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Journal: Bioinformatics

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]