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2014

Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul M. Seabury, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury, "A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene", PLOS ONE, March 2014, Volume 9, Issue 3  (Journal Publication)  [More Details]  [Online]

SEQC/MAQC-III Consortium, "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium", Nature Biotechnology (2014) doi:10.1038/nbt.2957  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan, Karina D. Garcia-Orozco, Patricia L. Chen, Adrian Ochoa-Leyva, Alonso A. Lopez-Zavala, J. Salvador Carrasco, Chris Hong, Luis G. Brieba, Enrique Rudiño-Piñera, Philip D. Blood, Jason E. Sawyer, Charles D. Johnson, Scott V. Dindot, Rogerio R. Sotelo-Mundo, Michael F. Criscitiello, "Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture", Nature Scientific Reports 4, Article number: 7081  (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]

MF Lensink, IH Moal, PA Bates, PL Kastritis, AS Melquiond, E Karaca, C Schmitz, M Van Dijk, AM Bonvin, M Eisenstein, B Jimenez-Garcia, S Grosdidier, A Solernou, L Perez-Cano, C Pallara, J Fernandez-Recio, J Xu, P Muthu, KP Kilambi, JJ Gray, S Grudinin, G Derevyanko, JC Mitchell, J Wieting, E Kanamori, Y Tsuchiya, Y Murakami, J Sarmiento, DM Standley, M Shirota, K Kinoshita, H Nakamura, M Chavent, DW Ritchie, H Park, J Ko, H Lee, C Seok, Y Shen, D Kozakov, S Vajda, PJ Kundrotas, IA Vakser, BG Pierce, H Hwang, T Vreven, Z Weng, I Buch, E Farkash, HJ Wolfson, M Zacharias, S Qin, HX Zhou, SY Huang, X Zou, JA Wojdyla, C Kleanthous, SJ Wodak, "Blind Prediction of Interfacial Water Positions in CAPRI", Proteins, 82: 620–632. doi: 10.1002/prot.24439  (Journal Publication)  [More Details]  [Online]

Madina BR, Kumar V1 Metz R, Mooers BH, Bundschuh R, Cruz-Reyes J., "Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition", RNA. 2014 Jul;20(7):1142-52. doi: 10.1261/rna.044495.114. Epub 2014 May 27.  (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]

Fangjun Li, Cheng Cheng, Fuhao Cui, Marcos VV de Oliveira, Xiao Yu, Xiangzong Meng, Aline C Intorne, Kevin Babilonia, Maoying Li, Bo Li, Sixue Chen, Xianfeng Ma, Shunyuan Xiao, Yi Zheng, Zhangjun Fei, Richard P Metz, Charles D Johnson, Hisashi Koiwa, Wenxian Sun, Zhaohu Li, Gonçalo A de Souza Filho, Libo Shan, Ping He, "Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity", Cell Host & Microbe doi:10.1016/j.chom.2014.10.018  (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]

2013

Yijie Wang, Xiaoning Qian, , "A novel subgradient-based optimization algorithm for blockmodel functional module identification", BMC Bioinformatics, 14(Suppl 2):S23, 2013  (Journal Publication)  [More Details]  [Online]

Yang Shen, Michael D. Altman, Akbar Ali, Madhavi N. L. Nalam, Hong Cao, Tariq M. Rana, Celia A. Schiffer, and Bruce Tidor, "Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds", ACS Chemical Biology 2013 8 (11), 2433-2441  (Journal Publication)  [More Details]  [Online]

Yang Shen, "Improved flexible refinement of protein docking in CAPRI rounds 22–27", Proteins, 81: 2129–2136. doi: 10.1002/prot.24404  (Journal Publication)  [More Details]  [Online]

Weiyi Toy, Yang Shen, Helen Won, Bradley Green, Rita A Sakr, Marie Will, Zhiqiang Li, Kinisha Gala, Sean Fanning, Tari A King, Clifford Hudis, David Chen, Tetiana Taran, Gabriel Hortobagyi, Geoffrey Greene, Michael Berger, José Baselga & Sarat Chandarlapaty, "ESR1 ligand-binding domain mutations in hormone-resistant breast cancer", Nature Genetics 45, 1439–1445 (2013) doi:10.1038/ng.2822  (Journal Publication)  [More Details]  [Online]

Tao Hu, Juan Nunez-Iglesias, Shiv Naga Prasad Vitaladevuni, Lou Scheffer, Shan Xu, Mehdi Bolorizadeh, Harald F. Hess, Richard Fetter, and Dmitri B. Chklovskii, "Electron Microscopy Reconstruction of Brain Structure Using Sparse Representations Over Learned Dictionaries.", IEEE Trans. Med. Imaging 32(12):2179-2188 (2013)  (Journal Publication)  [More Details]  [Online]

