
Ulisses BragaNeto's Publications
Book

U.M. BragaNeto and Edward Dougherty, Error Estimation for Pattern Recognition, WileyIEEE Press, July 2015.
Journal Papers in Reverse Chronological Order

M. Imani and U.M. BragaNeto, "MaximumLikelihood Adaptive Filter for PartiallyObserved Boolean Dynamical Systems," in press, IEEE Transactions on Signal Processing, 2016.

A. Karbalayghareh, U.M. BragaNeto, J. Hua, and E.R. Dougherty, "Classification of State Trajectories in Gene Regulatory Networks," in press, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016.

U. Banerjee and U.M. BragaNeto, "Bayesian ABCMCMC Classification of LiquidChromatography Mass Spectrometry Data," in press, Cancer Informatics, 2016.

T. Chen and U.M. BragaNeto, "Bayesian Estimation of the Discrete
Coefficient of Determination," EURASIP Journal on Bioinformatics and Systems Biology, Special Issue on Bayesian Methods for Computational Systems Biology, 2016, 2016:1

A. Bahadorinejad and U.M. BragaNeto, "Optimal Fault Detection and Diagnosis in Transcriptional Circuits using NextGeneration Sequencing," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. PP, No. 99, 2015.

T. Chen and U.M. BragaNeto, "Statistical Detection of Intrinsically Multivariate Predictive Genes," IEEE/ACM Transactions on
Computational Biology and Bioinformatics, Vol. 12, No. 4, JulAug 2015, pp. 951964.

U.M. BragaNeto, A. Zollanvari, and E.R. Dougherty,
"Crossvalidation under separate sampling: strong bias and how to
correct it," Bioinformatics, Vol. 30, No. 23, Dec 1 2014, pp. 33493355.

B. Afsari, U.M. BragaNeto, and D. Geman, "
Rank discriminants for predicting phenotypes from RNA expression," Annals of Applied Statistics, Vol. 8, No. 3, Sep 2014, pp. 14691491.

T.T. Vu, C. Sima, U.M. BragaNeto, and E.R. Dougherty,
"Unbiased Bootstrap Error Estimation for Linear Discriminant
Analysis," EURASIP Journal on Bioinformatics and Systems Biology, 2014, 2014:15

