HR job title
- Retired Distinguished Professor
- Contact Info
- 1 979 862 8154
- Websites
Dougherty, Edward Distinguished Professor
Positions
- Distinguished Professor, Electrical and Computer Engineering, College of Engineering
My research focuses on genomic signal processing and image analysis.
- Overview
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Overview
Publications
selected publications
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academic article
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Imani, M., Dougherty, E. R., & Braga-Neto, U.
(2020).
Boolean Kalman filter and smoother under model uncertainty. Automatica.
111, 108609-108609.
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Zollanvari, A., & Dougherty, E. R.
(2019).
Optimal Bayesian Classification With Vector Autoregressive Data Dependency. IEEE Transactions on Signal Processing.
67(12), 3073-3086.
-
Boluki, S., Zamani Dadaneh, S., Qian, X., & Dougherty, E. R.
(2019).
Optimal clustering with missing values. BMC Bioinformatics.
20(Suppl 12), 321.
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Boluki, S., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2019).
Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
16(2), 524-537.
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Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2019).
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data. 16(1), 193-207.
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Talapatra, A., Boluki, S., Duong, T., Qian, X., Dougherty, E., & Arroyave, R.
(2018).
Autonomous efficient experiment design for materials discovery with Bayesian model averaging. Physical Review Materials.
2(11), 113803.
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Dadaneh, S. Z., Dougherty, E. R., & Qian, X.
(2018).
Optimal Bayesian Classification With Missing Values. IEEE Transactions on Signal Processing.
66(16), 4182-4192.
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Karbalayghareh, A., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Transfer Learning. IEEE Transactions on Signal Processing.
66(14), 3724-3739.
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Dehghannasiri, R., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2018).
Optimal Bayesian Kalman Filtering With Prior Update. IEEE Transactions on Signal Processing.
66(8), 1982-1996.
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Oduola, W. O., Li, X. L., Duan, C., Qian, L., & Dougherty, E. R.
(2018).
Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach. 65(4), 866-874.
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Knight, J. M., Ivanov, I., Triff, K., Chapkin, R. S., & Dougherty, E. R.
(2018).
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(2), 484-493.
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Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
Intrinsically Bayesian robust Karhunen-Loeve compression. Signal Processing.
144, 311-322.
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Atashpaz-Gargari, E., Reis, M. S., Braga-Neto, U. M., Barrera, J., & Dougherty, E. R.
(2018).
A fast Branch-and-Bound algorithm for U-curve feature selection. Pattern Recognition.
73, 172-188.
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Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2018).
Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks. BMC Systems Biology.
12(Suppl 3), 23.
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Karbalayghareh, A., Braga-Neto, U., Hua, J., & Dougherty, E. R.
(2018).
Classification of State Trajectories in Gene Regulatory Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(1), 68-82.
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Dougherty, E. R., Boulesteix, A., Dalton, L. A., & Zhang, M.
(2018).
Guest Editorial-Special Collection Topic: Statistical Systems Theory in Cancer Modeling, Diagnosis, and Therapy. Cancer Informatics.
17, 1176935118760944-117693511876094.
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Mohsenizadeh, D. N., Dehghannasiri, R., & Dougherty, E. R.
(2018).
Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
15(1), 218-230.
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Boluki, S., Esfahani, M. S., Qian, X., & Dougherty, E. R.
(2017).
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. BMC Bioinformatics.
18(Suppl 14), 552.
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Li, X., Omotere, O., Qian, L., & Dougherty, E. R.
(2017).
Review of stochastic hybrid systems with applications in biological systems modeling and analysis. EURASIP Journal on Bioinformatics and Systems Biology.
2017(1), 8.
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Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2017).
Optimal experimental design in the context of canonical expansions. IET Signal Processing.
11(8), 942-951.
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Dehghannasiri, R., Esfahani, M. S., & Dougherty, E. R.
(2017).
Intrinsically Bayesian Robust Kalman Filter: An Innovation Process Approach. 65(10), 2531-2546.
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Dehghannasiri, R., Xue, D., Balachandran, P. V., Yousefi, M. R., Dalton, L. A., Lookman, T., & Dougherty, E. R.
(2017).
Optimal experimental design for materials discovery. COMPUTATIONAL MATERIALS SCIENCE.
129, 311-322.
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Grego, S., Dougherty, E. R., Alexander, F. J., Auerbach, S. S., Berridge, B. R., Bittner, M. L., ... Yoon, M.
(2017).
Systems biology for organotypic cell cultures. 34(2), 301-310.
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Kim, E., Ivanov, I., Hua, J., Lampe, J. W., Hullar, M. A., Chapkin, R. S., & Dougherty, E. R.
(2017).
The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data. Cancer Informatics.
16, 1176935117710530-15.
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Oduola, W. O., Li, X., Duan, C., Qian, L., Wu, F., & Dougherty, E. R.
(2017).
Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy. Cancer Informatics.
16, 1176935117706888-117693511770688.
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Qian, X., & Dougherty, E. R.
(2016).
Bayesian Regression with Network Prior: Optimal Bayesian Filtering Perspective. 64(23), 6243-6253.
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Zollanvari, A., & Dougherty, E. R.
(2016).
Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations. EURASIP Journal on Bioinformatics and Systems Biology.
2016(1), 2.
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Grigoryan, A. M., Dougherty, E. R., & Agaian, S. S.
(2016).
Optimal Wiener and homomorphic filtration: Review. Signal Processing.
121, 111-138.
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Mohsenizadeh, D. N., Hua, J., Bittner, M., & Dougherty, E. R.
(2015).
Dynamical modeling of uncertain interaction-based genomic networks. BMC Bioinformatics.
16 Suppl 13(Suppl 13), S3.
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Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics.
16 Suppl 13(Suppl 13), S2.
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Esfahani, M. S., & Dougherty, E. R.
(2015).
An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
12(6), 1304-1321.
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Zollanvari, A., & Dougherty, E. R.
(2015).
Generalized Consistent Error Estimator of Linear Discriminant Analysis. IEEE Transactions on Signal Processing.
63(11), 2804-2814.
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Dalton, L. A., Benalcazar, M. E., Brun, M., & Dougherty, E. R.
(2015).
Analytic Representation of Bayes Labeling and Bayes Clustering Operators for Random Labeled Point Processes. IEEE Transactions on Signal Processing.
63(6), 1605-1620.
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Li, X. L., Oduola, W. O., Qian, L., & Dougherty, E. R.
(2015).
Integrating Multiscale Modeling with Drug Effects for Cancer Treatment. Cancer Informatics.
14(Suppl 5), 21-31.
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Sima, C., Hua, J., Cypert, M., Miller, T., Wilson-Robles, H. M., Trent, J. M., Dougherty, E. R., & Bittner, M. L.
(2015).
Assessing Combinational Drug Efficacy in Cancer Cells by Using Image-based Dynamic Response Analysis. Cancer Informatics.
14(Suppl 5), 33-43.
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Broumand, A., Esfahani, M. S., Yoon, B., & Dougherty, E. R.
(2015).
Discrete optimal Bayesian classification with error-conditioned sequential sampling. Pattern Recognition.
48(11), 3766-3782.
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Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. BMC Bioinformatics.
16(1), 410.
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Braga-Neto, U. M., Zollanvari, A., & Dougherty, E. R.
(2014).
Cross-validation under separate sampling: strong bias and how to correct it. Bioinformatics.
30(23), 3349-3355.
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Knight, J. M., Ivanov, I., & Dougherty, E. R.
(2014).
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. BMC Bioinformatics.
15(1), 401.
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Vu, T., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2014).
Unbiased bootstrap error estimation for linear discriminant analysis. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 15-14.
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Fang, J., Ouyang, H., Shen, L., Dougherty, E. R., & Liu, W.
(2014).
Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 13-8.
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Ouyang, H., Fang, J., Shen, L., Dougherty, E. R., & Liu, W.
(2014).
Learning restricted Boolean network model by time-series data. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 10-12.
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Zollanvari, A., & Dougherty, E. R.
(2014).
Moments and Root-Mean-Square Error of the Bayesian MMSE Estimator of Classification Error in the Gaussian Model. Pattern Recognition.
47(6), 2178-2192.
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Yousefi, M. R., & Dougherty, E. R.
(2014).
A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 6.
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Dalton, L. A., & Dougherty, E. R.
(2014).
Intrinsically Optimal Bayesian Robust Filtering. IEEE Transactions on Signal Processing.
62(3), 657-670.
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Hua, J., Bittner, M. L., & Dougherty, E. R.
(2014).
Evaluating gene set enrichment analysis via a hybrid data model. 13(Suppl 1), 1-16.
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Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2014).
Modeling and systematic analysis of biomarker validation using selected reaction monitoring. EURASIP Journal on Bioinformatics and Systems Biology.
2014(1), 17-12.
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Shahrokh Esfahani, M., & Dougherty, E. R.
(2014).
Effect of separate sampling on classification accuracy. Bioinformatics.
30(2), 242-250.
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Yousefi, M. R., Datta, A., & Dougherty, E. R.
(2013).
Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug. IEEE Transactions on Biomedical Engineering.
60(12), 3542-3552.
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Qian, X., & Dougherty, E. R.
(2013).
Validation of gene regulatory network inference based on controllability. Frontiers in Genetics.
4(DEC), 272.
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Zollanvari, A., Hua, J., & Dougherty, E. R.
(2013).
Analytical Study of Performance of Linear Discriminant Analysis in Stochastic Settings. Pattern Recognition.
46(11), 3017-3029.
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Dougherty, E. R.
(2013).
On the impoverishment of scientific education. EURASIP Journal on Bioinformatics and Systems Biology.
2013(1), 15.
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Hsu, F., Dougherty, E. R., Chen, Y., & Serpedin, E.
(2013).
Estimating conditional probabilities for the detection of unfavorable copy number alterations in a targeted therapy. IEEE Transactions on Biomedical Engineering.
60(10), 2933-2942.
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Ghaffari, N., Yousefi, M. R., Johnson, C. D., Ivanov, I., & Dougherty, E. R.
(2013).
Modeling the next generation sequencing sample processing pipeline for the purposes of classification. BMC Bioinformatics.
14(1), 307.
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Dougherty, E. R., & Dalton, L. A.
(2013).
Scientific knowledge is possible with small-sample classification. EURASIP Journal on Bioinformatics and Systems Biology.
2013(1), 10.
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Yousefi, M. R., & Dougherty, E. R.
(2013).
Intervention in gene regulatory networks with maximal phenotype alteration. Bioinformatics.
29(14), 1758-1767.
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Dalton, L. A., & Dougherty, E. R.
(2013).
Optimal classifiers with minimum expected error within a Bayesian framework - Part II: Properties and performance analysis. Pattern Recognition.
46(5), 1288-1300.
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Dalton, L. A., & Dougherty, E. R.
(2013).
Optimal classifiers with minimum expected error within a Bayesian framework-Part I: Discrete and Gaussian models. Pattern Recognition.
46(5), 1301-1314.
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Yoon, B., Qian, X., & Dougherty, E. R.
(2013).
Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. 61(9), 2256-2266.
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Hanczar, B., & Dougherty, E. R.
(2013).
The reliability of estimated confidence intervals for classification error rates when only a single sample is available. Pattern Recognition.
46(3), 1067-1077.
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Agyepong, K. S., Hsu, F., Dougherty, E. R., & Serpedin, E.
(2013).
Spectral analysis on time-course expression data: detecting periodic genes using a real-valued iterative adaptive approach. Advances in Bioinformatics.
2013, 171530-10.
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Esfahani, M. S., Knight, J., Zollanvari, A., Yoon, B., & Dougherty, E. R.
(2013).
Classifier Design Given an Uncertainty Class of Feature Distributions via Regularized Maximum Likelihood and the Incorporation of Biological Pathway Knowledge in Steady-State Phenotype Classification. Pattern Recognition.
46(10), 2783-2797.
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Atashpaz-Gargari, E., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Relationship between the accuracy of classifier error estimation and complexity of decision boundary. Pattern Recognition.
46(5), 1315-1322.
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Hua, J., Sima, C., Cypert, M., Gooden, G. C., Shack, S., Alla, L., ... Bittner, M. L.
(2012).
DYNAMICAL ANALYSIS OF DRUG EFFICACY AND MECHANISM OF ACTION USING GFP REPORTERS. 20(4), 403-422.
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Li, X., Qian, L., & Dougherty, E. R.
(2012).
Dynamical modeling of drug effect using hybrid systems. EURASIP Journal on Bioinformatics and Systems Biology.
2012(1), 19.
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Dougherty, E. R., Yoon, B., Qian, X., & Pal, R.
(2012).
Special Issue on Genomic Signal Processing FOREWORD. 20(4), VII-VIII.
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Nounou, H. N., Nounou, M. N., Meskin, N., Datta, A., & Dougherty, E. R.
(2012).
Fuzzy intervention in biological phenomena. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
9(6), 1819-1825.
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Dougherty, E. R., & Shmulevich, I.
(2012).
On the limitations of biological knowledge. Current Genomics.
13(7), 574-587.
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Yousefi, M. R., & Dougherty, E. R.
(2012).
Performance reproducibility index for classification. Bioinformatics.
28(21), 2824-2833.
-
Hsu, F., Serpedin, E., Chen, Y., & Dougherty, E. R.
(2012).
Evaluating dynamic effects of copy number alterations on gene expression using a single transcription model. IEEE Transactions on Biomedical Engineering.
59(10), 2726-2736.
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Sun, Y., Braga-Neto, U., & Dougherty, E. R.
(2012).
A systematic model of the LC-MS proteomics pipeline. 13 Suppl 6(Suppl 6), S2.
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Hsu, F., Serpedin, E., Hsiao, T., Bishop, A., Dougherty, E. R., & Chen, Y.
(2012).
Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer. BMC GENOMICS.
13 Suppl 6(Suppl 6), S13.
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Nounou, M. N., Nounou, H. N., Meskin, N., Datta, A., & Dougherty, E. R.
(2012).
Multiscale denoising of biological data: a comparative analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
9(5), 1539-1544.
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Yousefi, M. R., Datta, A., & Dougherty, E. R.
(2012).
Optimal Intervention Strategies for Therapeutic Methods With Fixed-Length Duration of Drug Effectiveness. IEEE Transactions on Signal Processing.
60(9), 4930-4944.
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Zhao, C., Hua, J., Bittner, M. L., Ivanov, I., & Dougherty, E. R.
(2012).
Identifying mechanistic similarities in drug responses. Bioinformatics.
28(14), 1902-1910.
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Knight, J. M., Datta, A., & Dougherty, E. R.
(2012).
Generating stochastic gene regulatory networks consistent with pathway information and steady-state behavior. 59(6), 1701-1710.
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Dalton, L. A., & Dougherty, E. R.
(2012).
Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error-Part I: Representation. 60(5), 2575-2587.
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Dalton, L. A., & Dougherty, E. R.
(2012).
Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error-Part II: Consistency and Performance Analysis. IEEE Transactions on Signal Processing.
60(5), 2588-2603.
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Dougherty, E. R.
(2012).
Genomic Signal Processing. 29(3), 124-129.
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Dougherty, E. R.
(2012).
Biomarker development: prudence, risk, and reproducibility. BioEssays.
34(4), 277-279.
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Hua, J., Sima, C., Cypert, M., Gooden, G. C., Shack, S., Alla, L., ... Bittner, M. L.