Shaogang Ren, Bo Zeng, Xiaoning Qian, "Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints", BMC Bioinformatics, 14(Suppl 2):S17, 2013  (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]

Minna D Balbas, Michael J Evans, David J Hosfield, John Wongvipat, Vivek K Arora, Philip A Watson, Yu Chen, Geoffrey L Greene, Yang Shen, Charles L Sawyers, "Overcoming mutation-based resistance to antiandrogens with rational drug design", eLife 2013;2:e00499  (Journal Publication)  [More Details]  [Online]

L.X.E. de Alencar, U.M. Braga-Neto, E.J.M. Nascimento, M.T. Cordeiro, A.M. Silva, C.A.A. de Britto, M.P.C. da Silva, L.H.V.G. Gil, S. Montenegro, E.T.A. Marques, "HLA-B*44 is Associated with Dengue Severity Caused by DENV-3 in a Brazilian Population", Journal of Tropical Medicine. Volume 2013, Article ID 648475, 11 pages, 2013. doi:10.1155/2013/648475  (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]

Kahle JJ, Souroullas GP, Yu P, Zohren F, Lee Y, Shaw CA, Zoghbi HY, Goodell MA., "Ataxin1L is a regulator of HSC function highlighting the utility of cross-tissue comparisons for gene discovery", PLoS Genet. 2013 Mar;9(3):e1003359. doi: 10.1371/journal.pgen.1003359  (Journal Publication)  [More Details]  [Online]

Joshua Hill, Thomas S. Edrington, Guy H. Loneragan, Sara H. Gragg, David J. Nisbet. , "Rapid Detection of Salmonella in Bovine Lymph Nodes Using a Commercial Real-Time PCR System", Journal of Post Doctoral Research, Vol. 1, No. 2 Feb. 2013  (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]

Han K, Holder JL Jr, Schaaf CP, Lu H, Chen H, Kang H, Tang J, Wu Z, Hao S, Cheung SW, Yu P, Sun H, Breman AM, Patel A, Lu HC, Zoghbi HY., "SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties.", Nature. 2013 Nov 7;503(7474):72-7. doi: 10.1038/nature12630. Epub 2013 Oct 23.  (Journal Publication)  [More Details]  [Online]

Franco LM, Bucasas KL, Wells JM, Niño D, Wang X, Zapata GE, Arden N, Renwick A, Yu P, Quarles JM, Bray MS, Couch RB, Belmont JW, Shaw CA., "Integrative genomic analysis of the human immune response to influenza vaccination.", Elife. 2013 Jul 16;2:e00299. doi: 10.7554/eLife.00299. Print 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]

D.C. Martins, Jr., E.A. de Oliveira, U.M. Braga-Neto, R.F. Hashimoto and R.M. Cesar, Jr., "Signal Propagation in Bayesian Networks and its Relationship with Intrinsically Multivariate Predictive Variables", Information Sciences, Vol. 225, Mar 2013, pp. 18-34, doi:10.1016/j.ins.2012.10.027.  (Journal Publication)  [More Details]

Chen, T. and Braga-Neto, "Maximum-Likelihood Estimation of the Discrete Coefficient of Determination in Stochastic Boolean Systems", IEEE Transactions on Signal Processing, vol.61, no.15, pp.3880,3894, Aug.1, 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]

Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY., "An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders", Cell. 2013 Feb 28;152(5):984-96. doi: 10.1016/j.cell.2013.01.038  (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]

A.F. Pastor, L. Rodrigues, J.W.D. Neto, E.J.M. Nascimento, C.E. Calzavara-Silva, A.L.V. Gomes, A.M. da Silva, M.T. Cordeiro, U.M. Braga-Neto, S. Crovella, L.H.V.G. Gil, B. Acioli-Santos, E.T.A. Marques Jr., "Complement factor H gene (CFH) polymorphisms C-257T, G257A and haplotypes are associated with protection against Severe Dengue Phenotype, possible related with high CFH expression", Human Immunology Volume 74, Issue 9, September 2013, Pages 1225–1230  (Journal Publication)  [More Details]  [Online]

A.B. Melo, E.J.M. Nascimento, U.M. Braga-Neto, R. Dhalia, A.M. Silva, M. Oelke, J.P. Schneck, J. Sidney, A. Sette, S. Montenegro, E.T.A. Marques, "T-Cell Memory Responses Elicited by Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing Multiple HLA-I and -II Binding Motifs", PLoS Neglected Tropical Diseases, Vol. 7, No. 1, Jan 2013, p. e1938, doi:10.1371/journal.pntd.0001938  (Journal Publication)  [More Details]  [Online]