E. AtashpazGargari, U.M. BragaNeto, 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.
T. Chen and U.M. BragaNeto, "Statistical Detection of Boolean Regulatory
Relationships," IEEE/ACM Transactions on Computational Biology and Bioinformatics,
Vol. 10, No. 5, SepOct 2014, pp. 13101321. doi: 10.1109/TCBB.2013.118. [IEEE Explore]
[Preprint]
T. Chen and U.M. BragaNeto, "MaximumLikelihood
Estimation of the Discrete Coefficient of Determination in Stochastic
Boolean Systems," IEEE Transactions on
Signal Processing, Vol. 61, No. 15, August 1 2013, pp. 38803894.
[IEEE Explore]
[Preprint]
A.F. Pastor, L. Rodrigues, J.W.D. Neto, E.J.M. Nascimento,
C.E. CalzavaraSilva, A.L.V. Gomes, A.M. da Silva, M.T. Cordeiro,
U.M. BragaNeto, S. Crovella, L.H.V.G. Gil, B. AcioliSantos,
E.T.A. Marques Jr., "Complement factor H gene (CFH) polymorphisms
C257T, G257A and haplotypes are associated with protection against
Severe Dengue Phenotype, possible related with high CFH expression,"
Human Immunology, Vol. 74, No. 8, Sep 2013, pp. 12251230, doi:10.1016/j.humimm.2013.05.005. Epub 2013 Jun 6.
[PubMed]
L.X.E. de Alencar, U.M. BragaNeto, 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, "HLAB*44 is Associated
with Dengue Severity Caused by DENV3 in a Brazilian Population,"
Journal of Tropical Medicine.
Volume 2013, Article ID 648475, 11 pages, 2013. doi:10.1155/2013/648475
[Hindawi Open Access]
D.C. Martins, Jr., E.A. de Oliveira, U.M. BragaNeto, 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. 1834, doi:10.1016/j.ins.2012.10.027.
A.B. Melo, E.J.M. Nascimento, U.M. BragaNeto, R. Dhalia,
A.M. Silva, M. Oelke, J.P. Schneck, J. Sidney, A. Sette,
S. Montenegro, E.T.A. Marques, "TCell Memory Responses Elicited by
Yellow Fever Vaccine are Targeted to Overlapping Epitopes Containing
Multiple HLAI and II Binding Motifs," PLoS Neglected Tropical
Diseases, Vol. 7, No. 1, Jan 2013, p. e1938, doi:10.1371/journal.pntd.0001938.
[PubMed]
E. AtashpazGargari, C. Sima, U.M. BragaNeto 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 13151322,
doi:10.1016/j.patcog.2012.10.020.
Y. Sun, U.M. BragaNeto and E.R. Dougherty,
"A systematic model of the LCMS proteomics pipeline,"
BMC Genomics, GENSIPS'2011 Special Issue,
Vol. 13, Suppl. 6, October 2012, p. S2,
doi:10.1186/1471216413S6S2
[BMC Open Access]
[PubMed]
C.C. Allen, B.R.C. Alves, X. Li, L.O. Tedeschi, H. Zhou, J.A. Paschal,
P. Riggs, U.M. BragaNeto, 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 lowconcentrate diets," Journal of Animal Sciences, Vol. 90, No. 7,
July 2012, pp. 22222232. [PubMed]
Y. Sun, J. Zhang, U.M. BragaNeto and E.R. Dougherty,
"BPDA2d  A 2D global optimization based Bayesian peptide detection algorithm for LCMS,"
Bioinformatics, Vol. 28, No. 4,
February 2012, pp. 564572. [PubMed]
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty,
"Exact representation of the secondorder moments for resubstitution and
leaveoneout error estimation for linear discriminant analysis in the
univariate heteroskedastic Gaussian model," Pattern
Recognition, Vol. 45, No. 2,
February 2012, pp. 908917. [Preprint]
C. Sima, T.T. Vu, U.M. BragaNeto and E.R. Dougherty,
"HighDimensional Bolstered Error Estimation," Bioinformatics,
Vol. 27, No. 21, September 2011, pp. 30563064.
[PubMed]
Y. Wang, N. Ghaffari, C.D. Johnson, U.M. BragaNeto, H. Wang, R. Chen and H. Zhou,
"Evaluation of coverage and depth of transcriptome by RNASeq in chickens,"
BMC Bioinformatics, MCBIOS'2011 Special Issue,
Vol. 12, Suppl. 10, October 2011, p. S5,
doi:10.1186/1471210512S10S5
[BMC Open Access]
A.B. Melo, M. Silva, C. Magalhaes, L.H.V.G. Gil, E.M.F. Carvalho, G.R. Bertani, U.M. BragaNeto, 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. 739747.
