Computer Engineering and Systems Group

Publications (Braga)

Braga-Neto Homepage

Selected Publications

  • U.M. Braga-Neto and E.R. Dougherty, Error Estimation for Pattern Recognition, Wiley-IEEE, 2015.
  • M. Imani and U.M. Braga-Neto, “Finite-Horizon LQR Controller for Partially-Observed Boolean Dynamical Systems,” Automatica, Vol. 95, Sep 2018, pp. 172-179.
  • 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.
  • 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.
  • 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.
  • M. Imani and U.M. Braga-Neto, “Particle Filters for Partially-Observed Boolean Dynamical Systems,” Automatica, Vol. 87, Jan 2018, pp 238-250.
  • 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.
  • M. Imani and U.M. Braga-Neto, “Maximum-Likelihood Adaptive Filter for Partially-Observed Boolean Dynamical Systems,” IEEE Transactions on Signal Processing, Vol. 65, No. 2, Jan 2017, pp. 359-371.
  • 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.
  • T. Chen and U.M. Braga-Neto, “Maximum-Likelihood Estimation of the Discrete Coefficient of Determination in Stochastic Boolean Systems,” IEEE Transactions on Signal Processing, Vol. 61, No. 15, August 1 2013, pp. 3880-3894.
  • 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.
  • U.M. Braga-Neto, “Optimal State Estimation for Boolean Dynamical Systems,” Proceedings of the 45th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, November 2011.
  • A. Zollanvari, U.M. Braga-Neto and E.R. Dougherty, “Joint Sampling Distribution Between Actual and Estimated Classification Errors for Linear Discriminant Analysis,” IEEE Transactions on Information Theory, Vol. 56, No. 2, February 2010, pp. 784-804.
  • E.J.M. Nascimento, U.M. Braga-Neto, C. Calvazara, A.L. Gomes, F. Abath, B. Acioli, C.A.A. Brito, M.T. Cordeiro, A.M. Silva, C. Magalhaes, R. Andrade, L.H.V.G. Gil and E.T.A. Marques, Jr., “Gene Expression Profiling During Acute Stage of Dengue Infection,” PLoS ONE, Vol. 4, No. 11, Nov 2009, p. e7892, doi:10.1371/journal.pone.0007892.
  • U.M. Braga-Neto, “Fads and Fallacies in the Name of Small-Sample Microarray Classification,” IEEE Signal Processing Magazine, Special Issue on Signal Processing Methods in Genomics and Proteomics, Vol. 24, No. 1, January 2007, pp. 91-99.
  • U.M. Braga-Neto and E.A.T. Marques, Jr., “From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards,” PLoS Computational Biology, Vol. 2, No. 7, July 2006, p. e81
  • U.M. Braga-Neto and E. Dougherty, “Bolstered Error Estimation,” Pattern Recognition, Vol. 37, No. 6, June 2004, pp. 1267-1281.
  • U.M. Braga-Neto and E. Dougherty, “Is Cross-Validation Valid for Small-Sample Microarray Classification?” Bioinformatics, Vol. 20, No. 3, February 2004, pp. 374-380.