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]

2011

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]

Y. Wang, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, and H. Zhou, "Evaluation of Coverage and Depth of Transcriptome by RNA-Seq in Chickens", BMC Bioinformatics, 12 (Suppl 10):S5, 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]

Shah M.S., Schwartz S.L., Zhao C., Davidson L.A., Zhou B., Lupton J.R., Ivanov I, and Chapkin R.S., "Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: Effect of a chemoprotective diet", Physiological Genomics, 2011: 43(10)  (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]

Richardson WJ, Metz RP, Moreno MR, Wilson E, JE Moore, Jr., "A Device to Study the Effects of Stretch Gradients on Cell Behavior", J Biomech Eng. 2011 Oct;133(10):101008. doi: 10.1115/1.4005251  (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]

Fryer JD, Yu P, Kang H, Mandel-Brehm C, Carter AN, Crespo-Barreto J, Gao Y, Flora A, Shaw C, Orr HT, Zoghbi HY., "Exercise and genetic rescue of SCA1 via the transcriptional repressor Capicua.", Science. 2011 Nov 4;334(6056):690-3. doi: 10.1126/science.1212673.  (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]

A.B. Melo, M. Silva, C. Magalhaes, L.H.V.G. Gil, E.M.F. Carvalho, G.R. Bertani, U.M. Braga-Neto, E.T.A. Marques and M.T. Cordeiro, "Description of a Prospective 17DD Yellow Fever Vaccinee Cohort in Recife, Brazil", The American Journal of Tropical Medicine and Hygiene, Vol. 85, No. 4, Ocotber 2011, pp. 739-747.  (Journal Publication)  [More Details]  [Online]

2010

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]

Y. Mishchenko*, Tao Hu*, J. Spacek, J. Mendenhall, K.M. Harris and D.B. Chklovskii, "Ultrastructural analysis of hippocampal neuropil from the connectomics perspective", Neuron 67, 1009, (2010)  (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]

Ting Chen and Ulisses Braga-Neto, "Exact performance of CoD estimators in discrete prediction", Published in: · Journal EURASIP Journal on Advances in Signal Processing - Special issue on genomic signal processing archive Volume 2010, March 2010 Article No. 2   (Journal Publication)  [More Details]  [Online]

T. T. Vu and Braga-Neto, "Small-sample error estimation for bagged classification rules", Published in: · Journal EURASIP Journal on Advances in Signal Processing - Special issue on genomic signal processing archive Volume 2010, March 2010 Article No. 6   (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]

Leming et. al., "The MicroArray Quality Control (MAQC) Consortium. “MAQC-II Project: a comprehensive survey of common practices for the development and validation of microarray-based predictive models", Nat Biotechnology, 24(9), 2010, pp 827-838X.  (Journal Publication)  [More Details]  [Online]

Kozakov, D., Hall, D. R., Beglov, D., Brenke, R., Comeau, S. R., Shen, Y., Li, K., Zheng, J., Vakili, P., Paschalidis, I. Ch. and Vajda, S, "Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19", Proteins, 78: 3124–3130. doi: 10.1002/prot.22835 (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]

Dmitri Beglov, Ryan Brenke, Gwo-Yu Chuang, David Hall, Melissa Landon, Chi Ho Ngan, Yang Shen, Spencer Thiel, Brandon Zerbe, Dima Kozakov, Sandor Vajda, "Identification of Druggable Hot Spots on Proteins and in Protein–Protein Interfaces", In D Beglov, R Brenke, GY Chuang, D Hall, M Landon eds., Computational Protein-Protein Interactions, 2010, CRC Press  (Book Chapter)  [More Details]

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]

2009

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]

Lori Dalton, Virginia Ballarin, Marcel Brun, "Clustering Algorithms: On Learning, Validation, Performance, and Applications to Genomics", Curr Genomics. 2009 September; 10(6): 430–445.  (Book Chapter)  [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]

Chao Sima, Jianping Hua and Sungwon Jung, "Inference of Gene Regulatory Networks Using Time-Series Data: A Survey", Current Genomics - CURR GENOMICS , vol. 10, no. 6, pp. 416-429, 2009  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, "Hidden Markov Models and their Applications in Biological Sequence Analysis", Curr Genomics. 2009 September; 10(6): 402–415  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian , Sing-Hoi Sze, Byung-Jun Yoon, "Querying pathways in protein interaction networks based on hidden Markov models", Journal of Computational Biology, 16(2):145--157, 2009  (Journal Publication)  [More Details]  [Online]

2008

Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, "Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes", PLoS Comput Biol 4(10): e1000191. doi: 10.1371/journal.pcbi.1000191 (2008)  (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]