[PubMed]
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty,
"Analytic Study of Performance of Error Estimators for
Linear Discriminant Analysis," IEEE Transactions on
Signal Processing, Vol. 59, No. 9, September 2011, pp. 42384255.
[IEEE Explore]
[Preprint]
E.R. Dougherty, A. Zollanvari and U.M. BragaNeto,
"The Illusion of DistributionFree SmallSample Classification in Genomics,"
Current Genomics, Vol. 12, No. 5, August 2011, pp. 333341.
[Preprint]
T. Chen and U.M. BragaNeto, "Exact Performance of CoD
Estimators in Discrete Prediction," EURASIP Journal on Advances in
Signal Processing (JASP), Special Issue on Genomic Signal
Processing,
Volume 2010, Article ID 487893, 13 pages, 2010. doi:10.1155/2010/487893
[Hindawi Open Access]
T.T. Vu and U.M. BragaNeto, "SmallSample Error Estimation
for Bagged Classification Rules," EURASIP Journal on Advances in
Signal Processing (JASP), Special Issue on Genomic Signal
Processing.
Volume 2010, Article ID 548906, 12 pages, 2010. doi:10.1155/2010/548906
[Hindawi Open Access]
Y. Sun, J. Zhang, U.M. BragaNeto and E.R. Dougherty,
"BPDA  a Bayesian peptide detection algorithm for mass spectrometry,"
BMC Bioinformatics, Vol. 11, September 2010, p. 490,
doi:10.1186/1471210511490
[PubMed]
[BMC Open Access]
A. Zollanvari, U.M. BragaNeto 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. 784804.
[IEEE Explore]
[Preprint]
U.M. BragaNeto and E.R. Dougherty, "Exact Correlation
between Actual and Estimated Errors in Discrete Classification,"
Pattern Recogition Letters, Vol. 31, No. 5, April 2010, pp. 407412.
[Preprint]
E.R. Dougherty, C. Sima, J. Hua, B. Hanczar and U.M. BragaNeto,
"Performance of Error Estimators for Classification,"
Current Bioinformatics, Vol. 5, No. 1, March 2010, pp. 5367.
[Preprint]
Y. Sun, U.M. BragaNeto and E.R. Dougherty, "Impact of Missing
Value Imputation on Classification for DNA
Microarray Gene Expression Data  A ModelBased Study,"
EURASIP Journal on Bioinformatics and Systems Biology,
Volume 2009, Article ID 504069, November 2009, 17 pages,
doi:10.1155/2009/504069
[PubMed]
[Hindawi Open Access]
E.J.M. Nascimento, U.M. BragaNeto, 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, November 2009, p.
e7892, doi:10.1371/journal.pone.0007892
[PubMed]
[PLoS Open Access]
U.M. BragaNeto, "Classification and Error Estimation for Discrete Data," Current Genomics, Vol. 10, No. 7, November 2009, pp. 446462.
[PubMed]
[Preprint]
A. Zollanvari, M.J. Cunningham, U.M. BragaNeto and E.R. Dougherty,
"Analysis and Modeling of TimeCourse GeneExpression Profiles from
NanomaterialExposed Primary Human Epidermal Keratinocytes," BMC Bioinformatics,
MCBIOS'2009 Special Issue, Vol. 10, Suppl. 11, October 2009, p. S10.
[PubMed]
[BMC Open Access]
E.J.M. Nascimento, A.M. Silva, M.T. Cordeiro, C.A.A. Brito,
L.H.V.G. Gil, Ulisses BragaNeto and E.T.A. Marques, Jr.,
"Alternative Complement Pathway Deregulation Is Correlated with Dengue Severity,"
PLoS ONE, Vol. 4, No. 8, August 2009, p. e6782.
[PubMed]
[PLoS Open Access]
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty, "On the Sampling
Distribution of Resubstitution and LeaveOneOut Error Estimators for
Linear Classifiers," Pattern Recognition, Vol. 42, No. 11, November 2009, pp. 27052723. [Preprint]
T.T. Vu and U.M. BragaNeto, "Is Bagging Effective in the
Classification of SmallSample Genomic and Proteomic Data?" EURASIP
Journal on Bioinformatics and Systems Biology, Special Issue on
Applications of Signal Processing Techniques to Bioinformatics,
Genomics, and Proteomics,
Volume 2009, Article ID 158368, 10 pages, 2009. doi:10.1155/2009/158368
[PubMed]
[Hindawi Open Access]