(2012).
Tracking transcriptional activities with high-content epifluorescent imaging. Journal of Biomedical Optics.
17(4), 046008-04600815.
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Sun, Y., Zhang, J., Braga-Neto, U., & Dougherty, E. R.
(2012).
BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. Bioinformatics.
28(4), 564-572.
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Zollanvari, A., Braga-Neto, U., & Dougherty, E. R.
(2012).
Exact representation of the second-order moments for resubstitution and leave-one-out error estimation for linear discriminant analysis in the univariate heteroskedastic Gaussian model. Pattern Recognition.
45(2), 908-917.
-
Li, X., Qian, L., Bittner, M. L., & Dougherty, E. R.
(2012).
A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens-a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems. 11, 41-60.
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Bittner, M. L., & Dougherty, E. R.
(2012).
Newton, laplace, and the epistemology of systems biology. 11, 185-190.
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Qian, X., & Dougherty, E. R.
(2012).
Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior. 9(1), 123-136.
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Hsu, F., Serpedin, E., Chen, Y., & Dougherty, E. R.
(2012).
Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic. IEEE Transactions on Biomedical Engineering.
59(1), 272-280.
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ZHAO, C., IVANOV, I., BITTNER, M. L., & DOUGHERTY, E. R.
(2011).
PATHWAY REGULATORY ANALYSIS IN THE CONTEXT OF BAYESIAN NETWORKS USING THE COEFFICIENT OF DETERMINATION. Journal of Biological Systems.
19(04), 651-682.
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Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
High-dimensional bolstered error estimation. Bioinformatics.
27(21), 3056-3064.
-
Ghaffari, N., Ivanov, I., Qian, X., & Dougherty, E. R.
(2011).
A CoD-based stationary control policy for intervening in large gene regulatory networks. 12 Suppl 10(Suppl 10), S10.
-
Esfahani, M. S., Yoon, B., & Dougherty, E. R.
(2011).
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. BMC Bioinformatics.
12 Suppl 10(Suppl 10), S9.
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Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis. IEEE Transactions on Signal Processing.
59(9), 4238-4255.
-
Dougherty, E. R., Zollanvari, A., & Braga-Neto, U. M.
(2011).
The illusion of distribution-free small-sample classification in genomics. Current Genomics.
12(5), 333-341.
-
Dalton, L. A., & Dougherty, E. R.
(2011).
Application of the Bayesian MMSE estimator for classification error to gene expression microarray data. Bioinformatics.
27(13), 1822-1831.
-
Yousefi, M. R., Hua, J., & Dougherty, E. R.
(2011).
Multiple-rule bias in the comparison of classification rules. Bioinformatics.
27(12), 1675-1683.
-
Meskin, N., Nounou, H. N., Nounou, M., Datta, A., & Dougherty, E. R.
(2011).
Intervention in biological phenomena modeled by S-systems. IEEE Transactions on Biomedical Engineering.
58(5), 1260-1267.
-
Dougherty, E. R.
(2011).
Validation of gene regulatory networks: scientific and inferential. Briefings in Bioinformatics.
12(3), 245-252.
-
Li, X. L., Qian, L., Bittner, M. L., & Dougherty, E. R.
(2011).
Characterization of drug efficacy regions based on dosage and frequency schedules. IEEE Transactions on Biomedical Engineering.
58(3), 488-498.
-
Layek, R. K., Datta, A., & Dougherty, E. R.
(2011).
From biological pathways to regulatory networks. Molecular Biosystems.
7(3), 843-851.
-
Layek, R., Datta, A., Bittner, M., & Dougherty, E. R.
(2011).
Cancer therapy design based on pathway logic. Bioinformatics.
27(4), 548-555.
-
Dalton, L. A., & Dougherty, E. R.
(2011).
Bayesian Minimum Mean-Square Error Estimation for Classification Error-Part I: Definition and the Bayesian MMSE Error Estimator for Discrete Classification. 59(1), 115-129.
-
Dalton, L. A., & Dougherty, E. R.
(2011).
Bayesian Minimum Mean-Square Error Estimation for Classification Error-Part II: Linear Classification of Gaussian Models. 59(1), 130-144.
-
Qian, X., Ghaffari, N., Ivanov, I., & Dougherty, E. R.
(2010).
State reduction for network intervention in probabilistic Boolean networks. Bioinformatics.
26(24), 3098-3104.
-
Su, J., Yoon, B., & Dougherty, E. R.
(2010).
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinformatics.
11 Suppl 6(Suppl 6), S8.
-
Ivanov, I., Simeonov, P., Ghaffari, N., Qian, X., & Dougherty, E. R.
(2010).
Selection Policy-Induced Reduction Mappings for Boolean Networks. IEEE Transactions on Signal Processing.
58(9), 4871-4882.
-
Ghaffari, N., Ivanov, I., Qian, X., & Dougherty, E. R.
(2010).
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. Bioinformatics.
26(12), 1556-1563.
-
Dougherty, E. R., & Bittner, M. L.
(2010).
Causality, randomness, intelligibility, and the epistemology of the cell. Current Genomics.
11(4), 221-237.
-
Chapkin, R. S., Zhao, C., Ivanov, I., Davidson, L. A., Goldsby, J. S., Lupton, J. R., ... Dougherty, E. R.
(2010).
Noninvasive stool-based detection of infant gastrointestinal development using gene expression profiles from exfoliated epithelial cells. American Journal of Physiology: Gastrointestinal and Liver Physiology.
298(5), G582-G589.
-
Zhao, C., Bittner, M. L., Chapkin, R. S., & Dougherty, E. R.
(2010).
Characterization of the effectiveness of reporting lists of small feature sets relative to the accuracy of the prior biological knowledge. Cancer Informatics.
9, 49-60.
-
Wang, H., Qian, L., & Dougherty, E.
(2010).
Inference of gene regulatory networks using S-system: a unified approach. 4(2), 145-156.
-
Hanczar, B., & Dougherty, E. R.
(2010).
On the Comparison of Classifiers for Microarray Data. Current Bioinformatics.
5(1), 29-39.
-
Hanczar, B., Hua, J., Sima, C., Weinstein, J., Bittner, M., & Dougherty, E. R.
(2010).
Small-sample precision of ROC-related estimates. Bioinformatics.
26(6), 822-830.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2010).
Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis. IEEE TRANSACTIONS ON INFORMATION THEORY.
56(2), 784-804.
-
Sun, Y., Zhang, J., Braga-Neto, U., & Dougherty, E. R.
(2010).
BPDA - a Bayesian peptide detection algorithm for mass spectrometry. BMC Bioinformatics.
11(1), 490.
-
Braga-Neto, U. M., & Dougherty, E. R.
(2010).
Exact correlation between actual and estimated errors in discrete classification. Pattern Recognition Letters.
31(5), 407-412.
-
Dougherty, E. R., Sima, C., Hua, J., Hanczar, B., & Braga-Neto, U. M.
(2010).
Performance of Error Estimators for Classification. Current Bioinformatics.
5(1), 53-67.
-
Yousefi, M. R., Hua, J., Sima, C., & Dougherty, E. R.
(2010).
Reporting bias when using real data sets to analyze classification performance. Bioinformatics.
26(1), 68-76.
-
Yousefi, M. R., Hua, J., Sima, C., & Dougherty, E. R.
(2010).
Reporting bias when using real data sets to analyze classification performance. Bioinformatics (Oxford, England).
26(1), 68-76.
-
Dougherty, E. R., Pal, R., Qian, X., Bittner, M. L., & Datta, A.
(2010).
Stationary and structural control in gene regulatory networks: basic concepts. International Journal of Systems Science.
41(1), 5-16.
-
Su, J., Yoon, B., & Dougherty, E. R.
(2009).
Accurate and reliable cancer classification based on probabilistic inference of pathway activity. PLoS ONE.
4(12), e8161-e8161.
-
Sun, Y., Braga-Neto, U., & Dougherty, E. R.
(2009).
Impact of missing value imputation on classification for DNA microarray gene expression data--a model-based study. 2009(1), 504069-504069.
-
Zollanvari, A., Cunningham, M. J., Braga-Neto, U., & Dougherty, E. R.
(2009).
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. BMC Bioinformatics.
10(SUPPL. 11),
-
Pal, R., Datta, A., & Dougherty, E. R.
(2009).
Bayesian Robustness in the Control of Gene Regulatory Networks. 57(9), 3667-3678.
-
Dougherty, E. R., Huang, Y., Kim, S., Cai, X., & Yamaguchi, R.
(2009).
Genomic signal processing. Current Genomics.
10(6), 364-364.
-
Dougherty, E. R., Hua, J., & Sima, C.
(2009).
Performance of feature selection methods. Current Genomics.
10(6), 365-374.
-
Layek, R., Datta, A., Pal, R., & Dougherty, E. R.
(2009).
Adaptive intervention in probabilistic boolean networks. Bioinformatics.
25(16), 2042-2048.
-
Qian, X., Ivanov, I., Ghaffari, N., & Dougherty, E. R.
(2009).
Intervention in gene regulatory networks via greedy control policies based on long-run behavior. BMC Systems Biology.
3(1), 61.
-
Zhao, C., Ivanov, I., Dougherty, E. R., Hartman, T. J., Lanza, E., Bobe, G., ... Chapkin, R. S.
(2009).
Noninvasive detection of candidate molecular biomarkers in subjects with a history of insulin resistance and colorectal adenomas. Cancer Prevention Research.
2(6), 590-597.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2009).
Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 683463-683463.
-
Faryabi, B., Vahedi, G., Chamberland, J., Datta, A., & Dougherty, E. R.
(2009).
Intervention in context-sensitive probabilistic Boolean networks revisited. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 360864-13.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2009).
Spectral preprocessing for clustering time-series gene expressions. EURASIP Journal on Bioinformatics and Systems Biology.
2009(1), 713248-10.
-
Vahedi, G., Ivanov, I. V., & Dougherty, E. R.
(2009).
Inference of Boolean networks under constraint on bidirectional gene relationships. 3(3), 191-202.
-
Dougherty, E. R., Brun, M., Trent, J. M., & Bittner, M. L.
(2009).
Conditioning-based modeling of contextual genomic regulation. 6(2), 310-320.
-
Qian, X., & Dougherty, E. R.
(2009).
On the long-run sensitivity of probabilistic Boolean networks. Journal of Theoretical Biology.
257(4), 560-577.
-
Dougherty, E. R.
(2009).
Translational science: epistemology and the investigative process. Current Genomics.
10(2), 102-109.
-
Hua, J., Tembe, W. D., & Dougherty, E. R.
(2009).
Performance of feature-selection methods in the classification of high-dimension data. Pattern Recognition.
42(3), 409-424.
-
Vahedi, G., Faryabi, B., Chamberland, J., Datta, A., & Dougherty, E. R.
(2009).
Optimal intervention strategies for cyclic therapeutic methods. IEEE Transactions on Biomedical Engineering.
56(2), 281-291.
-
Xu, Q., Hua, J., Xiong, Z., Bittner, M. L., & Dougherty, E. R.
(2009).
The effect of microarray image compression on expression-based classification. Signal, Image and Video Processing.
3(1), 53-61.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
On the sampling distribution of resubstitution and leave-one-out error estimators for linear classifiers. Pattern Recognition.
42(11), 2705-2723.
-
Faryabi, B., Vahedi, G., Datta, A., Chamberland, J., & Dougherty, E. R.
(2009).
Recent advances in intervention in markovian regulatory networks. Current Genomics.
10(7), 463-477.
-
Vahedi, G., Faryabi, B., Chamberland, J., Datta, A., & Dougherty, E. R.
(2009).
Sampling-rate-dependent probabilistic Boolean networks. Journal of Theoretical Biology.
261(4), 540-547.
-
Choudhary, A., Hua, J., Bittner, M. L., & Dougherty, E. R.
(2008).
THE EFFECT OF POPULATION CONTEXTS ON CLASSIFIER PERFORMANCE. Journal of Biological Systems.
16(4), 495-517.
-
Qian, X., & Dougherty, E. R.
(2008).
Effect of function perturbation on the steady-state distribution of genetic regulatory networks: Optimal structural intervention. 56(10), 4966-4976.
-
Vahedi, G., Faryabi, B., Chamberland, J., Datta, A., & Dougherty, E. R.
(2008).
Intervention in gene regulatory networks via a stationary mean-first-passage-time control policy. IEEE Transactions on Biomedical Engineering.
55(10), 2319-2331.
-
Hanczar, B., & Dougherty, E. R.
(2008).
Classification with reject option in gene expression data. Bioinformatics.
24(17), 1889-1895.
-
Sima, C., & Dougherty, E. R.
(2008).
The peaking phenomenon in the presence of feature-selection. Pattern Recognition Letters.
29(11), 1667-1674.
-
Zhao, W., Agyepong, K., Serpedin, E., & Dougherty, E. R.
(2008).
Detecting periodic genes from irregularly sampled gene expressions: a comparison study. EURASIP Journal on Bioinformatics and Systems Biology.
2008(1), 769293-8.
-
Liu, W., Lhdesmki, H., Dougherty, E. R., & Shmulevich, I.
(2008).
Inference of Boolean networks using sensitivity regularization. EURASIP Journal on Bioinformatics and Systems Biology.
2008(1), 780541-12.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2008).
Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data. EURASIP Journal on Bioinformatics and Systems Biology.
2008(1), 248747-12.
-
Qian, L., Wang, H., & Dougherty, E. R.
(2008).
Inference of noisy nonlinear differential equation models for gene regulatory networks using genetic programming and Kalman filtering. IEEE Transactions on Signal Processing.
56(7), 3327-3339.
-
Faryabi, B., Vahedi, G., Chamberland, J., Datta, A., & Dougherty, E. R.
(2008).
Optimal constrained stationary intervention in gene regulatory networks. EURASIP Journal on Bioinformatics and Systems Biology.
2008(1), 620767-10.
-
Brun, M., Xu, Q., & Dougherty, E. R.
(2008).
Which is better: holdout or full-sample classifier design?. EURASIP Journal on Bioinformatics and Systems Biology.
2008(1), 297945-8.
-
Martins, D., Braga-Neto, U. M., Hashimoto, R. F., Bittner, M. L., & Dougherty, E. R.
(2008).
Intrinsically Multivariate Predictive Genes. IEEE Journal of Selected Topics in Signal Processing.
2(3), 424-439.
-
Faryabi, B., Chamberland, J., Vahedi, G., Datta, A., & Dougherty, E. R.
(2008).
Optimal Intervention in Asynchronous Genetic Regulatory Networks. IEEE Journal of Selected Topics in Signal Processing.
2(3), 412-423.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2008).
Inferring connectivity of genetic regulatory networks using information-theoretic criteria. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
5(2), 262-274.
-
Dougherty, E. R.
(2008).
On the epistemological crisis in genomics. Current Genomics.
9(2), 69-79.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2008).
Robust intervention in probabilistic Boolean networks. IEEE Transactions on Signal Processing.
56(3), 1280-1294.
-
Faryabi, B., Datta, A., & Dougherty, E. R.
(2007).
On approximate stochastic control in genetic regulatory networks. 1(6), 361-368.
-
Hanczar, B., Hua, J., & Dougherty, E. R.
(2007).
Decorrelation of the true and estimated classifier errors in high-dimensional settings. EURASIP Journal on Bioinformatics and Systems Biology.
2007(1), 38473-12.
