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Author: Braga-Neto, Ulisses

U.M. Braga-Neto, E. Arslan, U. Banerjee, and A. Bahadorinejad, "Bayesian Classification of Genomic Big Data", In Signal Processing and Machine Learning for Biomedical Big Data. Edited by E. Sedjic and T. Falk. CRC Press, 2018.  (Book Chapter)  [More Details]

M. Imani and U.M. Braga-Neto, , "Control of Gene Regulatory Networks using Bayesian Inverse Reinforcement Learning", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Special Issue on Advanced Machine Learning Techniques for Bioinformatics, 2018.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Particle Filters for Partially-Observed Boolean Dynamical Systems", Automatica, Vol. 87, Jan 2018, pp 238-250.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Point-Based Methodology to Monitor and Control Gene Regulatory Networks via Noisy Measurements", IEEE Transactions on Control Systems Technology, Early Access, Vol. PP, Issue 99, 2018, pp. 1-13.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Finite-Horizon LQR Controller for Partially-Observed Boolean Dynamical Systems", in press, Automatica, 2018  (Journal Publication)  [More Details]  [Online]

Karbalayghareh A, Braga-Neto U, Hua J, Dougherty ER., "Classification of State Trajectories in Gene Regulatory Networks.", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, Issue 1, Jan 2018, pp. 68-82.  (Journal Publication)  [More Details]  [Online]

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]

A. Karbalayghareh, U.M. Braga-Neto, and E.R. Dougherty, "Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks", BMC Systems Biology, Vol. 12 (Suppl 3), Mar 2018, p. 23.  (Journal Publication)  [More Details]  [Online]

A. Bahadorinejad and U.M. Braga-Neto, "Optimal Fault Detection and Diagnosis in Transcriptional Circuits using Next-Generation Sequencing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, Issue 2, Mar-Apr 2018  (Journal Publication)  [More Details]  [Online]

U. Banerjee and U.M. Braga-Neto, "Bayesian ABC-MCMC Classification of Liquid-Chromatography Mass Spectrometry Data", Cancer Informatics, Vol. 2015(Supp 5), Jan 2017, pp. 175-182.  (Journal Publication)  [More Details]  [Online]

R. Oliveira, M.T. Cordeiro, P. Moura, P. BaptistaFilho, U.M. Braga-Neto, E.T.A. Marques Júnior, L.H.V.G. Gil, "Serum cytokine/chemokine profiles in patients with dengue fever (DF) and dengue hemorrhagic fever (FHD) by using protein array", Journal of Clinical Virology, Vol. 89, Apr 2017, pp. 39-45.  (Journal Publication)  [More Details]  [Online]

P.K. Riggs, L.O. Tedeschi, N.D. Turner, U. Braga-Neto, A. Jayaraman, "The role of ‘omics’ technologies for livestock sustainability", Latin-American Archives of Animal Production, Vol. 25, 2017, pp. 147-153.  (Journal Publication)  [More Details]

M. Imani and U.M. Braga-Neto, "Gene regulatory network state estimation from arbitrary correlated measurements", EURASIP Journal on Advances in Signal Processing, Vol. 2018, Apr 2018, p. 22.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Maximum-Likelihood Adaptive Filter for Partially-ObservedBoolean Dynamical Systems", IEEE Transactions on Signal Processing, Vol. 65, No. 2, Jan 2017, pp. 359-371.  (Journal Publication)  [More Details]  [Online]

M. Imani and U.M. Braga-Neto, "Control of Gene Regulatory Networks with Noisy Measurements and Uncertain Inputs", IEEE Transactions on Control of Network Systems, Early Access, Vol. PP, Issue 99, 2017, pp. 1-1.  (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]

L.D. Mcclenny, M. Imani and U. M Braga-Neto, "BoolFilter: an R package for estimation and identification of Partially-Observed Boolean Dynamical Systems,", BMC Bioinformatics, Vol. 87, Jan 2018, pp 238-250.  (Journal Publication)  [More Details]  [Online]

T. Chen and U.M. Braga-Neto, "Bayesian Estimation of the Discrete Coefficient of Determination", Special Issue on Bayesian Methods for Computational Systems Biology, EURASIP Journal of Bioinformatics and Systems Biology, 2016 Jan 15;2016(1):1.  (Journal Publication)  [More Details]  [Online]

T. Chen and U.M. Braga-Neto, "Statistical Detection of Intrinsically Multivariate Predictive Genes", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, No. 4, Jul-Aug 2015, pp. 951-964.  (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]

B. Afsari, U.M. Braga-Neto, and D. Geman, "Rank Discriminants for Predicting Phenotypes from RNA Expression.", Annals of Applied Statistics, Vol. 8, No. 3, Sep 2014, pp. 1469-1491.  (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]

T. Chen and U.M. Braga-Neto, "Statistical Detection of Boolean Regulatory Relationships", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Sep-Oct 2013;10(5):1310-21,doi: 10.1109/TCBB.2013.118.  (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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]