M.T. Cordeiro, U.M. BragaNeto, R.M.R. Nogueira and E.T.A. Marques, Jr.,
"Reliable classifier to differentiate primary and secondary acute dengue infection based on IgG ELISA," PLoS ONE, Vol. 4, No. 4, April 2009, p. e4945.
[PubMed]
[PLoS Open Access]
D.C. Martins, Jr., U.M. BragaNeto, R.F. Hashimoto,
M.L. Bittner and E.R. Dougherty, "Intrinsically Multivariate Predictive Genes,"
IEEE Journal of Selected Topics in Signal Processing, Vol. 2, No. 3,
June 2008, pp. 424439. [IEEE Explore] [Preprint]
B. AcioliSantos, L. Segat, R. Dhalia,
C.A.A. Brito, U.M. BragaNeto, E.T.A. Marques
and S. Crovella,
"MBL2 Gene Polymorphisms Protect Against Development of
Thrombocytopenia Associated with Severe Dengue Phenotype,"
Human Immunology, Vol. 69, No. 2, February 2008, pp. 122128.
[PubMed]
U.M. BragaNeto,
"Fads and Fallacies in the Name of SmallSample Microarray Classification,"
IEEE Signal Processing Magazine,
Special Issue on Signal Processing Methods in Genomics and Proteomics,
Vol. 24, No. 1, January 2007, pp. 9199.
[IEEE Explore]
[Preprint]
Q. Xu, J. Hua, U.M. BragaNeto, Z. Xiong, E. Suh and E.R. Dougherty,
"Confidence Intervals for the True Classification Error Conditioned on the Estimated Error,"
Technology in Cancer Research and Treatment,
Vol. 5, No. 6, December 2006, pp. 579590.
[PubMed]
U.M. BragaNeto 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
[PubMed]
[PLoS Open Access]
E. Dougherty and U.M. BragaNeto,
"Epistemology of Computational Biology: Mathematical Models and Experimental
Prediction as the Basis of Their Validity,"
Journal of Biological Systems, Vol. 14, No. 1, March 2006, pp. 6590.
C. Sima, S. Attoor, U.M. BragaNeto, J. Lowey, E. Suh and E. Dougherty,
"Impact of Error Estimation on FeatureSelection Algorithms,"
Pattern Recognition, Vol. 38, No. 12, December 2005, pp. 24722482.
U.M. BragaNeto and E. Dougherty,
"Exact Performance of Error Estimators for Discrete Classifiers,"
Pattern Recognition, Vol. 38, No. 11, November 2005, pp. 17991814.
[Preprint]
U.M. BragaNeto and J. Goutsias,
"Constructing Multiscale Connectivities,"
Computer Vision and Image Understanding,
Vol. 99, No. 1, July 2005, pp. 126150.
[Preprint]
U.M. BragaNeto and J. Goutsias,
"ObjectBased Image Analysis Using Multiscale Connectivity,"
IEEE Transactions on Pattern Analysis and Machine Intelligence,
Vol. 27, No. 6, June 2005, pp. 892907.
[IEEE Explore]
[PubMed]
U.M. BragaNeto,
"Multiscale Connected Operators,"
Journal of Mathematical Imaging and Vision
(Special Issue on Mathematical Morphology After 40 Years),
Vol. 22, No. 23, May 2005, pp. 199216.
[Preprint]
C. Sima, U.M. BragaNeto and E. Dougherty,
"Superior FeatureSet Ranking for Small Samples
Using Bolstered Error Estimation,"
Bioinformatics,
Vol. 21, No. 7, April 2005, pp. 10461054.
[PubMed]
U.M. BragaNeto and J. Goutsias,
"Grayscale Level Connectivity: Theory and Applications,"
IEEE Transactions on Image Processing,
Vol. 13, No. 12, December 2004, pp. 15671580.
[IEEE Explore]
[PubMed]
U.M. BragaNeto and E. Dougherty,
"Bolstered Error Estimation,"
Pattern Recognition,
Vol. 37, No. 6, June 2004, pp. 12671281.
[Preprint]
U.M. BragaNeto and E. Dougherty,
"Is CrossValidation Valid for SmallSample Microarray Classification?"
Bioinformatics,
Vol. 20, No. 3, February 2004, pp. 374380.
[PubMed]
U.M. BragaNeto, R. Hashimoto, E. Dougherty, D. Nguyen and R. Carroll,
"Is CrossValidation Better Than Resubstitution for Ranking Genes?"
Bioinformatics,
Vol. 20, No. 2, January 2004, pp. 253258.
[PubMed]
U.M. BragaNeto, M. Choudhary and J. Goutsias,
"Automatic target detection and tracking on
forwardlooking infrared image sequences
using morphological connected operators,"
Journal of Electronic Imaging,
Vol. 13, No. 4, 2004, pp. 802813.