-
Dougherty, E. R., Akutsu, T., Cristea, P. D., & Tewfik, A. H.
(2007).
Genetic regulatory networks. EURASIP Journal on Bioinformatics and Systems Biology.
2007(1), 17321-2.
-
Dougherty, E. R.
(2007).
Validation of inference procedures for gene regulatory networks. Current Genomics.
8(6), 351-359.
-
Brun, M., Kim, S., Choi, W., & Dougherty, E. R.
(2007).
Comparison of gene regulatory networks via steady-state trajectories. EURASIP Journal on Bioinformatics and Systems Biology.
2007(1), 82702-11.
-
Marshall, S., Yu, L. e., Xiao, Y., & Dougherty, E. R.
(2007).
Inference of a probabilistic Boolean network from a single observed temporal sequence. EURASIP Journal on Bioinformatics and Systems Biology.
2007(1), 32454-15.
-
Ivanov, I., Pal, R., & Dougherty, E. R.
(2007).
Dynamics preserving size reduction mappings for probabilistic boolean networks. 55(5), 2310-2322.
-
Xiao, Y., & Dougherty, E. R.
(2007).
The impact of function perturbations in Boolean networks. Bioinformatics.
23(10), 1265-1273.
-
Xiao, Y., Hua, J., & Dougherty, E. R.
(2007).
Quantification of the impact of feature selection on the variance of cross-validation error estimation. EURASIP Journal on Bioinformatics and Systems Biology.
2007(1), 16354-11.
-
Brun, M., Sima, C., Hua, J., Lowey, J., Carroll, B., Suh, E., & Dougherty, E. R.
(2007).
Model-based evaluation of clustering validation measures. Pattern Recognition.
40(3), 807-824.
-
Doughtery, E. R., Jianping, H., & Bittner, M. L.
(2007).
Validation of computational methods in genomics. Current Genomics.
8(1), 1-19.
-
Dougherty, E. R., & Brun, M.
(2007).
On the number of close-to-optimal feature sets. Cancer Informatics.
2, 189-196.
-
Datta, A., Pal, R., Choudhary, A., & Dougherty, E. R.
(2007).
Control approaches for probabilistic gene regulatory networks. IEEE Signal Processing Magazine.
24(1), 54-63.
-
Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Tembe, W., ... Stephan, D. A.
(2007).
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics.
23(1), 57-63.
-
Dougherty, E. R., Stolovitzky, G. A., Tabus, l., & Wang, X.
(2007).
Signal Processing in Genomics [From The Guest Editors]. IEEE Signal Processing Magazine.
24(1), 16-16.
-
Xu, Q., Hua, J., Braga-Neto, U., Xiong, Z., Suh, E., & Dougherty, E. R.
(2006).
Confidence intervals for the true classification error conditioned on the estimated error. Technology in Cancer Research and Treatment.
5(6), 579-589.
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Xiao, Y., & Dougherty, E. R.
(2006).
Optimizing consistency-based design of context-sensitive gene regulatory networks. IEEE Transactions on Circuits and Systems I: Regular Papers.
53(11), 2431-2437.
-
Hua, J., Balagurunathan, Y., Chen, Y., Lowey, J., Bittner, M. L., Xiong, Z., Suh, E., & Dougherty, E. R.
(2006).
Normalization benefits microarray-based classification. EURASIP Journal on Bioinformatics and Systems Biology.
2006(1), 43056-13.
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Sima, C., & Dougherty, E. R.
(2006).
What should be expected from feature selection in small-sample settings. Bioinformatics.
22(19), 2430-2436.
-
Dougherty, E. R., & Xiao, Y.
(2006).
Design of probabilistic Boolean networks under the requirement of contextual data consistency. IEEE Transactions on Signal Processing.
54(9), 3603-3613.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2006).
Inferring gene regulatory networks from time series data using the minimum description length principle. Bioinformatics.
22(17), 2129-2135.
-
Dougherty, E., & Brun, M.
(2006).
On the Number of Close-to-Optimal Feature Sets. Cancer Informatics.
2, 189-196.
-
Sima, C., & Dougherty, E. R.
(2006).
Optimal convex error estimators for classification. Pattern Recognition.
39(9), 1763-1780.
-
Dougherty, E. R.
(2006).
Guest editorial - Genomic signal processing. IEEE Transactions on Signal Processing.
54(6), 2373-2374.
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Ivanov, I., & Dougherty, E. R.
(2006).
Modeling genetic regulatory networks: Continuous or discrete?. Journal of Biological Systems.
14(2), 219-229.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2006).
Optimal infinite-horizon control for probabilistic Boolean networks. IEEE Transactions on Signal Processing.
54(6), 2375-2387.
-
Hua, J., Lowey, J., Xiong, Z., & Dougherty, E. R.
(2006).
Noise-injected neural networks show promise for use on small-sample expression data. BMC Bioinformatics.
7(1), 274.
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Choudhary, A., Brun, M., Hua, J., Lowey, J., Suh, E. d., & Dougherty, E. R.
(2006).
Genetic test bed for feature selection. Bioinformatics.
22(7), 837-842.
-
Dougherty, E. R., & Braga-Neto, U.
(2006).
Epistemology of computational biology: Mathematical models and experimental prediction as the basis of their validity. Journal of Biological Systems.
14(1), 65-90.
-
Zhou, X., Wang, X., & Dougherty, E. R.
(2006).
Multi-class cancer classification using multinomial probit regression with Bayesian gene selection. IET Systems Biology.
153(2), 70-78.
-
Choudhary, A., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2006).
Intervention in a family of Boolean networks. Bioinformatics.
22(2), 226-232.
-
Braga-Neto, U., & Dougherty, E. R.
(2005).
Classification. Eurasip Book Series on Signal Processing and Communications.
2, 93-128.
-
Dougherty, E. R., Shmulevich, I., Chen, J., & Jane Wang, Z.
(2005).
Genomic signal processing: Perspectives. Eurasip Book Series on Signal Processing and Communications.
2, 1-14.
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Sima, C., Attoor, S., Brag-Neto, U., Lowey, J., Suh, E., & Dougherty, E. R.
(2005).
Impact of error estimation on feature selection. Pattern Recognition.
38(12), 2472-2482.
-
Shmulevich, I., & Dougherty, E. R.
(2005).
Modeling genetic regulatory networks with probabilistic Boolean networks. Eurasip Book Series on Signal Processing and Communications.
2, 241-279.
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Dougherty, E. R.
(2005).
The fundamental role of pattern recognition for gene-expression/microarray data in bioinformatics. Pattern Recognition.
38(12), 2226-2228.
-
Forman, G., Liu, H., Dougherty, E. R., Dy, J. G., Torkkola, K., Tuv, E., ... Zhao, Z.
(2005).
Feature selection: We've barely scratched the surface. IEEE Intelligent Systems.
20(6), 74-76.
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Dougherty, E. R.
(2005).
Feature-selection overfitting with small-sample classifier design. IEEE Intelligent Systems.
20(6), 64-66.
-
Pal, R., Ivanov, I., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2005).
Generating Boolean networks with a prescribed attractor structure. Bioinformatics.
21(21), 4021-4025.
-
Dougherty, E. R., Datta, A., & Sima, C.
(2005).
Research issues in genomic signal processing. IEEE Signal Processing Magazine.
22(6), 46-68.
-
Dougherty, E. R., Hua, J. P., Xiong, Z. X., & Chen, Y. D.
(2005).
Optimal robust classifiers. Pattern Recognition.
38(10), 1520-1532.
-
Brun, M., Dougherty, E. R., & Shmulevich, I.
(2005).
Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Processing.
85(10), 1993-2013.
-
Silva, P., Hashimoto, R. F., Kim, S. C., Barrera, J., Brandao, L. O., Suh, E., & Dougherty, E. R.
(2005).
Feature selection algorithms to find strong genes. Pattern Recognition Letters.
26(10), 1444-1453.
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Hsing, T. L., Liu, L. Y., Brun, M., & Dougherty, E. R.
(2005).
The coefficient of intrinsic dependence (feature selection using el CID). Pattern Recognition.
38(5), 623-636.
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Hua, J., Xiong, Z., Lowey, J., Suh, E., & Dougherty, E. R.
(2005).
Optimal number of features as a function of sample size for various classification rules. Bioinformatics.
21(8), 1509-1515.
-
Pal, R., Datta, A., Fornace, A. J., Bittner, M. L., & Dougherty, E. R.
(2005).
Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS. Bioinformatics.
21(8), 1542-1549.
-
Pal, R., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2005).
Intervention in context-sensitive probabilistic Boolean networks. Bioinformatics.
21(7), 1211-1218.
-
Sima, C., Braga-Neto, U., & Dougherty, E. R.
(2005).
Superior feature-set ranking for small samples using bolstered error estimation. Bioinformatics.
21(7), 1046-1054.
-
Leyk, M., Nguyen, D. V., Attoor, S. N., Dougherty, E. R., Turner, N. D., Bancroft, L. K., ... Carroll, R. J.
(2005).
Comparing automatic and manual image processing in FLARE assay analysis for colon carcinogenesis. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY.
4(1), 1-20.
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Hua, J. P., Xiong, Z. X., & Dougherty, E. R.
(2005).
Determination of the optimal number of features for quadratic discriminant analysis via the normal approximation to the discriminant distribution. Pattern Recognition.
38(3), 403-421.
-
Braga-Neto, U., & Dougherty, E.
(2005).
Exact performance of error estimators for discrete classifiers. Pattern Recognition.
38(11), 1799-1814.
-
Dougherty, E. R., & Datta, A.
(2005).
Genomic signal processing: Diagnosis and therapy. IEEE Signal Processing Magazine.
22(1), 107-112.
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Chen, J., Dougherty, E., Demir, S. S., Friedman, C., Li, C. S., & Wong, S.
(2005).
Grand challenges for multimodal bio-medical systems. IEEE Circuits and Systems Magazine.
5(2), 46-52.
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Fu, W. J., Dougherty, E. R., Mallick, B., & Carroll, R. J.
(2005).
How many samples are needed to build a classifier: a general sequential approach. Bioinformatics.
21(1), 63-70.
-
Zhou, X. B., Wang, X. D., & Dougherty, E. R.
(2004).
Gene prediction using multinomial probit regression with Bayesian gene selection. 2004(1), 115-124.
-
Wang, X. D., Dougherty, E. R., Chen, Y. D., & Peterson, C. O.
(2004).
Genomic signal processing - Editorial. 2004(1), 3-4.
-
Dougherty, E. R., Shmulevich, I., & Bittner, M. L.
(2004).
Genornic signal processing: The salient issues. 2004(1), 146-153.
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Ivanov, I., & Dougherty, E. R.
(2004).
Reduction mappings between Probabilistic Boolean networks. EURASIP Journal on Advances in Signal Processing.
2004(1), 125-131.
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Zhou, X., Wang, X., Pal, R., Ivanov, I., Bittner, M., & Dougherty, E. R.
(2004).
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics.
20(17), 2918-2927.
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Attoor, S., Dougherty, E. R., Chen, Y., Bittner, M. L., & Trent, J. M.
(2004).
Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics.
20(16), 2513-2520.
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Davidson, L. A., Nguyen, D. V., Hokanson, R. M., Callaway, E. S., Isett, R. B., Turner, N. D., ... Chapkin, R. S.
(2004).
Chemopreventive n-3 polyunsaturated fatty acids reprogram genetic signatures during colon cancer initiation and progression in the rat. Cancer Research.
64(18), 6797-6804.
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Zhou, X. B., Wang, X. D., & Dougherty, E. R.
(2004).
Nonlinear probit gene classification using mutual information and wavelet-based feature selection. Journal of Biological Systems.
12(3), 371-386.
-
Attoor, S. N., & Dougherty, E. R.
(2004).
Classifier performance as a function of distributional complexity. Pattern Recognition.
37(8), 1641-1651.
-
Dougherty, E. R.
(2004).
A lattice-based minimal gray-scale switching algorithm for obtaining the optimal increasing filter from the optimal filter. Journal of Mathematical Imaging and Vision.
21(1), 43-52.
-
Dougherty, E. R.
(2004).
Automatic design of morphological operators. Journal of Electronic Imaging.
13(3), 486-491.
-
Balagurunathan, Y., Wang, N., Dougherty, E. R., Nguyen, D., Chen, Y., Bittner, M. L., Trent, J., & Carroll, R.
(2004).
Noise factor analysis for cDNA microarrays. Journal of Biomedical Optics.
9(4), 663-678.
-
Brun, M., Hirata, R., Barrera, J., & Dougherty, E. R.
(2004).
Nonlinear filter design using envelopes. Journal of Mathematical Imaging and Vision.
21(1), 81-97.
-
Dougherty, E. R., & Brun, M.
(2004).
A probabilistic theory of clustering. Pattern Recognition.
37(5), 917-925.
-
Hashimoto, R. F., Kim, S., Shmulevich, I., Zhang, W., Bittner, M. L., & Dougherty, E. R.
(2004).
Growing genetic regulatory networks from seed genes. Bioinformatics.
20(8), 1241-1247.
-
Green, A. C., Dougherty, E. R., Marshall, S., & Greenhalgh, D.
(2004).
Optimal filters with multiresolution apertures. Journal of Mathematical Imaging and Vision.
20(3), 237-250.
-
Datta, A., Choudhary, A., Bittner, M. L., & Dougherty, E. R.
(2004).
External control in Markovian genetic regulatory networks: the imperfect information case. Bioinformatics.
20(6), 924-930.
-
Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpisheh, M. H., Brun, M., Walker, M. K., Dougherty, E. R., & Ramos, K. S.
(2004).
Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environmental Health Perspectives.
112(4), 403-412.
-
Braga-Neto, U. M., & Dougherty, E. R.
(2004).
Is cross-validation valid for small-sample microarray classification?. Bioinformatics.
20(3), 374-380.
-
Braga-Neto, U., & Dougherty, E.
(2004).
Bolstered error estimation. Pattern Recognition.
37(6), 1267-1281.
-
Zhou, X., Wang, X., Dougherty, E. R., Russ, D., & Suh, E.
(2004).
Gene clustering based on clusterwide mutual information. Journal of Computational Biology.
11(1), 147-161.
-
Braga-Neto, U., Hashimoto, R., Dougherty, E. R., Nguyen, D. V., & Carroll, R. J.
(2004).
Is cross-validation better than resubstitution for ranking genes?. Bioinformatics.
20(2), 253-258.
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Shmulevich, I., Gluhovsky, I., Hashimoto, R. F., Dougherty, E. R., & Zhang, W.
(2003).
Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks. International Journal of Genomics.
4(6), 601-608.
-
Zhou, X., Wang, X., & Dougherty, E. R.
(2003).
Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics.
19(17), 2302-2307.
-
Franciskovic-Bilinski, S., Bilinski, H., Vdovic, N., Balagurunathan, Y., & Dougherty, E. R.
(2003).
Application of image-based granulometry to siliceous and calcareous estuarine and marine sediments. Estuarine, Coastal and Shelf Science.
58(2), 227-239.
-
Mousses, S., Caplen, N. J., Cornelison, R., Weaver, D., Basik, M., Hautaniemi, S., ... Kallioniemi, O.
(2003).
RNAi microarray analysis in cultured mammalian cells. Genome Research.
13(10), 2341-2347.
-
Green, A. C., Marshall, S., Greenhalgh, D., & Dougherty, E. R.
