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Author: Dougherty, Edward Rusell

Mohammad Shahrokh Esfahani and Edward R. Dougherty, "Effect of separate sampling on classification accuracy", Bioinformatics (2014) 30 (2): 242-250.  (Journal Publication)  [More Details]  [Online]

Jianping Hua, Michael L. Bittner, and Edward R. Dougherty, "Evaluating gene set enrichment analysis via a hybrid data model", Cancer Inform. 2014 Feb 12;13(Suppl 1):1-16  (Journal Publication)  [More Details]  [Online]

Dalton L.A. and Dougherty E.R., "Intrinsically Optimal Bayesian Robust Filtering", IEEE Transactions on Signal Processing 62(3): 657-670 (2014).   (Journal Publication)  [More Details]  [Online]

Rezaei Yousefi, Datta, A. ; Dougherty, E., "Optimal Intervention in Markovian Gene Regulatory Networks with Random-Length Therapeutic Response to Antitumor Drug", Biomedical Engineering, IEEE Transactions on , vol.60, no.12, pp.3542,3552, Dec. 2013  (Journal Publication)  [More Details]  [Online]

Qian X, Dougherty ER., "Validation of gene regulatory network inference based on controllability", Front Genet. 2013 Dec 12;4:272.   (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Mohammadmahdi R Yousefi, Charles D Johnson, Ivan Ivanov and Edward R Dougherty, "Modeling the next generation sequencing sample processing pipeline for the purposes of classification", BMC Bioinformatics 2013, 14:307  (Journal Publication)  [More Details]  [Online]

Mohammadmahdi R. Yousefi, Edward R. Dougherty, "Intervention in gene regulatory networks with maximal phenotype alteration", Bioinformatics first published online April 29, 2013 doi:10.1093/bioinformatics/btt242  (Journal Publication)  [More Details]  [Online]

Mohammad Shahrokh Esfahania, Jason Knighta, Amin Zollanvaria, Byung-Jun Yoona, Edward R. Dougherty, "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 Volume 46, Issue 10, October 2013, Pages 2783–2797  (Journal Publication)  [More Details]  [Online]

Kwadwo S. Agyepong, Fang-Han Hsu, Edward R. Dougherty, and Erchin Serpedin, "Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach", Advances in Bioinformatics Volume 2013 (2013), Article ID 171530, 10 pages  (Journal Publication)  [More Details]  [Online]

Hsu, F., Dougherty, E. ; Chen, Y. ; Serpedin, E., "Estimating conditional probabilities for the detection of unfavorable copy number alterations in targeted therapy", Biomedical Engineering, IEEE Transactions on (Volume:PP , Issue: 99 )  (Journal Publication)  [More Details]  [Online]

Hanczar, B., and Dougherty E. R., "The reliability of estimated confidence intervals for classification error rates when only a single sample is available", Pattern Recognition, Vol. 46, No. 3, 1067-1077, 2013  (Journal Publication)  [More Details]  [Online]

Edward R Dougherty and Lori A Dalton, "Scientific knowledge is possible with small-sample classification", EURASIP Journal on Bioinformatics and Systems Biology 2013, 2013:10  (Journal Publication)  [More Details]  [Online]

Edward R Dougherty, "On the impoverishment of scientific education", EURASIP Journal on Bioinformatics and Systems Biology 2013, 2013:15  (Journal Publication)  [More Details]  [Online]

E. Atashpaz-Gargari, C. Sima, U.M. Braga-Neto and E.R. Dougherty, "Relationship Between the Accuracy of Classifier Error Estimation and Complexity of the Decision Boundary", Pattern Recognition, Volume 46, Issue 5, May 2013, Pages 1315-1322, doi:10.1016/j.patcog.2012.10.020.   (Journal Publication)  [More Details]  [Online]

Dalton, L., and Dougherty, E. R., "Optimal classifiers with minimum expected error within a Bayesian framework — Part II: Properties and performance analysis", Pattern Recognition, Vol. 46, No. 5, 1301-1314, 2013  (Journal Publication)  [More Details]  [Online]