Tao Hu and B.I. Shklovskii, "Theory of DNA translocation through narrow ion channels and nanopores with charged walls", Physical Review E 78, 032901 (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]

2007

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]

Tao Hu, R. Zhang and B.I. Shklovskii, "Electrostatic theory of viral self-assembly: a toy model", Physica A 387, 3059 (2008)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "How a protein searches for its specific site on DNA: role of intersegment transfer", Physical Review E 76, 051909 (2007)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Kinetics of viral self-assembly: the role of ss RNA antenna", Physical Review E 75, 051901 (2007)  (Journal Publication)  [More Details]  [Online]

Shen, Y., Brenke, R., Kozakov, D., Comeau, S. R., Beglov, D. and Vajda, S. , "Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI", Proteins, 69: 734–742. doi: 10.1002/prot.21754  (Journal Publication)  [More Details]  [Online]

IC Paschalidis, Y Shen, P Vakili, S Vajda, "SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking", Automatic Control, IEEE Transactions on 52 (4), 664-676   (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]

Dmitriy Ovcharenko, Kevin Kelnar, Charles Johnson, Nan Leng, David Brown, "Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway", Cancer Res 2007;67(22):10782–8  (Journal Publication)  [More Details]  [Online]

Comeau, S. R., Kozakov, D., Brenke, R., Shen, Y., Beglov, D. and Vajda, S, "ClusPro: Performance in CAPRI rounds 6–11 and the new server", Proteins, 69: 781–785. doi: 10.1002/prot.21795  (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]

Charles D Johnson, Aurora Esquela-Kerscher, Giovanni Stefani, Mike Byrom, Kevin Kelnar, Dmitriy Ovcharenko, Mike Wilson, Xiaowei Wang, Jeffrey Shelton, Jaclyn Shingara, Lena Chin, David Brown, Frank J Slack, "The let-7 MicroRNA Represses Cell Proliferation Pathways in Human Cells", Cancer Res 2007; 67: (16). August 15, 2007  (Journal Publication)  [More Details]  [Online]

2006

Y.J. Sun, W.S. Gao,Tao Hu and Q.J. Xing, "Photoelastic Waveguides Induced by Thin Film Composite Structure in InGaAsP/InP Double Heterostructures", Semiconductor Science and Technology 21, 575 (2006)  (Journal Publication)  [More Details]  [Online]

Timothy S. Davison, Charles D. Johnson, Bernard F. Andruss, "[2] Analyzing Micro‐RNA Expression Using Microarrays", Methods in Enzymology Volume 411, 2006, Pages 14–34  (Journal Publication)  [More Details]  [Online]

Tao Hu, A.Yu. Grosberg and B.I. Shklovskii, "How proteins search for their specific sites on DNA: the role of DNA conformation", Biophysical Journal. 90, 2731 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu, A.Yu. Grosberg and B.I. Shklovskii, "Conductivity of a suspension of nanowires in a weakly conducting medium", Physical Review B 73, 155434 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "How does a protein search for the specific site on DNA: the role of disorder", Physical Review E 74, 021903 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Hopping conductivity of a suspension of flexible wires in an insulator", Physical Review B 74, 174201 (2006)  (Journal Publication)  [More Details]  [Online]

Tao Hu and B.I. Shklovskii, "Theory of hopping conductivity of a suspension of nanowires in an insulator", Physical Review B 74, 054205 (2006)  (Journal Publication)  [More Details]  [Online]

MAQC Consortium, "The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements", Nat Biotechnol. 2006 September; 24(9): 1151–1161.  (Journal Publication)  [More Details]  [Online]

2004

Tao Hu, Y. Fu, H. Zhang, S.L. Zhang, J. Ouyang and X.S. Zhao, "Temperature-dependent Raman Spectra of α-Fe2O3 Nano-wire and Bulk Material", Chinese Journal of Light Scattering 16, 303 (2004)  (Journal Publication)  [More Details]

Tao Hu, X. Lu, Y. Yan, Y. Fu, H. Zhang and S. L. Zhang, "Raman Spectroscopic Study on Iron Oxides Prepared by Oxidation of Iron", Spectroscopy and Spectral Analysis 24, 1072 (2004)  (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]

2003

W.S. Gao, Q.J. Xing, Z.J. Yuan and Tao Hu, "W0.95Ni0.05 Compressive Strain Thin Film Stripe Window Induced Photoelastic Waveguide Structure in InGaAsP/InP Double Heterostructure", 2003 Chinese Phys. Lett. 20 1296 doi:10.1088/0256-307X/20/8/333  (Journal Publication)  [More Details]  [Online]