(2003).
Design of multi-mask aperture filters. 83(9), 1961-1971.
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Shmulevich, I., Lhdesmki, H., Dougherty, E. R., Astola, J., & Zhang, W.
(2003).
The role of certain Post classes in Boolean network models of genetic networks. Proceedings of the National Academy of Sciences of the United States of America.
100(19), 10734-10739.
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Zhou, X., Wang, X., & Dougherty, E. R.
(2003).
Binarization of microarray data on the basis of a mixture model. MOLECULAR CANCER THERAPEUTICS.
2(7), 679-684.
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Datta, A., Choudhary, A., Bittner, M. L., & Dougherty, E. R.
(2003).
External control in Markovian Genetic Regulatory Networks. Machine Learning.
52(1-2), 169-191.
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Hsing, T., Attoor, S., & Dougherty, E.
(2003).
Relation Between Permutation-Test P Values and Classifier Error Estimates. Machine Learning.
52(1-2), 11-30.
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Balagurunathan, Y., & Dougherty, E. R.
(2003).
Morphological quantification of surface roughness. Optical Engineering.
42(6), 1795-1804.
-
Brun, M., Sabbagh, D. L., Kim, S., & Dougherty, E. R.
(2003).
Corrected small-sample estimation of the Bayes error. Bioinformatics.
19(8), 944-951.
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Johnson, C. D., Balagurunathan, Y., Lu, K. P., Tadesse, M., Falahatpisheh, M. H., Carroll, R. J., ... Ramos, K. S.
(2003).
Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiological Genomics.
13(3), 263-275.
-
Zhou, X. B., Wang, X. D., & Dougherty, E. R.
(2003).
Construction of genomic networks using mutual-information clustering and reversible jump Markov-chain-Monte-Carlo predictor design. Signal Processing.
83(4), 745-761.
-
Brun, M., Dougherty, E. R., Hirata, R., & Barrera, J.
(2003).
Design of optimal binary filters under joint multiresolution-envelope constraint. Pattern Recognition Letters.
24(7), 937-945.
-
Hashimoto, R. F., Dougherty, E. R., Brun, M., Zhou, Z. Z., Bittner, M. L., & Trent, J. M.
(2003).
Efficient selection of feature sets possessing high coefficients of determination based on incremental determinations. Signal Processing.
83(4), 695-712.
-
Astola, J., Dougherty, E., Shmulevich, I., & Tabus, I.
(2003).
Genomic signal processing. Signal Processing.
83(4), 691-694.
-
Dougherty, E. R., & Shmulevich, I.
(2003).
Mappings between probabilistic Boolean networks. Signal Processing.
83(4), 799-809.
-
McKenzie, J., Marshall, S., Gray, A. J., & Dougherty, E. R.
(2003).
Morphological texture analysis using the texture evolution function. International Journal of Pattern Recognition and Artificial Intelligence.
17(2), 167-185.
-
Lee, K. E., Sha, N., Dougherty, E. R., Vannucci, M., & Mallick, B. K.
(2003).
Gene selection: a Bayesian variable selection approach. Bioinformatics.
19(1), 90-97.
-
Balagurunathan, Y., & Dougherty, E. R.
(2003).
Granulometric parametric estimation for the random Boolean model using optimal linear filters and optimal structuring elements. Pattern Recognition Letters.
24(1-3), 283-293.
-
Kobayashi, T., Yamaguchi, M., Kim, S., Morikawa, J., Ogawa, S., Ueno, S., ... Zhang, W.
(2003).
Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas. Cancer Research.
63(1), 60-66.
-
Kim, S., Li, H., Dougherty, E. R., Cao, N. W., Chen, Y. D., Bittner, M., & Suh, E. B.
(2002).
Can Markov chain models mimic biological regulation?. Journal of Biological Systems.
10(4), 337-357.
-
Shmulevich, I., Dougherty, E. R., & Zhang, W.
(2002).
Control of stationary behavior in probabilistic Boolean networks by means of structural intervention. Journal of Biological Systems.
10(4), 431-445.
-
Shmulevich, I., Dougherty, E. R., & Mang, W.
(2002).
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proceedings of the Institute of Electrical and Electronics Engineers (IEEE).
90(11), 1778-1792.
-
Dougherty, E. R.
(2002).
Granulometric size density for segmented random-disk models. Journal of Mathematical Imaging and Vision.
17(3), 271-281.
-
Kim, S., Dougherty, E. R., Shmulevich, I., Hess, K. R., Hamilton, S. R., Trent, J. M., Fuller, G. N., & Zhang, W.
(2002).
Identification of combination gene sets for glioma classification. MOLECULAR CANCER THERAPEUTICS.
1(13), 1229-1236.
-
Shmulevich, I., Dougherty, E. R., & Zhang, W.
(2002).
Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics.
18(10), 1319-1331.
-
Chen, Y., Kamat, V., Dougherty, E. R., Bittner, M. L., Meltzer, P. S., & Trent, J. M.
(2002).
Ratio statistics of gene expression levels and applications to microarray data analysis. Bioinformatics.
18(9), 1207-1215.
-
Balagurunathan, Y., Dougherty, E. R., Chen, Y., Bittner, M. L., & Trent, J. M.
(2002).
Simulation of cDNA microarrays via a parameterized random signal model. Journal of Biomedical Optics.
7(3), 507-523.
-
Balagurunathan, Y., & Dougherty, E. R.
(2002).
Optimal linear granulometric estimation for random sets. Pattern Recognition.
35(6), 1315-1325.
-
Grigoryan, A. M., Hostetter, G., Kallioniemi, O., & Dougherty, E. R.
(2002).
Simulation toolbox for 3D-FISH spot-counting algorithms. Real Time Imaging.
8(3), 203-212.
-
Grigoryan, A. M., & Dougherty, E. R.
(2002).
Automatic counting of illuminated spheres in a random Boolean model. Proceedings of SPIE.
4667(1), 170-180.
-
Hirata Junior, R., Brun, M., Barrera, J., & Dougherty, E. R.
(2002).
Multiresolution Design of Aperture Operators. Journal of Mathematical Imaging and Vision.
16(3), 199-222.
-
Dougherty, E. R., & Barrera, J.
(2002).
Pattern recognition theory in nonlinear signal processing. Journal of Mathematical Imaging and Vision.
16(3), 181-197.
-
Dougherty, E. R., & Astola, J.
(2002).
Untitled. Journal of Mathematical Imaging and Vision.
16(3), 179-180.
-
Shmulevich, I., Dougherty, E. R., Kim, S., & Zhang, W.
(2002).
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics.
18(2), 261-274.
-
Dougherty, E. R., Barrera, J., Brun, M., Kim, S., Cesar, R. M., Chen, Y., Bittner, M., & Trent, J. M.
(2002).
Inference from clustering with application to gene-expression microarrays. Journal of Computational Biology.
9(1), 105-126.
-
Grigoryan, A. M., Dougherty, E. R., Kononen, J., Bubendorf, L., Hostetter, G., & Kallioniemi, O.
(2002).
Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization. Journal of Biomedical Optics.
7(1), 109-122.
-
Kim, S., Dougherty, E. R., Barrera, J., Chen, Y., Bittner, M. L., & Trent, J. M.
(2002).
Strong feature sets from small samples. Journal of Computational Biology.
9(1), 127-146.
-
Sivakumar, K., Balagurunathan, Y., & Dougherty, E. R.
(2001).
Asymptotic joint normality of the granulometric moments. Pattern Recognition Letters.
22(14), 1537-1543.
-
Grigoryan, A. M., & Dougherty, E. R.
(2001).
Bayesian robust optimal linear filters. Signal Processing.
81(12), 2503-2521.
-
Theera-Umpon, N., Dougherty, E. R., & Gader, P. D.
(2001).
Non-homothetic granulometric mixing theory with application to blood cell counting. Pattern Recognition.
34(12), 2547-2560.
-
Dougherty, E. R., & Chen, Y. D.
(2001).
Optimal and adaptive design of logical granulometric filters. Advances in Imaging and Electron Physics.
117(C), 1-71.
-
Dougherty, E. R., & Chen, Y. D.
(2001).
Robust optimal granulometric bandpass filters. Signal Processing.
81(7), 1357-1372.
-
Balagurunathan, Y., Dougherty, E. R., Chen, Y. D., Bittner, M. L., & Trent, J. M.
(2001).
A random signal model for cDNA microarrays. Proceedings of SPIE.
4266, 163-170.
-
Kim, S., Dougherty, E. R., Barrera, J., Chen, Y. D., Bittner, M., & Trent, J. M.
(2001).
Finding robust linear expression-based classifiers. Proceedings of SPIE.
4266, 207-212.
-
Batman, S., & Dougherty, E. R.
(2001).
Morphological granulometric estimation of random patterns in the context of parameterized random sets. Pattern Recognition.
34(6), 1207-1217.
-
Dougherty, E. R., Barrera, J., Brun, M., Kim, S., Cesar, R. M., Chen, Y. D., Bittner, M., & Trent, J. M.
(2001).
Time series inference from clustering. Proceedings of SPIE.
4266, 222-227.
-
Kamat, V. G., & Dougherty, E. R.
(2001).
Bayesian iterative binary filter design. Proceedings of SPIE.
4304, 197-208.
-
Hirata, R., Brun, M., Barrera, .., & Dougherty, E. R.
(2001).
Image restoration by multiresolution nonlinear filters. Proceedings of SPIE.
4304, 256-264.
-
Grigoryan, A. M., & Dougherty, E. R.
(2001).
Morphological slice-based counting of illuminated 3D bodies. Proceedings of SPIE.
4304, 18-24.
-
Kamat, V. G., & Dougherty, E. R.
(2001).
Real-time large-window binary filter design. Proceedings of SPIE.
4303, 89-100.
-
Dougherty, E. R.
(2001).
Small sample issues for microarray-based classification. 2(1), 28-34.
-
Jeanne, M., Marshall, S., & Dougherty, E. R.
(2001).
Design of binary filters by sequential basis expansion. Proceedings of SPIE.
4303, 101-106.
-
Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., ... Sauter, G.
(2001).
Gene-expression profiles in hereditary breast cancer. 344(8), 539-548.
-
Dougherty, E. R., Barrera, J., Mozelle, G., Kim, S., & Brun, M.
(2001).
Multiresolution analysis for optimal binary filters. Journal of Mathematical Imaging and Vision.
14(1), 53-72.
-
Chen, Y., Yakhini, Z., Ben-Dor, A., Dougherty, E., Trent, J. M., & Bittner, M.
(2001).
Analysis of expression patterns: the scope of the problem, the problem of scope. Disease Markers.
17(2), 59-65.
-
Dougherty, E. R.
(2001).
Editorial. Journal of Electronic Imaging.
10(1), 6-6.
-
Grigoryan, A. M., & Dougherty, E. R.
(2001).
Optimization of linear filters under power-spectral-density stabilization. IEEE Transactions on Signal Processing.
49(10), 2292-2300.
-
Hirata, N., Dougherty, E. R., & Barrera, J.
(2000).
Iterative design of morphological binary image operators. Optical Engineering.
39(12), 3106-3123.
-
Dougherty, E. R., Kim, S., & Chen, Y. D.
(2000).
Coefficient of determination in nonlinear signal processing. Signal Processing.
80(10), 2219-2235.
-
Kim, S., Dougherty, E. R., Bittner, M. L., Chen, Y., Sivakumar, K., Meltzer, P., & Trent, J. M.
(2000).
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. Journal of Biomedical Optics.
5(4), 411-424.
-
Barrera, .., Dougherty, E. R., & Brun, M.
(2000).
Hybrid humanmachine binary morphological operator design. An independent constraint approach. Signal Processing.
80(8), 1469-1487.
-
Bittner, M., Meltzer, P., Chen, Y., Jiang, Y., Seftor, E., Hendrix, M., ... Sondak, V.
(2000).
Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature.
406(6795), 536-540.
-
Kamat, V. G., Dougherty, E. R., & Barrera, J.
(2000).
Multiresolution Bayesian design of binary filters. Journal of Electronic Imaging.
9(3), 283-295.
-
Kim, S., Dougherty, E. R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., & Bittner, M.
(2000).
Multivariate measurement of gene expression relationships. Genomics.
67(2), 201-209.
-
Sivakumar, K., Patel, M. J., Kehtarnavaz, N., Balagurunathan, Y., & Dougherty, E. R.
(2000).
A constant-time algorithm for erosions/dilations with application to morphological texture feature computation. Real Time Imaging.
6(3), 223-239.
-
Hirata, N., Dougherty, E. R., & Barrera, J.
(2000).
A switching algorithm for design of optimal increasing binary filters over large windows. Pattern Recognition.
33(6), 1059-1081.
-
Batman, S., Dougherty, E. R., & Sand, F.
(2000).
Heterogeneous morphological granulometries. Pattern Recognition.
33(6), 1047-1057.
-
Hirata, R., Dougherty, E. R., & Barrera, J.
(2000).
Aperture filters. Signal Processing.
80(4), 697-721.
-
Chen, Y., Kamat, V. G., Dougherty, E. R., Bittner, M. L., Meltzer, P. S., & Trent, J. M.
(2000).
Expression ratio statistics and its applications to microarray data analysis. Proceedings of SPIE.
3926, 142-149.
-
Grigoryan, A. M., & Dougherty, E. R.
(1999).
Design and analysis of robust binary filters in the context of a prior distribution for the states of nature. Journal of Mathematical Imaging and Vision.
11(3), 239-254.
-
Handley, J. C., & Dougherty, E. R.
(1999).
Maximum-likelihood estimation and optimal filtering in the nondirectional, one-dimensional binomial germ-grain model. 32(9), 1529-1541.
-
Sand, F., & Dougherty, E. R.
(1999).
Robustness of granulometric moments. 32(9), 1657-1665.
-
Sarca, O. V., Dougherty, E. R., & Astola, J.
(1999).
Two-stage binary filters. Journal of Electronic Imaging.
8(3), 219-232.
-
Chen, Y., Ermolaeva, O., Bittner, M. L., Meltzer, P. S., Trent, J. M., Dougherty, E. R., & Batman, S.
(1999).
Clustering analysis for gene expression data. Proceedings of SPIE.
3602, 422-428.
-
Chen, Y. D., & Dougherty, E. R.
(1999).
Markovian analysis of adaptive reconstructive multiparameter tau-openings. Journal of Mathematical Imaging and Vision.
10(3), 253-267.
-
Baeg, S., Kehtarnavaz, N., & Dougherty, E. R.
(1999).
Morphological texture-based classification of abnormalities in mammograms. Proceedings of SPIE.
3661(II), 1208-1218.
-
Hirata, N., Dougherty, E. R., & Barrera.
(1999).
Efficient switching algorithm for designing increasing binary filters. Proceedings of SPIE.
3646, 185-196.
-
Barrera, .., Dougherty, E. R., & Brun, M.
(1999).
Hybrid human-machine binary morphological operator design. Proceedings of SPIE.
3646, 162-173.
-
Hirata, R., Dougherty, E. R., & Barrera.
(1999).
Optimal range-domain window filters. Proceedings of SPIE.
3646, 38-45.
-
Baeg, S., Batman, S., Dougherty, E. R., Kamat, V. G., Kehtarnavaz, N., Kim, S., ... Shah, R.
(1999).