Dalton, L., and Dougherty, E. R., "Optimal Classifiers with Minimum Expected Error within a Bayesian Framework–Part I: Discrete and Gaussian Models", Pattern Recognition, Vol. 46, No. 5, 1288-1300, 2013  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, Xiaoning Qian, and Edward R. Dougherty, "Quantifying the objective cost of uncertainty in complex dynamical systems", IEEE Transactions on Signal Processing, vol. 61, no. 9, pp. 2256-2266, May 2013  (Journal Publication)  [More Details]  [Online]

Amin Zollanvaria, Jianping Hua, Edward R. Dougherty, "Analytical study of performance of linear discriminant analysis in stochastic settings", Pattern Recognition Volume 46, Issue 11, November 2013, Pages 3017–3029  (Journal Publication)  [More Details]  [Online]

Zollanvari, A., Braga-Neto, U. M., and Dougherty, E. R., "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, Vol. 45, No. 2, 908-917, February, 2012  (Journal Publication)  [More Details]  [Online]

Zhao, C., Hua, J., Bittner, M. L., Ivanov, I., and Dougherty, E. R., "Identifying Mechanistic Similarities in Drug Responses", Bioinformatics, Vol. 28, No. 14, 1902-1910, 2012  (Journal Publication)  [More Details]  [Online]

Yousefi, M. R., Datta, A., and Dougherty, E. R., "Optimal Intervention Strategies for Therapeutic Methods With Fixed-Length Duration of Drug Effectiveness", IEEE Transactions on Signal Processing, Vol. 60, No. 9, 4930-4944  (Journal Publication)  [More Details]  [Online]

Y. Sun, U.M. Braga-Neto and E.R. Dougherty, "A systematic model of the LC-MS proteomics pipeline", BMC Genomics, GENSIPS'2011 Special Issue, Vol. 13, Suppl. 6, October 2012, p. S2, doi:10.1186/1471-2164-13-S6-S2  (Journal Publication)  [More Details]  [Online]

Y. Sun, J. Zhang, U.M. Braga-Neto and E.R. Dougherty,, "BPDA2d — A 2D global optimization based Bayesian peptide detection algorithm for LC-MS", Bioinformatics, Vol. 28, No. 4, February 2012, pp. 564-572  (Journal Publication)  [More Details]  [Online]

Xiangfang Li, Lijun Qian and Edward R Dougherty, "Dynamical modeling of drug effect using hybrid systems", EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012:19  (Journal Publication)  [More Details]  [Online]

Sun, Y., Braga-Neto, U. M., and Dougherty, E. R., "Modeling and Systematic Analysis of the LC-MS Proteomics Pipeline", BMC Genomics, 2012, Vol. 13 (supp 6):S2  (Journal Publication)  [More Details]  [Online]

Nounou, M., Nounou, H., Meskin, N., Datta, A., and Dougherty, E. R., "Multiscale Denoising of Biological Data: A Comparative Analysis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 9, No. 5, 1539-1545.  (Journal Publication)  [More Details]  [Online]

Nounou HN, Nounou MN, Meskin N, Datta A, Dougherty ER., "Fuzzy Intervention in Biological Phenomena", IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1819-25.   (Journal Publication)  [More Details]  [Online]

Lori A. Dalton, Edward R. Dougherty, "Application of the Bayesian MMSE estimator for classification error to gene expression microarray data", Bioinformatics [ISMB/ECCB] 27(13): 1822-1831 (2011)  (Journal Publication)  [More Details]  [Online]

Li, X., Qian, L., Hua, J., Bittner, M. L., and Dougherty, E. R., "Assessing the Efficacy of Molecularly Targeted Agents on Cell Line-based Platforms by Using System Identification", BMC Genomics, , 2012, Vol. 13 (supp 6):S11.   (Journal Publication)  [More Details]  [Online]

Li, X., Qian, L., Bittner, M. L., and Dougherty, E. R., "A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens—a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems", Cancer Informatics, 2012:11, 41-60, March, 2012  (Journal Publication)  [More Details]  [Online]

Knight, J., Datta, A., and Dougherty, E. R., "Generating Stochastic Gene Regulatory Networks Consistent With Pathway Information and Steady-State Behavior", IEEE Transactions on Biomedical Engineering, Vol. 59, No. 6, 1701-1710, 2012  (Journal Publication)  [More Details]  [Online]

