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Author: Dougherty, Edward Rusell

E. Atashpaz-Gargari, M.S. Reis, U.M. Braga-Neto, J. Barrera and E.R. Dougherty, "A fast Branch-and-Bound algorithm for U-curve feature selection", Pattern Recognition, Vol. 73, Jan 2018, pp. 172-188  (Journal Publication)  [More Details]  [Online]

ShahinBoluki, Mohammad ShahrokhEsfahani, Xiaoning Qian, Edward R. Dougherty, "Constructing pathway-based priors within a Gaussian Mixture Model for Bayesian regression and classification", IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, DOI: 10.1109/TCBB.2017.2778715, 2017  (Journal Publication)  [More Details]  [Online]

A. Karbalayghareh, U.M. Braga-Neto, and E.R. Dougherty, "Classification of Single-cell Gene Expression Trajectories from Incomplete and Noisy Data", IEEE/ACM Transactions on Computational Biology and Bioinformatics,Early Access, Vol. PP, Issue 99, 2018, pp. 1-1.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "Bayesian regression with network prior: Optimal Bayesian filtering perspective", IEEE Transactions on Signal Processing, 64(23):6243-6253, 2016.  (Book Chapter)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Efficient experimental design for uncertainty reduction in gene regulatory networks", BMC Bioinformatics, 16(Suppl 13):S2, 2015.  (Journal Publication)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Optimal experimental design for gene regulatory networks in the presence of uncertainty", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, no.4, pp.938-950, 2015.  (Journal Publication)  [More Details]  [Online]

U.M. Braga-Neto, A. Zollanvari, and E.R. Dougherty, "Cross-validation under separate sampling: strong bias and how to correct it", Bioinformatics, Vol. 30, No. 23, Dec 1 2014, pp. 3349-3355.  (Journal Publication)  [More Details]  [Online]

E. Atashpaz-Gargari, U.M. Braga-Neto, and E.R. Dougherty, "Modeling and Systematic Analysis of Biomarker Validation using Selected Reaction Monitoring", EURASIP Journal on Bioinformatics and Systems Biology, 2014, 2014:17.  (Journal Publication)  [More Details]  [Online]

T.T. Vu, C. Sima, U.M. Braga-Neto, and E.R. Dougherty, "Unbiased Bootstrap Error Estimation for Linear Discriminant Analysis", EURASIP Journal on Bioinformatics and Systems Biology, 2014, 2014:15.  (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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]