Unsupervised morphological granulometric texture segmentation of digital mammograms. Journal of Electronic Imaging.
8(1), 65-75.
-
Sarca, O. V., Dougherty, E. R., & Astola, J.
(1998).
Secondarily constrained Boolean filters. Signal Processing.
71(3), 247-263.
-
Handley, J. C., & Dougherty, E. R.
(1998).
Probability distributions for discrete one-dimensional coverage processes. Signal Processing.
69(2), 163-168.
-
Dougherty, E. R., & Chen, Y. D.
(1998).
Logical structural filters. Optical Engineering.
37(6), 1668-1676.
-
Sand, F., & Dougherty, E. R.
(1998).
Asymptotic granulometric mixing theorem: Morphological estimation of sizing parameters and mixture proportions. Pattern Recognition.
31(1), 53-61.
-
Grigoryan, A. M., & Dougherty, E. R.
(1998).
Robustness of optimal binary filters. Journal of Electronic Imaging.
7(1), 117-126.
-
Sinha, D., Sinha, P., Dougherty, E. R., & Batman, S.
(1997).
Design and analysis of fuzzy morphological algorithms for image processing. IEEE transactions on fuzzy systems.
5(4), 570-584.
-
Chen, Y., Dougherty, E. R., & Bittner, M. L.
(1997).
Ratio-based decisions and the quantitative analysis of cDNA microarray images. Journal of Biomedical Optics.
2(4), 364-374.
-
Chen, Y., & Dougherty, E. R.
(1997).
Optimal and adaptive reconstructive granulometric bandpass filters. Signal Processing.
61(1), 65-81.
-
Handley, J. C., & Dougherty, E. R.
(1997).
Maximum-likelihood estimation for the two-dimensional discrete Boolean random set and function models using multidimensional linear samples. Graphical Models and Image Processing.
59(4), 221-231.
-
Batman, S., & Dougherty, E. R.
(1997).
Size distributions for multivariate morphological granulometries: Texture classification and statistical properties. Optical Engineering.
36(5), 1518-1529.
-
Dougherty, E. R.
(1997).
Optimal binary morphological bandpass filters induced by granulometric spectral representation. Journal of Mathematical Imaging and Vision.
7(2), 175-192.
-
Loce, R. P., Dougherty, E. R., Jodoin, R. E., & Cianciosi, M. S.
(1997).
Logically efficient spatial resolution conversion using paired increasing operators. Real Time Imaging.
3(1), 7-16.
-
Barrera, J., Dougherty, E. R., & Tomita, N. S.
(1997).
Automatic programming of binary morphological machines by design of statistically optimal operators in the context of computational learning theory. Journal of Electronic Imaging.
6(1), 54-67.
-
Dougherty, E. R., & CuciureanZapan, C.
(1997).
Optimal reconstructive tau-openings for disjoint and statistically modeled nondisjoint grains. Signal Processing.
56(1), 45-58.
-
Dougherty, E. R.
(1996).
Existence and synthesis of minimal-basis morphological solutions for a restoration-based boundary-value problem. Journal of Mathematical Imaging and Vision.
6(4), 315-333.
-
Dougherty, E. R., Zhang, Y. Q., & Chen, Y. D.
(1996).
Optimal iterative increasing binary morphological filters. Optical Engineering.
35(12), 3495-3507.
-
Cuciurean-Zapan, C., Dougherty, E. R., & Chen, Y.
(1996).
Behavior of adaptive digital erosions. Proceedings of SPIE.
2823, 100-108.
-
Handley, J. C., & Dougherty, E. R.
(1996).
Maximum-likelihood estimation for the discrete Boolean random function. Proceedings of SPIE.
2823, 32-39.
-
Chen, Y. D., & Dougherty, E. R.
(1996).
Adaptive reconstructive tau-openings: Convergence and the steady-state distribution. Journal of Electronic Imaging.
5(3), 266-282.
-
Dougherty, E. R., Chen, Y., & Waks, A.
(1996).
Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In situ hybridization. Pattern Recognition.
29(6), 987-996.
-
Handley, J. C., & Dougherty, E. R.
(1996).
Optimal nonlinear filter for signal-union-noise and runlength analysis in the directional one-dimensional discrete Boolean random set model. Signal Processing.
51(3), 147-166.
-
HANDLEY, J. C., & DOUGHERTY, E. R.
(1996).
Maximumlikelihood estimation for discrete Boolean models using linear samples. Journal of Microscopy.
182(1), 67-78.
-
Dougherty, E. R., & Loce, R. P.
(1996).
Optimal binary differencing filters: design, logic complexity, precision analysis, and application to digital document processing. Journal of Electronic Imaging.
5(1), 66-86.
-
Dougherty, E. R., & Sinha, D.
(1995).
Computational Gray-scale Mathematical Morphology on Lattices (A Comparator-based Image Algebra) Part II: Image Operators. Real Time Imaging.
1(4), 283-295.
-
Dougherty, E. R., & Sinha, D.
(1995).
Computational Gray-scale Mathematical Morphology on Lattices (A Comparator-based Image Algebra) Part 1: Architecture. Real Time Imaging.
1(1), 69-85.
-
Dougherty, E. R., & Handley, J. C.
(1995).
Recursive maximum-likelihood estimation in the one-dimensional discrete Boolean random set model. Signal Processing.
43(1), 1-15.
-
Dougherty, E. R., & Sand, F.
(1995).
Representation of Linear Granulometric Moments for Deterministic and Random Binary Euclidean Images. Journal of Visual Communication and Image Representation.
6(1), 69-79.
-
Sinha, D., & Dougherty, E. R.
(1995).
A general axiomatic theory of intrinsically fuzzy mathematical morphologies. IEEE transactions on fuzzy systems.
3(4), 389-403.
-
Loce, R. P., & Dougherty, E. R.
(1995).
Mean-Absolute-Error Representation and Optimization of Computational-Morphological Filters. Graphical Models and Image Processing.
57(1), 27-37.
-
Haralick, R. M., Katz, P. L., & Dougherty, E. R.
(1995).
Model-Based Morphology: The Opening Spectrum. Graphical Models and Image Processing.
57(1), 1-12.
-
Dougherty, E. R., & Cheng, Y.
(1995).
Morphological pattern-spectrum classification of noisy shapes: Exterior granulometries. Pattern Recognition.
28(1), 81-98.
-
Dougherty, E. R., & Loce, R. P.
(1994).
Precision of morphological-representation estimators for translation-invariant binary filters: Increasing and nonincreasing. Signal Processing.
40(2-3), 129-154.
-
Dougherty, E. R.
(1994).
Minimal representation of -openings via pattern bases. Pattern Recognition Letters.
15(10), 1029-1033.
-
Chen, Y., & Dougherty, E. R.
(1994).
Gray-scale morphological granulometric texture classification. Optical Engineering.
33(8), 2713-2722.
-
Dougherty, E. R., & Sinha, D.
(1994).
Computational mathematical morphology. Signal Processing.
38(1), 21-29.
-
Dougherty, E. R.
(1994).
Optimal mean-absolute-error filtering of gray-scale signals by the morphological hit-or-miss transform. Journal of Mathematical Imaging and Vision.
4(3), 255-271.
-
Haralick, R. M., Dougherty, E., Ha, J., Kanungo, T., Karasu, S., Lee, C. K., ... Phillips, I.
(1994).
Statistical morphology. Journal of Applied Statistics.
21(1-2), 341-354.
-
Kraus, E. J., Heijmans, H., & Dougherty, E. R.
(1993).
Gray-scale granulometries compatible with spatial scalings. Signal Processing.
34(1), 1-17.
-
Mathew, A. V., Dougherty, E. R., & Swarnakar, V.
(1993).
Efficient derivation of the optimal mean-square binary morphological filter from the conditional expectation via a switching algorithm for discrete power-set lattice. Circuits, Systems and Signal Processing.
12(3), 409-430.
-
Bettoli, B., & Dougherty, E. R.
(1993).
Linear granulometric moments of noisy binary images. Journal of Mathematical Imaging and Vision.
3(3), 299-319.
-
Sinha, D., & Dougherty, E. R.
(1993).
Erratum. Fuzzy Sets and Systems.
57(3), 381-381.
-
Sinha, D., & Dougherty, E. R.
(1993).
Fuzzification of set inclusion: Theory and applications. Fuzzy Sets and Systems.
55(1), 15-42.
-
Chen, Y., Dougherty, E. R., Totterman, S. M., & Hornak, J. P.
(1993).
Classification of trabecular structure in magnetic resonance images based on morphological granulometries. Magnetic Resonance in Medicine.
29(3), 358-370.
-
Li, B. o., & Dougherty, E. R.
(1993).
Size-distribution estimation in process fluids by ultrasound for particle sizes in the wavelength range. Optical Engineering.
32(8), 1967-1980.
-
Dougherty, E. R., Haralick, R. M., Chen, Y., Agerskov, C., Jacobi, U., & Sloth, P. H.
(1992).
Estimation of optimal morphological -opening parameters based on independent observation of signal and noise pattern spectra. Signal Processing.
29(3), 265-281.
-
Loge, R. P., & Dougherty, E. R.
(1992).
Optimal morphological restoration: The morphological filter mean-absolute-error theorem. Journal of Visual Communication and Image Representation.
3(4), 412-432.
-
Dougherty, E. R., & Haralick, R. M.
(1992).
Unification of nonlinear filtering in the context of binary logical calculus, part I: Binary filters. Journal of Mathematical Imaging and Vision.
2(2-3), 173-183.
-
Dougherty, E. R.
(1992).
Unification of nonlinear filtering in the context of binary logical calculus, part II: Gray-scale filters. Journal of Mathematical Imaging and Vision.
2(2-3), 185-192.
-
Dougherty, E. R., Newell, J. T., & Pelz, J. B.
(1992).
Morphological texture-based maximum-likelihood pixel classification based on local granulometric moments. Pattern Recognition.
25(10), 1181-1198.
-
Sinha, D., & Dougherty, E. R.
(1992).
Fuzzy mathematical morphology. Journal of Visual Communication and Image Representation.
3(3), 286-302.
-
Dougherty, E. R., & Haralick, R. M.
(1992).
Hole-spectrum representation and model-based optimal morphological restoration of binary images degraded by subtractive noise. Journal of Mathematical Imaging and Vision.
1(3), 257-278.
-
Sand, F., & Dougherty, E. R.
(1992).
Statistics of the morphological pattern-spectrum moments for a random-grain model. Journal of Mathematical Imaging and Vision.
1(2), 121-135.
-
Sand, F., & Dougherty, E. R.
(1992).
Asymptotic normality of the morphological pattern-spectrum moments and orthogonal granulometric generators. Journal of Visual Communication and Image Representation.
3(2), 203-214.
-
Dougherty, E. R., & Zhao, D.
(1992).
Model-based characterization of statistically optimal design for morphological shape recognition algorithms via the hit-or-miss transform. Journal of Visual Communication and Image Representation.
3(2), 147-160.
-
Dougherty, E. R.
(1992).
Euclidean gray-scale granulometries: Representation and umbra inducement. Journal of Mathematical Imaging and Vision.
1(1), 7-21.
-
Dougherty, E. R., & Kraus, E.
(1992).
Morphological pseudoconvolutions: One-parameter families of derived filters with increased invariant classes. Circuits, Systems and Signal Processing.
11(1), 195-228.
-
Weisman, A. D., Dougherty, E. R., Mizes, H. A., & Miller, R.
(1992).
Nonlinear digital filtering of scanningprobemicroscopy images by morphological pseudoconvolutions. Journal of Applied Physics.
71(4), 1565-1578.
-
Dougherty, E. R.
(1992).
Optimal mean-square N-observation digital morphological filters I. Optimal binary filters. CVGIP. Image understanding.
55(1), 36-54.
-
Dougherty, E. R.
(1992).
Optimal mean-square N-observation digital morphological filters II. Optimal gray-scale filters. CVGIP. Image understanding.
55(1), 55-72.
-
Dougherty, E. R., & Kraus, E. J.
(1991).
Shape Analysis and Reduction of the Morphological Basis for Digital Moving-Average Filters. SIAM Journal on Applied Mathematics.
51(6), 1764-1781.
-
Dougherty, E. R.
(1991).
Application of the Hausdorff metric in gray-scale mathematical morphology via truncated umbrae. Journal of Visual Communication and Image Representation.
2(2), 177-187.
-
Dougherty, E. R., Pelz, J. B., & Marsh, D. G.
(1990).
Morphological Granulometric Analysis Of Electrophotographic Images. Proceedings of SPIE.
1153, 387-399.
-
Dougherty, E. R., & Sehdev, P.
(1989).
Implementation of the umbra transform in the SLIP image processing language. Technical Paper - Society of Manufacturing Engineers. MS.
-
Dougherty, E. R., & Pelz, J. B.
(1989).
Pixel Classification By Morphologically Derived Texture Features. Proceedings of SPIE.
1199, 440-449.
-
Dougherty, E. R., & Giardina, C. R.
(1988).
Universal Systolic Architecture For Morphological And Convolutional Image Filters. Proceedings of SPIE.
1001, 739-746.
-
Dougherty, E. R., & Giardina, C. R.
(1987).
Error Bounds for Morphologically Derived Measurements. SIAM Journal on Applied Mathematics.
47(2), 425-440.
-
Imani, M., Dougherty, E. R., & Braga-Neto, U.
(2020).
Boolean Kalman filter and smoother under model uncertainty. Automatica.
111, 108609-108609.
-
book
-
Braga-Neto, U. M., & Dougherty, E. R.
(2015).
Error Estimation for Pattern Recognition. John Wiley & Sons, Inc..
-
Shmulevich, I., & Dougherty, E. R.
(2014).
Genomic signal processing
-
Dougherty, E. R., & Bittner, M. L.
(2011).
Epistemology of the Cell. Wiley.
-
Hirata, R., Brun, M., Barrera, J., & Dougherty, E. R.
(2006).
Aperture filters: Theory, application, and multiresolution analysis. Ed. 6.
-
Braga-Neto, U. M., & Dougherty, E. R.
(2015).
Error Estimation for Pattern Recognition. John Wiley & Sons, Inc..
-
chapter
-
Hua, J., Sima, C., Cypert, M., Dougherty, E. R., Trent, J. M., & Bittner, M. L.
(2017).
Dynamical Analysis of Drug Efficacy and Mechanism of Action Using GFP Reporters. Biometrics.
(pp. 1145-1174).
IGI Global.
-
Huang, Y., & Dougherty, E. R.
(2008).
Probabilistic Boolean Networks as Models for Gene Regulation. ANALYSIS OF MICROARRAY DATA: A NETWORK-BASED APPROACH.
(pp. 205-242).
Wiley.
-
Datta, A., Choudhary, A., Bittner, M. L., & Dougherty, E. R.
(2008).
Modeling and Control in Cancer Genomics. MODELING AND CONTROL OF COMPLEX SYSTEMS.
(pp. 339-365).
-
Dougherty, E. R., & Attoor, S. N.
(2006).
Design Issues and Comparison of Methods for Microarray-Based Classification. Computational and Statistical Approaches to Genomics.
(pp. 119-136).
Springer Nature.
-
Chen, Y., Dougherty, E. R., Bittner, M. L., Meltzer, P., & Trent, J.
(2006).
Microarray Image Analysis and Gene Expression Ratio Statistics. Computational and Statistical Approaches to Genomics.
(pp. 1-19).