Hua, J., Sima, C., Cypert, M., Gooden, C., Shack, S., Alla, L., Smith, E., Trent, J. M., Dougherty, E. R., and Bittner, M. L., "Tracking transcriptional activities with high-content epifluorescent imaging", Biomedical Optics, Vol. 17, 046008, DOI:10.1117/1.JBO.17.4.046008, May, 2012  (Journal Publication)  [More Details]  [Online]

Hsu, F-H., Serpedin, E., Hsiao, T-H., Bishop, A., E. R. Dougherty, and Chen, Y., "Reducing Confounding and Suppression Effects in TCGA Data: An Integrated Analysis of Chemotherapy Response in Ovarian Cancer", BMC Genomics, , 2012, Vol. 13 (supp 6):S13  (Journal Publication)  [More Details]  [Online]

Hsu, F-H., Serpedin, E., Chen, Y., and Dougherty, E. R., "Evaluating Dynamic Effects of Copy Number Alterations On Gene Expression Using a Single-Transcription Model", IEEE Transactions on Biomedical Engineering, Vo. 59, No. 10, 2726-2736  (Journal Publication)  [More Details]  [Online]

Hsu, F-H., Serpedin, E., Chen, Y., and Dougherty, E. R., "Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic", IEEE Transactions on Biomedical Engineering, Vol. 59, No. 1, 272-280, January, 2012  (Book Chapter)  [More Details]  [Online]

Hsu FH, Serpedin E, Hsiao TH, Bishop AJ, Dougherty ER, Chen Y., "Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer", BMC Genomics. 2012;13 Suppl 6:S13.   (Journal Publication)  [More Details]  [Online]

Dougherty, E. R., and Shmulevich, I., "On the Limitations of Biological Knowledge", Current Genomics, Vol. 13, No. 7, 574-587  (Journal Publication)  [More Details]  [Online]

Dougherty, E. R., "Genomic Signal Processing", IEEE Signal Processing Magazine, Vol. 29. No. 3, 124-129, 2012  (Epistemology Paper)  [More Details]  [Online]

Dougherty, E. R., "Biomarker development: Prudence, risk, and reproducibility", BioEssays, Vol. 34, No. 4, 277-279, 2012  (Journal Publication)  [More Details]  [Online]

Dougherty Edward Russell, M. R., Yousefi, "Performance Reproducibility Index for Classification", Bioinformatics, Vol. 28, No. 21, pp. 2824-2833, 2012  (Journal Publication)  [More Details]  [Online]

Dalton, L., and Dougherty, E. R., "Optimal MSE Calibration of Error Estimators under Bayesian Models", Pattern Recognition, Vol. 45, No. 6, 2308-2320, 2012  (Book Chapter)  [More Details]  [Online]

Dalton, L., and Dougherty, E. R., "Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error – Part I: Representation", IEEE Transactions on Signal Processing, Vol. 60, No. 5, 2575-2587, 2012  (Journal Publication)  [More Details]  [Online]

Dalton, L., and Dougherty, E. R., "Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error—Part II: Consistency and Performance Analysis", IEEE Transactions on Signal Processing, Vol. 60, No. 5, 2588-2603, 2012  (Journal Publication)  [More Details]  [Online]

Bittner, M. L., and Dougherty, E. R., "Newton, Laplace, and the Epistemology of Systems Biology", Cancer Informatics, 2012:5, 185-190  (Journal Publication)  [More Details]  [Online]

A. Zollanvari, U.M. Braga-Neto and E.R. Dougherty, "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, Vol. 45, No. 2, February 2012, pp. 908-917  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Edward R Dougherty, "Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 9, No. 1, 123-136, January, 2012  (Journal Publication)  [More Details]  [Online]

Zollanvari, A., Braga-Neto, U. M., and Dougherty E. R., "Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis", IEEE Transactions on Signal Processing, Vol. 59, No. 9, 4238-4255, September, 2011  (Journal Publication)  [More Details]  [Online]

