Operator Design: An Independent Constraint Approach" in Signal Processing, Vol. 80, No. 8, 1469-1487.

Kamat, V. G., Dougherty, E. R., and Barrera, J., "Multiresolution Bayesian Design of Binary Filters" in Electronic Imaging, Vol. 9, No. 3, 283-295.

Sivakumar, K., Patel, M. J., Kehtarnavaz, N., Balagurunathan, Y., and Dougherty, E. R., "A Constant-time Algorithm for Erosions/Dilations with Applications to Morphological Texture Feature Computation" in Real-Time Imaging, Vol. 6, 223-239.

Batman, S., Dougherty, E. R., and Sand, F., "Heterogeneous Morphological Granulometries" in Pattern Recognition, Vol. 33, No. 6, 1047-1057.

Hirata, N., Dougherty, E. R., and Barrera, J., "A Switching Algorithm for Design of Optimal Increasing Binary Filters over Large Windows" in Pattern Recognition, Vol. 33, No. 6, 1059-1081.

Hirata, R., Dougherty, E. R., and Barrera, J., "Aperture Filters" in Signal Processing, Vol. 80, No. 4, 697-721.

Kim, S., Dougherty, E. R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., and Bittner, M., "Multivariate Measurement of Gene Expression Relationships" in Genomics, Vol. 67, 201-209. [More Details] [PDF]

Kim, S., Dougherty, E. R., Bittner, M. L., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., "General Nonlinear Framework for the Analysis of Gene Interaction via Multivariate Expression Arrays" in Journal of Biomedical Optics, Vol. 5, No. 4, 411–424. [More Details] [PDF]

Dougherty, E. R., Kim, S., Chen, Y., "Coeffcient of Determination in Nonlinear Signal Processing" in Signal Processing,  Vol. 80, 2219-2235. [More Details] [PDF]

Bittner, M., Meltzer, P. S. J., Chen, Y. D., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., Sampas, N., Dougherty, E. R., Wang, E. L., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P. C. A., Carpten, J., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C.,Berens, M., Alberts, D., Sondak, V., Hayward, N., Trent, J., "Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling" in Nature, Vol. 406, No. 6795, 536-540. [More Details] [PDF]

1999

Dougherty, E. R., Bittner, M., Chen, Y., Kim, S., Sivakumar, K., Barrera, J., Meltzer, P., and Trent, J., "Nonlinear Filters in Genomic Control" in Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing, Antalya, Turkey. [More Details] [PDF]

1997

Chen, Y., Dougherty, E. R., and Bittner, M. L., "Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images" in Journal Of Biomedical Optics, Vol. 2, No. 4, 364–374. [More Details] [PDF]