Springer Nature.
-
Suh, E. B., Dougherty, E. R., Kim, S., Bittner, M. L., Chen, Y., Russ, D. E., & Martino, R. L.
(2006).
Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene Expression Relations. Computational and Statistical Approaches to Genomics.
(pp. 297-310).
Springer Nature.
-
Shmulevich, I., & Dougherty, E. R.
(2003).
Nonlinear Signal and Image Processing. Barner, K. E., & Arce, G. R. (Eds.),
Nonlinear Signal and Image Processing: Theory, Methods, and Applications.
(pp. 507-524).
CRC Press.
-
Hua, J., Sima, C., Cypert, M., Dougherty, E. R., Trent, J. M., & Bittner, M. L.
(2017).
Dynamical Analysis of Drug Efficacy and Mechanism of Action Using GFP Reporters. Biometrics.
(pp. 1145-1174).
IGI Global.
-
conference paper
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
Robust Smoothing for State-Space Models with Unknown Noise Statistics. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1024-1028.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2017).
CLASSIFICATION OF GAUSSIAN TRAJECTORIES WITH MISSING DATA IN BOOLEAN GENE REGULATORY NETWORKS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
1078-1082.
-
Karbalayghareh, A., Braga-Neto, U., & Dougherty, E. R.
(2017).
Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks. 766-767.
-
Dehghannasiri, R., Esfahani, M. S., & Dougherty, E. R.
(2016).
A Bayesian Framework for Robust Kalman Filtering Under Uncertain Noise Statistics. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1545-1549.
-
Xue, D., Balachandran, P. V., Yuan, R., Hu, T., Qian, X., Dougherty, E. R., & Lookman, T.
(2016).
Accelerated search for BaTiO3-based piezoelectrics with vertical morphotropic phase boundary using Bayesian learning. Proceedings of the National Academy of Sciences of the United States of America.
13301-13306.
-
Coveney, P. V., Dougherty, E. R., & Highfield, R. R.
(2016).
Big data need big theory too. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
20160153-20160153.
-
Kim, E., Ivanov, I., Hua, J., Chapkin, R. S., & Dougherty, E. R.
(2016).
Model-based study of the Effectiveness of Reporting Lists of Small Feature Sets using RNA-Seq Data. 470-471.
-
Dehghannasiri, R., Esfahani, M. S., & Dougherty, E. R.
(2016).
Inference of Nonlinear ODE-Based Gene Regulatory Networks via Intrinsically Bayesian Robust Kalman Filtering. 542-543.
-
Oduola, W., Li, X., Duan, C., Qian, L., Wu, F., & Dougherty, E. R.
(2016).
Analysis and Control of Genetic Regulatory Systems with Switched Drug Inputs. 533-536.
-
Mohsenizadeh, D. N., Dehghannasiri, R., & Dougherty, E. R.
(2016).
Optimal Dynamics Uncertainty Reduction in Gene Networks in the Presence of Experimental Error. 581-582.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2016).
OPTIMAL EXPERIMENTAL DESIGN IN CANONICAL EXPANSIONS WITH APPLICATIONS TO SIGNAL COMPRESSION. 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP).
94-98.
-
Dalton, L. A., & Dougherty, E. R.
(2016).
Small-Sample Classification. Springer Series in Materials Science.
77-101.
-
Dougherty, E. R., Dalton, L. A., & Alexander, F. J.
(2015).
Small Data Is the Problem. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
418-422.
-
Mohsenizadeh, D. N., Dehghannasiri, R., & Dougherty, E. R.
(2015).
An experimental design to reduce dynamics uncertainty in genomic networks. 644-645.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2015).
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
938-950.
-
Marshall, S., & Dougherty, E. R.
(2015).
New challenges in non-linear signal and image processing. European Signal Processing Conference.
1883-1886.
-
Li, X. L., Ogedengbe, S., Qian, L., & Dougherty, E. R.
(2014).
SENSITIVITY ANALYSIS FOR DRUG EFFECT STUDY: AN NF - kappa B PATHWAY EXAMPLE. 1418-1421.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2014).
Computationally Efficient Experimental Design Strategy for Reducing Gene Network Uncertainty. 1380-1381.
-
Esfahani, M. S., & Dougherty, E. R.
(2014).
Incorporation of Biological Pathway Knowledge in the Construction of Priors for Optimal Bayesian Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
202-218.
-
Zollanvari, A., & Dougherty, E. R.
(2013).
Application of Double Asymptotics and Random Matrix Theory in Error Estimation of Regularized Linear Discriminant Analysis. 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP).
57-59.
-
Qian, L., Li, X., & Dougherty, E.
(2013).
Robust Identification of Molecularly Targeted Drug Effect Coefficient using $H_{infty}$ Filter. 99-102.
-
Dalton, L. A., Benalcazar, M. E., Brun, M., & Dougherty, E. R.
(2013).
Bayes Clustering Operators for Known Random Labeled Point Processes. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
893-897.
-
Knight, J., Ivanov, I., & Dougherty, E.
(2013).
Bayesian Multivariate Poisson Model for RNA-Seq Classification. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
96-97.
-
Yousefi, M. R., & Dougherty, E. R.
(2013).
Bayesian Optimal Control of Markovian Genetic Regulatory Networks. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
980-984.
-
Li, X. L., Qian, L., Bittner, M. L., & Dougherty, E. R.
(2013).
DRUG EFFECT STUDY ON PROLIFERATION AND SURVIVAL PATHWAYS ON CELL LINE-BASED PLATFORM: A STOCHASTIC HYBRID SYSTEMS APPROACH. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
54-57.
-
Esfahani, M. S., & Dougherty, E. R.
(2013).
Effect of Separate Sampling on Classification and the Minimax Criterion. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
72-73.
-
Qian, X., & Dougherty, E. R.
(2013).
PHENOTYPICALLY CONSTRAINED BOOLEAN NETWORK INFERENCE WITH PRESCRIBED STEADY STATES. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
82-83.
-
Zollanvari, A., & Dougherty, E. R.
(2013).
Random Matrix Theory in Pattern Classification: An Application to Error Estimation. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
884-887.
-
Esfahani, M. S., & Dougherty, E. R.
(2013).
Sample-Based Prior Probability Construction Using Biological Pathway Knowledge. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1405-1409.
-
Zollanvari, A., Hua, J., & Dougherty, E. R.
(2013).
PERFORMANCE OF LINEAR DISCRIMINANT ANALYSIS IN STOCHASTIC SETTINGS. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
3437-3441.
-
Dehghannasiri, R., Yoon, B., & Dougherty, E. R.
(2013).
Designing Experiments for Optimal Reduction of Uncertainty in Gene Regulatory Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
88-89.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Effect of Mixing Probabilities on the Bias of Cross-Validation Under Separate Sampling. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
98-99.
-
Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2013).
Improved Branch-and-Bound Algorithm for U-Curve Optimization. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
100-101.
-
Dalton, L., & Dougherty, E. R.
(2012).
Optimal Bayesian Classification and Its Application to Gene Regulatory Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
164-167.
-
Yousefi, M. R., Datta, A., & Dougherty, E. R.
(2012).
Optimal Therapeutic Methods with Random-Length Response in Probabilistic Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
50-53.
-
Li, X., Qian, L., Hua, J., Bittner, M. L., & Dougherty, E. R.
(2012).
Assessing the efficacy of molecularly targeted agents on cell line-based platforms by using system identification. BMC GENOMICS.
S11.
-
Yousefi, M. R., Datta, A., & Dougherty, E. R.
(2012).
OPTIMAL CANCER THERAPY BASED ON A TUMOR GROWTH INHIBITION MODEL. 568-571.
-
Dalton, L. A., & Dougherty, E. R.
(2012).
OPTIMAL CLASSIFIERS WITHIN A BAYESIAN FRAMEWORK. 564-567.
-
Meskin, N., Nounou, H., Nounou, M., Datta, A., & Dougherty, E. R.
(2012).
Output-Feedback Model Predictive Control of Biological Phenomena Modeled by S-Systems. Proceedings of the ... American Control Conference. American Control Conference.
1979-1984.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2012).
STRUCTURAL INTERVENTION OF GENE REGULATORY NETWORKS BY GENERAL RANK-K MATRIX PERTURBATION. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
729-732.
-
Li, X., Qian, L., Bittner, M. L., & Dougherty, E. R.
(2011).
Assessing the Efficacy of Molecularly Targeted Agents by Using Kalman Filter. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
50-51.
-
Dalton, L., Dougherty, E. R., Dougherty, E. R., & Dougherty, E. R.
(2011).
Classifier Error Estimator Performance in a Bayesian Context. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
135-138.
-
Layek, R., Datta, A., Bittner, M., & Dougherty, E. R.
(2011).
Combination Therapy Design for Cancer: A Digital Systems Approach. Proceedings of the ... IEEE Conference on Decision & Control / IEEE Control Systems Society. IEEE Conference on Decision & Control.
4377-4382.
-
Hsu, F., Serpedin, E., Hsiao, T., Bishop, A., Douzherty, E. R., & Chen, Y.
(2011).
Identifying Genes Associated with Chemotherapy Response in Ovarian Carcinomas Based on DNA Copy Number and Expression Profiles. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
46-49.
-
Yousefi, M. R., Datta, A., & Doughrty, E. R.
(2011).
Modeling Cyclic and Acyclic Therapeutic Methods with Persistent Intervention Effect in Probabilistic Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
38-41.
-
Meskin, N., Nounou, H., Nounou, M., Datta, A., & Dougherty, E. R.
(2011).
Parameter Estimation of Biological Phenomena Modeled by S-systems: An Extended Kalman Filter Approach. Proceedings of the ... IEEE Conference on Decision & Control / IEEE Control Systems Society. IEEE Conference on Decision & Control.
4424-4429.
-
Zhao, C., Ivanov, I., Bittner, M. L., & Dougherty, E. R.
(2011).
Pathway Analysis in the Context of Bayesian Networks Mathematical Modeling of Master and Canalizing Genes. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
64-65.
-
Hsu, F., Serpedin, E., Chen, Y., & Dougherty, E. R.
(2011).
Stochastic Modeling of Dynamic Effects of Copy Number Alterations upon Gene Expression Levels. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
83-86.
-
Qian, X., Yoon, B., & Dougherty, E. R.
(2011).
UNCERTAINTY-BASED ESSENTIALITY IN GENE REGULATORY NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
17-20.
-
Dalton, L., & Dougherty, E. R.
(2011).
Exact MSE Performance of the Bayesian MMSE Estimator for Classification Error. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
997-1001.
-
Yousefi, M. R., Datta, A., & Dougherty, E. R.
(2011).
Optimal Intervention Strategies for Cyclic Therapeutic Methods with Fixed-Length Duration of Effect. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1007-1011.
-
Meskin, N., Nounou, H., Nounou, M., Datta, A., & Dougherty, E. R.
(2011).
Intervention in Biological Phenomena Modeled by S-Systems: A Model Predictive Control Approach. Proceedings of the ... American Control Conference. American Control Conference.
3519-3523.
-
Zhang, Z., Sun, Y., Braga-Neto, U., Dougherty, E., & Zhang, J.
(2011).
A parallel programming framework with Markovian messaging for LC-MS peptide detection. 1057-1059.
-
Esfahani, M. S., Zollanvari, A., Yoon, B., & Dougherty, E. R.
(2011).
Designing Enhanced Classifiers Using Prior Process Knowledge: Regularized Maximum-Likelihood. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
91-94.
-
Sun, Y., Ulisses, B., & Dougherty, E. R.
(2011).
Modeling and systematic analysis of LC-MS proteomics pipeline. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
112-116.
-
Atashpaz-Gargari, E., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Multiple Reaction Monitoring: Modeling and Systematic Analysis. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
105-107.
-
Atashpaz-Gargari, E., Sima, C., Braga-Neto, U. M., & Dougherty, E. R.
(2011).
Relationship between the accuracy of classifier error estimation and distribution complexity. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
147-149.
-
Layek, R., Datta, A., & Dougherty, E. R.
(2010).
From Biological Pathways to Regulatory Networks. Proceedings of the ... IEEE Conference on Decision & Control / IEEE Control Systems Society. IEEE Conference on Decision & Control.
5781-5786.
-
Qian, X., & Dougherty, E. R.
(2010).
A COMPARATIVE STUDY ON SENSITIVITIES OF BOOLEAN NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Dalton, L. A., & Dougherty, E. R.
(2010).
BAYESIAN MMSE ESTIMATION OF CLASSIFICATION ERROR AND PERFORMANCE ON REAL GENOMIC DATA. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Zhao, C., Ivanov, I., Shah, M., Davidson, L. A., Chapkin, R. S., & Dougherty, E. R.
(2010).
CONDITIONING-BASED MODEL FOR THE REGULATORY ACTIVITIES OF microRNAs IN SPECIFIC DIETARY CONTEXTS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Yousefi, M. R., Hua, J., Chao, S., & Dougherty, E. R.
(2010).
EFFECTS OF PARTIAL REPORTING OF CLASSIFICATION RESULTS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Li, X., Qian, L., & Dougherty, E. R.
(2010).
Modeling treatment and drug effects at the molecular level using hybrid system theory. 1-7.
-
Zollanvari, A., Braga-Neto, U. M., & Dougherty, E. R.
(2010).
RMS BOUNDS AND SAMPLE SIZE CONSIDERATIONS FOR ERROR ESTIMATION IN LINEAR DISCRIMINANT ANALYSIS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-4.
-
Ghaffari, N., Ivanov, I., & Dougherty, E.
(2009).
A COD BASED REDUCTION ALGORITHM FOR BOOLEAN AND PROBABILISTIC BOOLEAN NETWORKS. 1-2.
-
Qian, X., & Dougherty, E. R.
(2009).
CONTROL-COMPATIBLE STATE REDUCTION FOR BOOLEAN NETWORKS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
41-42.
-
Vahedi, G., Shmulevich, I., Liu, W., & Dougherty, E.
(2009).
CRITICAL BOOLEAN NETWORKS REQUIRE MINIMAL INTERVENTION RATE. 1-2.
-
Pal, R., Datta, A., & Dougherty, E.
(2009).
QUANTIFICATION OF DATA EXTRACTION NOISE IN PROBABILISTIC BOOLEAN NETWORK MODELING. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
9-+.
-
Vu, T. T., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
BAGGING DEGRADES THE PERFORMANCE OF LINEAR DISCRIMINANT CLASSIFIERS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
78-79.
-
Sima, C., Vu, T., Braga-Neto, U. M., & Dougherty, E. R.
(2009).
BOLSTERED ERROR ESTIMATOR WITH FEATURE SELECTION. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
17-+.
-
Faryabi, B., Vahedi, G., Chamberland, J., Datta, A., & Dougherty, E. R.
(2009).
OPEN-LOOP FEEDBACK INTERVENTION: CONTROL OF GENE REGULATORY NETWORKS WITH UNMEASURABLE CONTEXT. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
19-20.
-
Zollanvari, A., Braga-Neto, M. M., & Dougherty, E. R.
(2009).
SAMPLE SIZE CALCULATION FROM SPECIFIED RMS OF THE RESUBSTITUTION ERROR FOR LINEAR CLASSIFIERS. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
76-77.
-
Wang, H., Qian, L., & Dougherty, E. R.
(2009).
Steady-state Analysis of Genetic Regulatory Networks Modeled by Nonlinear Ordinary Differential Equations. 1-4.