Zhao, C., Ivanov, I., Bittner, M. L., and Dougherty, E. R., "Pathway Regulatory Analysis in the Context of Bayesian Networks Using the Coefficient of Determination", Biological Systems, Vol. 19, No. 4, 651-682, December, 2011  (Journal Publication)  [More Details]  [Online]

Xiangfang Li, Lijun Qian, Michael L. Bittner, Edward R. Dougherty, "Characterization of Drug Efficacy Regions Based on Dosage and Frequency Schedules", IEEE Trans. Biomed. Engineering 58(3): 488-498 (2011)  (Journal Publication)  [More Details]  [Online]

Sima, C., Braga-Neto, U. M., and Dougherty, E. R., "High-Dimensional Bolstered Error Estimation", Bioinformatics, Vol. 27, No. 21, 3056-3064, November, 2011  (Journal Publication)  [More Details]  [Online]

Ritwik Layek, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty, "Cancer therapy design based on pathway logic", Bioinformatics 27(4): 548-555 (2011)  (Journal Publication)  [More Details]  [Online]

Nader Meskin, Hazem N. Nounou, Mohamed N. Nounou, Aniruddha Datta, Edward R. Dougherty, "Intervention in Biological Phenomena Modeled by S-Systems", IEEE Trans. Biomed. Engineering 58(5): 1260-1267 (2011)  (Journal Publication)  [More Details]  [Online]

Mohammadmahdi R. Yousefi, Jianping Hua, Edward R. Dougherty, "Multiple-rule bias in the comparison of classification rules", Bioinformatics 27(12): 1675-1683 (2011)  (Journal Publication)  [More Details]  [Online]

Lori A. Dalton, Edward R. Dougherty, "Bayesian Minimum Mean-Square Error Estimation for Classification Error – Part I: Definition and the Bayesian MMSE Error Estimator for Discrete Classification", IEEE Transactions on Signal Processing 59(1): 115-129 (2011)  (Journal Publication)  [More Details]  [Online]

Lori A. Dalton, Edward R. Dougherty, "Bayesian Minimum Mean-Square Error Estimation for Classification Error – Part II: Linear Classification of Gaussian Models", IEEE Transactions on Signal Processing 59(1): 130-144 (2011)  (Journal Publication)  [More Details]  [Online]

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

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

Dougherty, E. R., Zollanvari, A., and Braga-Neto, U. M., "The Illusion of Distribution-Free Small-Sample Classification in Genomics", Current Genomics, Vol. 12, No. 5, 333-341, August, 2011  (Journal Publication)  [More Details]  [Online]

Dougherty ER., "Validation of gene regulatory networks: scientific and inferential", Briefings in Bioinformatics, 2011 May;12(3):245-52  (Journal Publication)  [More Details]  [Online]

Zollanvari, A, Braga-Neto and Dougherty, E.R., "Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis", Published in: Information Theory, IEEE Transactions on (Volume:56 , Issue: 2 ) Date of Publication: Feb. 2010 Page(s): 784 - 804 ISSN : 0018-9448 INSPEC Accession Number: 11152615 Digital Object Identifier : 10.1109/TIT.2009.2037034 Date of Current Version : 25 febrero 2010 Issue Date : Feb. 2010 Sponsored by : IEEE Information Theory Society  (Journal Publication)  [More Details]  [Online]

Zhao C, Bittner ML, Chapkin RS, Dougherty ER., "Characterization of the effectiveness of reporting lists of small feature sets relative to the accuracy of the prior biological knowledge", Cancer Inform. 2010 Mar 18;9:49-60.  (Journal Publication)  [More Details]  [Online]

Youting Sun, Jianqiu Zhang, Ulisses Braga-Neto and Edward R Dougherty, "BPDA – A Bayesian peptide detection algorithm for mass spectrometry", BMC Bioinformatics 2010, 11:490 doi:10.1186/1471-2105-11-490  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Noushin Ghaffari, Ivan Ivanov and Edward R. Dougherty, "State reduction for network intervention in probabilistic Boolean networks", Bioinformatics, 26(24): 3098--3104, 2010  (Journal Publication)  [More Details]  [Online]

Ulisses M. Braga-Neto and Edward R. Dougherty, "Exact Correlation between Actual and Estimated Errors in Discrete Classification", Published in: Journal Pattern Recognition Letters archive Volume 31 Issue 5, April, 2010 Pages 407-412   (Journal Publication)  [More Details]  [Online]

