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Year: 2012

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]

Yang Shen, Michael K. Gilson, and Bruce Tidor, "Charge Optimization Theory for Induced-Fit Ligands", Journal of Chemical Theory and Computation 2012 8 (11), 4580-4592  (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]

Tao Hu, A. Genkin and D.B. Chklovskii, "Computing sparse representations using a network of sparsely communicating nodes", Neural Computation 24, 2852 (2012)  (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]

Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin R., "A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response", Genome Biol. 2012 Apr 30;13(4):R32.  (Journal Publication)  [More Details]  [Online]

Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charles D Johnson, Scott V Dindot, "Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare", BMC Genomics, 2012; 13 (1): 78  (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]

Metz RP, Patterson JL, Wilson E., "Vascular smooth muscle cells: isolation, culture, and characterization", Methods Mol Biol. 2012;843:169-76.  (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]

Kessler JD, Kahle KT, Sun T, Meerbrey KL, Schlabach MR, Schmitt EM, Skinner SO, Xu Q, Li MZ, Hartman ZC, Rao M, Yu P, Dominguez-Vidana R, Liang AC, Solimini NL, Bernardi RJ, Yu B, Hsu T, Golding I, Luo J, Osborne CK, Creighton CJ, Hilsenbeck SG, Schiff R, Shaw CA, Elledge SJ, Westbrook TF., "A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis", Science. 2012 Jan 20;335(6066):348-53. doi: 10.1126/science.1212728. Epub 2011 Dec 8.  (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]

C.C. Allen, B.R.C. Alves, X. Li, L.O. Tedeschi, H. Zhou, J.A. Paschal, P. Riggs, U.M. Braga-Neto, D.H. Keisler, G.L. Williams and M. Amstalden, "Gene expression in the arcuate nucleus of heifers is affected by controlled intake of high- and low-concentrate diets", Journal of Animal Sciences, Vol. 90, No. 7, July 2012, pp. 2222-2232  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, "Comparative analysis of biological networks using Markov chains and hidden Markov models", IEEE Signal Processing Magazine, Special Issue on Genomic and Proteomic Signal Processing in Biomolecular Pathways, 29(1): 22--34, 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]

Alfonso Clavijo, Amir Nikooienejad, Mohammad Shahrokh , Richard P. Metz, Scott Schwartz, Esmaeil Atashpaz Gargari, Thomas J. Deliberto, Mark W. Lutman, Kerri Pedersen , Luis R. Bazan, Leo G. Koster, Melinda Jenkins-Moore, Sabrina L. Swenson, Mike Zang, Tammy Beckham, Charles D. Johnson , Mangkey Bounpheng, "Identification and Analysis of the First 2009 Pandemic H1N1 Influenza Virus from U.S. Feral Swine", Zoonoses and Public Health. DOI: 10.1111/zph.12006  (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]