-
Layek, R., Datta, A., Pal, R., & Dougherty, E. R.
(2009).
Adaptive Intervention in Probabilistic Boolean Networks. Proceedings of the ... American Control Conference. American Control Conference.
5647-+.
-
Qian, X., & Dougherty, E. R.
(2008).
A New Sensitivity Measure for Probabilistic Boolean Networks based on Steady-State Distributions. 136-139.
-
Brun, M., Xu, Q., & Dougherty, E. R.
(2008).
A criterion for choosing between full-sample and hold-out classifier design. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
30-+.
-
Qian, X., & Dougherty, E. R.
(2008).
Analytic formulation of optimal structural intervention strategies in Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Choudhary, A., Hua, J., Bittner, M. L., & Dougherty, E. R.
(2008).
CLASSIFICATION PERFORMANCE ON A POPULATION WITH CONTEXTS. 1-2.
-
Pal, R., Datta, A., & Dougherty, E.
(2008).
Comparison of robust strategies for the control of gene regulatory networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
55-+.
-
Hua, J., Tembe, W., & Dougherty, E. R.
(2008).
Feature selection in the classification of high-dimension data. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
39-+.
-
Vahedi, G., Faryabi, B., Chamberland, J., Datta, A., & Dougherty, E. R.
(2008).
Mean first-passage time control policy versus reinforcement-learning control policy in gene regulatory networks. Proceedings of the ... American Control Conference. American Control Conference.
1394-1399.
-
Pal, R., Lahdesmaki, H., Shmulevich, I., Yli-Harja, O., & Dougherty, E.
(2008).
ON THE CONSTRAINT OF GENE REGULATORY NETWORKS TO CANALIZING FUNCTIONS AND POST CLASSES. 1-2.
-
Faryabi, B., Chamberland, J., Vahedi, G., Datta, A., & Dougherty, E. R.
(2008).
Optimal intervention in semi-Markov-based asynchronous genetic regulatory networks. Proceedings of the ... American Control Conference. American Control Conference.
1388-1393.
-
Ghaffari, N., Ivanov, I., & Dougherty, E.
(2008).
REDUCTION MAPPINGS AND CONTROL POLICIES FOR INTERVENTION IN BOOLEAN NETWORKS. 1-2.
-
Sima, C., & Dougherty, E. R.
(2008).
THE PEAKING PHENOMENON REVISITED: THE CASE WITH FEATURE SELECTION. 1-2.
-
Zhao, W., Agyepong, K., Serpedin, E., & Dougherty, E. R.
(2008).
Identifying Drosophila cell-cycle regulated genes from irregular microarray data. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
633-636.
-
Faryabi, B., Vahedi, G., Chamberland, J., Datta, A., & Dougherty, E. R.
(2008).
Constrained intervention in a cancerous mammalian cell cycle network. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
51-52.
-
Vahedi, G., Faryabi, B., Chamberland, J., Datta, A., & Dougherty, E.
(2008).
Modeling cyclic therapy in gene regulatory networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
53-54.
-
Martins-D, C. J., Braga-Neto, U., Bittner, M. L., & Dougherty, E. R.
(2008).
Network properties of intrinsically multivariate predictive genes. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
9-+.
-
Vu, T. T., Braga-Neto, U., & Dougherty, E. R.
(2008).
Preliminary study on bolstered error estimation in high-dimensional spaces. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
110-111.
-
Ivanov, I., Vahedi, G., & Dougherty, E.
(2007).
Constrained Reduction Mapping for a Class of Network Models of Genomic Regulation. 192-195.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2007).
Robust intervention in Probabilistic Boolean Networks. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
29-+.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2007).
Bayesian robustness in the control of gene regulatory networks. 31-35.
-
Ranczar, B., Hua, B. J., & Dougherty, E. R.
(2007).
Is there correlation between the estimated and true classification errors in small-sample settings?. 16-+.
-
Wang, H., Qian, L., & Dougherty, E.
(2007).
Modeling Genetic Regulatory Networks by Sigmoidal Functions: A Joint Genetic Algorithm and Kalman Filtering Approach. 324-328.
-
Faryabi, B., Datta, A., & Dougherty, E. R.
(2007).
On reinforcement learning in genetic regulatory networks. 11-15.
-
Vahedi, G., Datta, A., & Dougherty, E. R.
(2007).
Which control gene should be used in genetic regulatory networks?. 6-10.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2007).
Robust Intervention in Probabilistic Boolean Networks. Proceedings of the ... American Control Conference. American Control Conference.
2405-2410.
-
Yin, Y., Huang, Y., Shanmugam, V., Brun, M., Hua, J., & Dougherty, E. R.
(2007).
A Bayesian Approach for Uncovering Gene Network Motifs. 1-2.
-
Vahedi, G., Ivanov, I., & Dougherty, E. R.
(2007).
Bidirectional relationships and attractor structure of Boolean networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
7-+.
-
Marshall, S., Yu, L., Xiao, Y., & Dougherty, E. R.
(2007).
Effect of parameter variations on the inference of context-sensitive Probabilistic Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
99-+.
-
Kim, S., Roy, I., Raghavan, S., Dougherty, E. R., & Bittner, M.
(2007).
Learning Context-Specific Gene Regulatory Networks via In-Silico Conditioning. 1-4.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2007).
Recovering genetic regulatory networks by integrating multiple data sources. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
1-2.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2007).
Robustness of intervention strategies for probabilistic Boolean networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
87-90.
-
Zhao, W., Agyepong, K., Serpedin, E., & Dougherty, E. R.
(2007).
Reconstruction of Genetic Regulatory Networks Based on the Posterior Probabilities of Gene Regulations. Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing / sponsored by the Institute of Electrical and Electronics Engineers Signal Processing Society. ICASSP (Conference).
i-357-i-360-360.
-
Choudhary, A., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2006).
Optimal Control in a Family of Boolean Networks. IEEE Conference on Decision and Control.
4200-4205.
-
Ivanov, I., Pal, R., & Dougherty, E.
(2006).
Applying Reduction Mappings in Designing Genomic Regulatory Networks. 1-2.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2006).
Inferring the Structure of Genetic Regulatory Networks Using Information Theoretic Tools. 1-2.
-
Taverna, D. M., Brun, M., Dougherty, E. R., & Chen, Y.
(2006).
Quality-Based Distance Measures and Applications to Clustering. 1-2.
-
Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Joshipura, K., ... Stephan, D. A.
(2006).
SNiPer 500K: A Novel SNP Genotype Calling Algorithm. 1-2.
-
Xu, Q., Hua, J., Xiong, Z., Bittner, M. L., & Dougherty, E. R.
(2006).
Accuracy of differential expression detection with compressed microarray images. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
43-+.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2006).
Altering steady-state probabilities in Probabilistic Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
75-+.
-
Ruusuvuori, P., Yli-Harja, O., Sima, C., & Dougherty, E. R.
(2006).
Classification of quantized small sample data. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
93-+.
-
Xu, Q., Hua, J., Xiong, Z., Suh, E., & Dougherty, E. R.
(2006).
Conditional confidence intervals for the true classification error. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
97-+.
-
Choudhary, A., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2006).
Control in a family of Boolean networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
15-+.
-
Hua, J., Balagurunathan, Y., Chen, Y., Lowey, D., Bittner, M. L., Xiong, Z., Suh, E., & Dougherty, E. R.
(2006).
Effect of normalization on microarray-based classification. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
7-+.
-
Xiao, Y., Hua, J., & Dougherty, E. R.
(2006).
Feature selection increases cross-validation imprecision. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
17-+.
-
Wang, H., Qian, L., & Dougherty, E.
(2006).
Inference of Gene Regulatory Networks Using Genetic Programming and Kalman Filter. 27-28.
-
Zhao, W., Serpedin, E., & Dougherty, E. R.
(2006).
Information theoretic inference of direct gene regulation from time series data. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
5-+.
-
Ivanov, I., Pal, R., & Dougherty, E. R.
(2006).
Reducing the complexity of a PBN while preserving its dynamical structure. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
77-+.
-
Pal, R., Ivanov, I., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2006).
Synthesizing Boolean networks with a given attractor structure. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
73-+.
-
Marshall, S., Yu, L., Xiao, Y., & Dougherty, E. R.
(2006).
Temporal inference of Probabilistic Boolean Networks. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
71-+.
-
Sima, C., & Dougherty, E. R.
(2006).
What can we expect from high-dimensional feature selection. IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.
91-+.
-
Pal, R., Datta, A., & Dougherty, E. R.
(2006).
Optimal infinite horizon control for probabilistic Boolean networks. Proceedings of the ... American Control Conference. American Control Conference.
668-+.
-
Brun, M., & Dougherty, E. R.
(2005).
Clustering algorithms do not learn, but they can be learned. Proceedings of SPIE.
59160t-59160t-9-9.
-
Choudhary, A., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2005).
Assignment of terminal penalties in controlling genetic regulatory networks. Proceedings of the ... American Control Conference. American Control Conference.
417-422.
-
Pal, R., Datta, A., Bittner, M. L., & Dougherty, E. R.
(2005).
External control in a special class of Probabilistic Boolean Networks. Proceedings of the ... American Control Conference. American Control Conference.
411-416.
-
Zhou, X. B., Wang, X. D., & Dougherty, E. R.
(2004).
A Bayesian approach to nonlinear probit gene selection and classification. Journal of the Franklin Institute.
137-156.
-
Datta, A., Choudhary, A., Bittner, M. L., & Dougherty, E. R.
(2003).
Application of dynamic programming in genetic regulatory networks. IEEE Conference on Decision and Control.
2817-2822.
-
Datta, A., Choudhary, A., Bittner, M. L., & Dougherty, E. R.
(2003).
External control in Markovian Genetic Regulatory Networks. Proceedings of the ... American Control Conference. American Control Conference.
3614-3619.
-
Brun, M., Balagurunathan, Y., Barrera, J., & Dougherty, E. R.
(2002).
Clustering granulometric features. Proceedings of SPIE.
36-42.
-
Balagurunathan, Y., Hashimoto, R. F., Kim, S., Barrera, J., & Dougherty, E. R.
(2002).
Granulometric classifiers from small samples. Proceedings of SPIE.
100-107.
-
Armelin, H. A., Barrera, .., Dougherty, E. R., Ferreira, J. E., Gubitoso, M. D., Hirata, N., & Neves, E. J.
(2001).
Simulator for gene expression networks. Proceedings of SPIE.
248-259.
-
Barrera, .., Dougherty, E. R., Gubitoso, M. D., & Hirata, N.
(2001).
Modeling temporal morphological systems via lattice dynamical systems. Proceedings of SPIE.
265-276.
-
Dougherty, E. R., & Barrera, J.
(2001).
Nonlinear filtering and pattern recognition: Are they the same?. Proceedings of SPIE.
1-6.
-
Dumitrescu, B., Tbu, I., Peltonen, S., Astola, J., & Dougherty, E.
(2001).
Efficient Design of Minmax Odif Robust Stack Filters. 44-47.
-
Brun, M., Hirata, R., Barrera, .., & Dougherty, E. R.
(2001).
Hybrid Human-machine Non-linear Filter Design Using Envelopes. Brazilian Symposium of Computer Graphic and Image Processing.
106-111.
-
Balagurunathan, Y., & Dougherty, E. R.
(2000).
Estimation of random-model parameters via linear systems with granulometric inputs. Proceedings of SPIE.
11-15.
-
Grigoryan, A. M., Dougherty, E. R., Bubendorf, L., Kononen, J., & Kallioniemi, O.
(2000).
Rapid analysis of gene copy numbers by FISH and automated spot counting from stacked confocal images. Proceedings of SPIE.
96-107.
-
Kim, S. C., Dougherty, E. R., Bittner, M. L., Chen, Y. D., Sivakumar, K., Meltzer, P., & Trent, J. M.
(2000).
Automated analysis of multivariate nonlinear gene relations based on cDNA microarray expression data. 150-155.
-
Kamat, V. G., Dougherty, E. R., & Barrera, J.
(2000).
Bayesian multiresolution filter design. Proceedings of SPIE.
22-33.
-
Hirata, R., Dougherty, E. R., & Barrera, J.
(2000).
Design of gray-scale nonlinear filters via multiresolution apertures. European Signal Processing Conference.
-
Barrera, J., & Dougherty, E. R.
(2000).
Design of statistically optimal morphological operators. European Signal Processing Conference.
-
Grigoryan, A. M., Agaian, S. S., & Dougherty, E. R.
(2000).
Fibonacci thresholding, signal representation and morphological filters. European Signal Processing Conference.
-
Dougherty, E. R., Barrera, J., Mozelle, G., Kim, S. C., & Brun, M.
(2000).
Multiresolution filter design. Proceedings of SPIE.
12-21.
-
Dougherty, E. R.
(2000).
Parametric design of nonlinear optimal filters. European Signal Processing Conference.
-
Sabbagh, D. L., & Dougherty, E. R.
(2000).
Small-sample estimation of the error of the optimal binary filter. European Signal Processing Conference.
-
Dougherty, E. R., & Chen, Y. D.
(1999).
Robust openings in the context of a prior distribution governing the parameters of the random set model. Proceedings of SPIE.
57-65.
-
Hirata, N., Barrera, J., & Dougherty, E. R.
(1999).
Design of statistically optimal stack filters. 265-274.
-
Dougherty, E. R.
(1999).
The granulometric size density in filter optimization. 257-264.
-
Dougherty, E. R., & Astola, J. T.
(1998).
Erratum: (Nonlinear Image Processing IX (26-27 January 1998)). Proceedings of SPIE.
323.
-
Hirata, N., Dougherty, E. R., & Barrera.
(1998).
Design of large-window binary filters via iteration. Proceedings of SPIE.
173-182.
-
Popov, A. T., & Dougherty, E. R.
(1998).
Fuzzy adaptive Voronoi-diagram-based clustering of textured images. Proceedings of SPIE.
286-292.
-
Balagurunathan, Y., & Dougherty, E. R.
(1998).
Morphological measurement of surface roughness. Proceedings of SPIE.
95-103.
-
Chen, Y., & Dougherty, E. R.
(1998).
Adaptive design of logical structure filters. Proceedings of SPIE.
43-51.
-
Dougherty, E. R., Grigoryan, A. M., Barrera, J., & Hirata, N.
(1998).
Binary filter design: Optimization, prior information, and robustness. Proceedings of SPIE.
230-241.
-
Kim, S., Batman, S., & Dougherty, E. R.
(1998).
Fast run-length-based algorithm for one-dimensional flat opening. Proceedings of SPIE.
158-163.
-
Patel, M. J., Kehtarnavaz, N., Dougherty, E. R., Batman, S., Sivakumar, K., & Popov, A. T.
(1998).
Computation of morphological texture features for medical imaging applications. Proceedings of SPIE.
192-201.
-
Grigoryan, A. M., & Dougherty, E. R.
(1998).
Designing robust binary filters. Proceedings of SPIE.
14-24.
-
Sarca, O. V., Dougherty, E. R., & Astola, J. T.
(1998).
Optimal binary filters with linearly separable preprocessing. Proceedings of SPIE.
25-35.
-
Chen, Y., & Dougherty, E. R.
(1998).
Queueing interpretation of adaptive reconstructive multiparameter -opening filters. Proceedings of SPIE.
59-65.
-
Dougherty, E. R.