M.R. Yousefi, J. Hua, C. Sima, E.R. Dougherty, "Reporting bias when using real data sets to analyze classification performance", Bioinformatics vol. 26(1), 68-76 2010  (Journal Publication)  [More Details]  [Online]

Dougherty, E. R., Sima, C., Hua, J., Hanczar, B., and Braga-Neto, U. M., "Performance of Error Estimators for Classification", Current Bioinformatics, Vol. 5, No. 1, 53-67, March, 2010.  (Journal Publication)  [More Details]  [Online]

Dougherty ER, Bittner ML., "Causality, randomness, intelligibility, and the epistemology of the cell", Curr Genomics. 2010 Jun;11(4):221-37  (Journal Publication)  [More Details]  [Online]

B. Hanczar, J. Hua, C. Sima, J. Weinstein, M. Bittner, and E. R. Dougherty, "Small-sample precision of ROC-related estimates", Bioinformatics vol. 26(6), 822-830 2010  (Journal Publication)  [More Details]  [Online]

Youting Sun, Ulisses Braga-Neto and Edward R. Dougherty, "Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data – A Model-Based Study", Published in: ·Journal EURASIP Journal on Bioinformatics and Systems Biology Volume 2009, January 2009 Article No. 4   (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Ivan Ivanov, Noushin Ghaffari and Edward R. Dougherty, "Intervention in gene regulatory networks via greedy control policies based on long-run behavior", BMC Systems Biology, 3(61): 16 pages, 2009.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "On the long-run sensitivity of probabilistic Boolean network", Journal of Theoretical Biology, 257(4): 560--577, 2009  (Journal Publication)  [More Details]  [Online]

Q. Xu, J. Hua, Z. Xiong, M.L. Bittner, and E. R. Dougherty, "The Effect of Microarray Image Compression on Expression-Based Classification", Signal, Image and Video Processing February 2009, Volume 3, Issue 1, pp 53-61  (Journal Publication)  [More Details]  [Online]

J. Hua, W. Tembe and E. R. Dougherty, "Performance of feature-selection methods in the classification of high-dimension data", Pattern Recognition vol. 42, 409-424 2009  (Journal Publication)  [More Details]  [Online]

E.R. Dougherty, J. Hua, and C. Sima, "Performance of Feature Selection Methods", Current Genomics Vol. 10(6), 365-374 2009  (Journal Publication)  [More Details]  [Online]

Dougherty ER, Brun M, Trent JM, Bittner ML., "Conditioning-based modeling of contextual genomic regulation", IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):310-20  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "Effect of function perturbation on the steady state distribution of genetic regulatory networks: optimal structural intervention", IEEE Transactions on Signal Processing, 56(10):4966--4976, 2008.  (Journal Publication)  [More Details]  [Online]

A. Choudhary, J. Hua, M. Bittner and E. R. Dougherty, "The Effects of Population Contexts on Classifier Performance", Journal of Biological Systems vol. 16, 495-517. 2008  (Journal Publication)  [More Details]  [Online]

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

Hua, J, Craig DW, Brun M, Webster J, Zismann VL, Tembe W, Joshipura K, Huentelman MJ, Dougherty ER, Stephan DA, "SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays", Bioinformatics 23(1):57-63 2007  (Journal Publication)  [More Details]  [Online]

E.R. Dougherty, J. Hua, and M.L. Bittner, "Validation of computational methods in genomics", Current Genomics vol. 8, 1-19. 2007  (Journal Publication)  [More Details]  [Online]

Charles D Johnson, Yoganand Balagurunathan, Edward R Dougherty, Cynthia A Afshari, Qiang He, Kenneth S Ramos, "Insight into redox-regulated gene networks in vascular cells", Bioinformation, 2007; 1(10); 379-383  (Journal Publication)  [More Details]  [Online]

Brun Marcel, Dougherty Edward Russell, "A Probabilistic Theory of Clustering", Pattern Recognition, Vol. 37, No. 5, pp. 917-925, 2004  (Journal Publication)  [More Details]  [Online]