(1998).
Binary filter estimation for large windows. 20-27.
-
Baeg, S., Popov, A. T., Kamat, V. G., Batman, S., Sivakumar, K., Kehtarnavaz, N., Dougherty, E. R., & Shah, R. B.
(1998).
Segmentation of mammograms into distinct morphological texture regions. Proceedings / IEEE International Symposium on Computer-Based Medical Systems. IEEE International Symposium on Computer-Based Medical Systems.
20-25.
-
Handley, J. C., & Dougherty, E. R.
(1997).
Comparative analysis of discrete and continuous Boolean models. Proceedings of SPIE.
210-219.
-
Sarca, O. V., Astola, J. T., & Dougherty, E. R.
(1997).
New training method for linear separable threshold Boolean filters. Proceedings of SPIE.
23-34.
-
Dougherty, E. R., & Grigoryan, A. M.
(1997).
Robustness of optimal binary filters for sparse noise. Proceedings of SPIE.
130-137.
-
Dougherty, E. R., Chen, Y. D., Batman, S., & Bittner, M. L.
(1997).
Digital measurement of gene expression in a cDNA micro-array. Proceedings of SPIE.
68-73.
-
Zhang, Y., Loce, R. P., & Dougherty, E. R.
(1997).
Document restoration and enhancement using optimal iterative and paired morphological filters. Proceedings of SPIE.
109-123.
-
Dougherty, E. R., & Barrera.
(1996).
Morphological paradigm for loss-function-based design of digital filters. Proceedings of SPIE.
90-97.
-
Swarnakar, V., Mathew, A. V., Dougherty, E. R., & Sibata, C. H.
(1996).
Optimal restoration of compressed biomedical images: a discrete lattice theoretic approach. Proceedings of SPIE.
468-476.
-
Batman, S., & Dougherty, E. R.
(1996).
Granulometric estimation of distorted shapes. Proceedings of SPIE.
60-69.
-
Handley, J. C., & Dougherty, E. R.
(1996).
Maximum-likelihood estimation for the two-dimensional discrete Boolean model using cross-windowed observations. Proceedings of SPIE.
49-59.
-
Dougherty, E. R., Handley, J. C., & Chen, Y.
(1995).
Texture-region coding based on Boolean random sets. Proceedings of SPIE.
74-79.
-
Dougherty, E. R.
(1995).
Filtering clutter by optimal granulometric bandpass filters. Proceedings of SPIE.
70-76.
-
Batman, S., Dougherty, E. R., Rzadca, M. C., & Chapa, J. O.
(1995).
Multivariate morphological granulometric texture classification using Walsh and wavelet features. Proceedings of SPIE.
46-56.
-
Chen, Y., & Dougherty, E. R.
(1995).
Adaptive multiparameter openings. Proceedings of SPIE.
37-47.
-
Sinha, D., & Dougherty, E. R.
(1995).
Computational representation of lattice operators. Proceedings of SPIE.
168-175.
-
Loce, R. P., & Dougherty, E. R.
(1995).
Design and application of binary differencing filters. Proceedings of SPIE.
338-349.
-
Sand, F. M., & Dougherty, E. R.
(1995).
Granulometric estimation of sizing parameters and proportions for gamma-distributed grain sizes. Proceedings of SPIE.
102-106.
-
Handley, J. C., & Dougherty, E. R.
(1995).
Optimal nonlinear filter in the random Boolean model. Proceedings of SPIE.
28-36.
-
Laplante, P. A., & Dougherty, E. R.
(1995).
Optimization techniques for real-time image processing. Proceedings of SPIE.
116-122.
-
Handley, J. C., & Dougherty, E. R.
(1995).
Binary texture estimation using linear samples. Proceedings of SPIE.
257-266.
-
Handley, J. C., & Dougherty, E. R.
(1994).
Optimal nonlinear fax restoration. Proceedings of SPIE.
232-242.
-
Kraus, E. J., & Dougherty, E. R.
(1994).
Segmentation-free morphological character recognition. Proceedings of SPIE.
14-23.
-
Dougherty, E. R.
(1994).
Fuzzy morphological algorithms. Proceedings of SPIE.
103120a-103120a-49-263.
-
Cuciurean-Zapan, C., & Dougherty, E. R.
(1993).
Computational morphology and representation of operators between complete lattices. Proceedings of SPIE.
152-158.
-
Dougherty, E. R., Sinha, D., & Sinha, P.
(1992).
Fuzzy morphological filters. Proceedings of SPIE.
414-426.
-
Dougherty, E. R., & Loce, R. P.
(1992).
Hausdorff-metric continuity of projection-generated Fourier descriptors. Proceedings of SPIE.
632-640.
-
Chen, Y., & Dougherty, E. R.
(1992).
Texture classification by gray-scale morphological granulometries. Proceedings of SPIE.
931-942.
-
Sand, F. M., & Dougherty, E. R.
(1992).
Morphological granulometric simulation: distribution of the pattern-spectrum mean and variance for binary images with overlapping elements. Proceedings of SPIE.
372-379.
-
Sand, F. M., & Dougherty, E. R.
(1992).
Asymptotic distributions for morphological granulometric moments. Proceedings of SPIE.
21-31.
-
Sinha, D., & Dougherty, E. R.
(1992).
Characterization of fuzzy Minkowski algebra. Proceedings of SPIE.
59-69.
-
Dougherty, E. R., Chen, Y., Totterman, S., & Hornak, J. P.
(1992).
Detection of osteoporosis by morphological granulometries. Proceedings of SPIE.
666-680.
-
Loce, R. P., & Dougherty, E. R.
(1992).
Optimal restoration using the morphological hit-or-miss transform. Proceedings of SPIE.
94-105.
-
Kraus, E. J., Heijmans, H., & Dougherty, E. R.
(1992).
Spatial-scaling-compatible morphological granulometries on locally convex topological vector spaces. Proceedings of SPIE.
283-291.
-
Newell, J. T., & Dougherty, E. R.
(1992).
Maximum-likelihood morphological granulometric classifiers. Proceedings of SPIE.
386-395.
-
McCabe, J. M., & Dougherty, E. R.
(1992).
Shape characterization of silver halide crystals. Proceedings of SPIE.
563-571.
-
Sinha, D., & Dougherty, E. R.
(1992).
Fuzzification of set inclusion. Proceedings of SPIE.
440-449.
-
Dougherty, E. R., & Sinha, D.
(1992).
Need for fuzzy morphology: erosion as a fuzzy marker. Proceedings of SPIE.
431-439.
-
Dougherty, E. R., & Zhao, D.
(1992).
Noise-model-based morphological shape recognition. Proceedings of SPIE.
736-747.
-
Sinha, D., & Dougherty, E. R.
(1992).
Intrinsically fuzzy approach to mathematical morphology. Proceedings of SPIE.
477-488.
-
Loce, R. P., & Dougherty, E. R.
(1992).
The use of first-order structuring-element libraries to design morphological filters. International Conference on Pattern Recognition.
256-259.
-
Dougherty, E. R., Haralick, R. M., Chen, Y., Li, B. o., Agerskov, C., Jacobi, U., & Sloth, P. H.
(1991).
Morphological pattern-spectra-based Tau-opening optimization. Proceedings of SPIE.
141-152.
-
Dougherty, E. R., & Haralick, R. M.
(1991).
Hole spectrum: model-based optimization of morphological filters. Proceedings of SPIE.
224-232.
-
Loce, R. P., & Dougherty, E. R.
(1991).
Using structuring-element libraries to design suboptimal morphological filters. Proceedings of SPIE.
233-246.
-
Dougherty, E. R., Mathew, A. V., & Swarnakar, V.
(1991).
Conditional-expectation-based implementation of the optimal mean-square binary morphological filter. Proceedings of SPIE.
137-147.
-
Dougherty, E. R., & Sand, F. M.
(1991).
Distribution of the pattern spectrum mean for convex base images. Proceedings of SPIE.
114-124.
-
Haralick, R. M., Dougherty, E. R., & Katz, P. L.
(1991).
Model-based morphology (Invited Paper). Proceedings of SPIE.
108-117.
-
Mathew, A. V., Dougherty, E., & Swarnakar, V.
(1991).
The optimal-morphological-=basis switching algorithm. IEEE Region 10 Annual International Conference, Proceedings/TENCON.
373-378.
-
Dougherty, E. R.
(1990).
Characterization of gray-scale morphological granulometries. Proceedings of SPIE.
129-137.
-
Dougherty, E. R., & Loce, R. P.
(1990).
Projection-generated Fourier descriptors that are robust with respect to both random point noise and occlusion. Proceedings of SPIE.
84-95.
-
Dougherty, E. R., & Kraus, E. J.
(1990).
Role of shape in morphological bases for digital moving-average filters. Proceedings of SPIE.
14-24.
-
Dougherty, E. R.
(1990).
Minimal search for the optimal mean-square digital gray-scale morphological filter. Proceedings of SPIE.
214-226.
-
Dougherty, E. R., & Kraus, E. J.
(1990).
Filtering by morphological pseudoconvolutions. Proceedings of SPIE.
157-168.
-
Dougherty, E. R.
(1990).
Hausdorf-metric interpretation of convergence in the Matheron topology for binary mathematical morphology. 870-875 vol.1-875.
-
Dougherty, E. R., Kraus, E. J., & Pelz, J. B.
(1989).
Image segmentation by local morphological granulometries. 1220-1223.
-
Dougherty, E. R.
(1989).
The dual representation of gray-scale morphological filters. Proceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition.
172-177.
-
Dougherty, E. R., & Giardina, C. R.
(1988).
Closed-form representation of convolution, dilation, and erosion in the context of image algebra. 754-759.
-
Dougherty, E. R., & Sehdev, P.
(1988).
Robust image processing language in the context of image algebra. 748-753.
-
Dougherty, E. R., & Giardina, C. R.
(1986).
DIGITAL VERSION OF THE MATHERON REPRESENTATION THEOREM FOR INCREASING tau -MAPPINGS IN TERMS OF A BASIS FOR THE KERNEL. 534-536.
-
Dehghannasiri, R., Qian, X., & Dougherty, E. R.
(2018).
Robust Smoothing for State-Space Models with Unknown Noise Statistics. Conference record / Asilomar Conference on Signals, Systems & Computers. Asilomar Conference on Signals, Systems & Computers.
1024-1028.
-
patent
-
Dougherty, E., Balagurunathan, Y., & Chen, Y.
(2008).
Simulating microarrays using a parameterized model
-
Shmulevich, I., Dougherty, E., & Zhang, W.
(2007).
Probabilistic boolean networks
-
Dougherty, E., Balagurunathan, Y., & Chen, Y.
(2008).
Simulating microarrays using a parameterized model
Research
principal investigator on
- AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems awarded by Brookhaven National Laboratory - (Upton, New York, United States) 2018 - 2022
- Quantifying Performance for Classification based on Multi-Gene Dynamics Relative to the Number of Simultaneously Measured Live-Cell Expression Levels awarded by Brookhaven National Laboratory - (Upton, New York, United States) 2018
co-principal investigator on
- NRT-DESE: Data-Enabled Discovery and Design of Energy Materials awarded by National Science Foundation - (Arlington, Virginia, United States) 2015 - 2021
- DMREF: Accelerating the Development of High Temperature Shape Memory Alloys awarded by National Science Foundation - (Arlington, Virginia, United States) 2015 - 2019
investigator on
Teaching
teaching activities
- ECEN489 Sptp: Found Mod Science & Eng Instructor
- ECEN684 Professional Internship Instructor
- ECEN684 Professional Internship: In-ab Instructor
- ECEN685 Directed Studies Instructor
- ECEN689 Sptp:opt Sig Proc Und Uncerta Instructor
- ECEN691 Research Instructor
Works By Students
chaired theses and dissertations
-
Agyepong, Kwadwo (2012-10). Comparative Performance Analysis of the Algorithms for Detecting Periodically Expressed Genes.
-
Atashpazgargari, Esmaeil (2014-08). Biomarker Discovery and Validation for Proteomics and Genomics: Modeling And Systematic Analysis.
-
Attoor, Sanju Nair (2004-11). Relationship between classifier performance and distributional complexity for small samples.
-
Dalton, Lori Anne (2012-07). Analysis and Optimization of Classifier Error Estimator Performance within a Bayesian Modeling Framework.
-
Dehghannasiri, Roozbeh (2016-08). Optimal Experimental Design in the Context of Objective-Based Uncertainty Quantification.
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Ghaffari, Noushin (2012-07). Genomic Regulatory Networks, Reduction Mappings and Control.
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Hsu, Fang-Han (2013-05). Copy Number and Gene Expression: Stochastic Modeling and Therapeutic Application.
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Knight, Jason Matthew (2015-05). Optimal Model-Based Approaches for Predictive Inference in Biology.
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Layek, Ritwik (2012-07). Pathways, Networks and Therapy: A Boolean Approach to Systems Biology.
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Rezaei Yousefi, Mohammadmahdi (2013-04). Optimal Intervention in Markovian Genetic Regulatory Networks for Cancer Therapy.
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Shahrokh Esfahani, Mohammad (2014-04). Using Prior Knowledge in the Design of Classifiers.
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Sima, Chao (2007-09). Small sample feature selection.
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Sun, Youting (2012-07). Model-based Biomarker Detection and Systematic Analysis in Translational Science.
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Vahedi, Golnaz (2010-10). An Engineering Approach Towards Personalized Cancer Therapy.
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Xiao, Yufei (2009-05). Boolean models for genetic regulatory networks.
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Zhao, Chen (2012-07). Stochastic Modeling and Analysis of Pathway Regulation and Dynamics.
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Zhao, Wentao (2009-05). Genomic applications of statistical signal processing.
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Zollanvari, Amin (2012-02). Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis with Applications in Genomics.
Background
education and training
- M.S. in Computer Science, Stevens Institute of Technology - (Hoboken, New Jersey, United States) 1986
- Ph.D. in Mathematics, Rutgers University - (New Brunswick, New Jersey, United States) 1974
- M.S. in Mathematics, Fairleigh Dickinson University - (Teaneck, New Jersey, United States) 1969
- B.S. in Mathematics, Fairleigh Dickinson University - (Teaneck, New Jersey, United States) 1967
awards and honors
- Highly Cited Researcher, conferred by Thomson Reuters - (New York, New York, United States), 2014
- Fellow, conferred by Institute of Electrical and Electronics Engineers - (Piscataway, New Jersey, United States), 2012
- Doctor Honoris Causa, conferred by Tampere University of Technology - (Tampere, Pirkanmaa, Finland), 2007
- Robert M. Kennedy Class of '26 Professorship, conferred by Texas A&M University - (College Station, Texas, United States), 2007
- Association of Former Students University-Level Distinguished Achievement Award, The, conferred by Texas A&M University - (College Station, Texas, United States), 2005
- President's Award, conferred by International Society for Optics and Photonics, 2004
- Halliburton Professorship Award, conferred by Texas A&M University - (College Station, Texas, United States), 2001
- Fellow, conferred by International Society for Optics and Photonics, 2000
Contact
first name
- Edward
has last name
- Dougherty
mailing address
-
Texas A&M University
Electrical Engineering
3128 TAMU
College Station, TX 77843-3128
USA
Other
In the News
- Data, sustainability: ceding research advantages to China News Release
- Does socialism sound good? News Release
- e-dougherty@tamu.edu