[Preprint]
U.M. BragaNeto and J. Goutsias,
"Supremal Multiscale Signal Analysis,"
SIAM Journal of Mathematical Analysis,
Vol. 36, No. 1, 2004, pp. 94120.
U.M. BragaNeto and J. Goutsias,
"A Theoretical Tour of Connectivity
in Image Processing and Analysis,"
Journal of Mathematical Imaging and Vision,
Vol. 19, No. 1, 2003, pp. 531.
U.M. BragaNeto and J. Goutsias,
"A Multiscale Approach to Connectivity,"
Computer Vision and Image Understanding,
Vol. 89, No. 1, 2003, pp. 70107.
U.M. BragaNeto and J. Goutsias,
"Connectivity on Complete Lattices: New Results,"
Computer Vision and Image Understanding,
Vol. 85, No. 1, 2002, pp. 2253.
X. Han, C. Xu, U.M. BragaNeto and J.L. Prince,
"Topology Correction in Brain Cortex Segmentation
Using a Multiscale, GraphBased Algorithm,"
IEEE Transactions on Medical Imaging,
Vol. 21, No. 2, 2002, pp. 109121.
[IEEE Explore]
[PubMed]
A.J. Candéas, U.M. BragaNeto and E.C.B. Carvalho Filho,
"A Mathematical Morphology Approach to
the Star/Galaxy Characterization Problem,"
Journal of the Brazilian Computer Society,
Special Issue on Computer Graphics
and Image Processing, Vol. 3, No. 3, 1997, pp. 1429. [HTML]
Book Chapters
R. Dhalia, L. Gil, E. Nascimento, U.M. BragaNeto and E.T.A. Marques Jr.,
"Epitope Mapping: Rational Search for the Development of vaccines Against
Chronic Diseases" (in Portuguese),
In Epidemiology, Policy, and Determining Factors of Chronic Diseases
in Brazil (in Portuguese).
Edited by Eduardo Freese.
Editora Universitária UFPE, Recife, Brazil, 2006, pp. 321340.
U.M. BragaNeto and E. Dougherty,
"Classification,"
In Genomic Signal Processing and Statistics,
Edited by E. Dougherty, I. Shmulevich, J. Chen and Z. J. Wang,
EURASIP Book Series on Signal Processing and Communication,
Hindawi Publishing Corporation, 2005.
[Preprint]
Note: The preprint PDF linked above already contains the correct
Figures 3.8 and 3.9 (see Erratum).
Selected Conference Papers, Posters, and Abstracts
M. Imani and U.M. BragaNeto, "PointBased Value Iteration for PartiallyObserved Boolean Dynamical Systems with Finite Observation Spaces," 55th IEEE Conference on Decision and Control, Las Vegas, December 2016.
M. Imani and U.M. BragaNeto, "Optimal Intervention Strategy for Boolean Dynamical Systems Observed through RNASeq Data," American Control Conference, Boston, July 2016.
X. Jiang, Y. Che, U.M. BragaNeto and M. Dickman, "Identification of Biotic and Abiotic Stress Induced Pathways in Bananas," Plant Biology 2016 Conference, Austin, July 2016.
M. Imani and U.M. BragaNeto, "Optimal Gene Regulatory Network Inference using the Boolean Kalman Filter and Multiple Model Adaptive Estimation," Proceedings of the 3rd IEEE Global Conference on Signal and Information Processing (GlobalSip'2015), Orlando, FL, December 2015.
M. Imani and U.M. BragaNeto, "Optimal State Estimation for Boolean Dynamical Systems using a Boolean Kalman Smoother," Proceedings of the 49th Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, November 2015. [Finalist Paper Award]
M. Imani and U.M. BragaNeto, "Adaptive Estimation and Control of Boolean Dynamical Systems," Poster presented at the Eighth Annual Winedale Workshop, Winedale, TX, October 2015.
X. Jiang, Y. Che, U.M. BragaNeto and M. Dickman, "Gene Expression Profiling of Transgenic Banana under Infection Conditions," Poster presented at the Eighth Annual Winedale Workshop, Winedale, TX, October 2015.
M. Imani and U.M. BragaNeto, "Control and Inference of Gene Regulatory Networks," Poster presented at the 1st Annual Symposium for Genome Sciences and Society (TIGSS), College Station, TX, October 2015.
A. Bahadorinejad and U.M. BragaNeto,
"Optimal Fault Detection in Stochastic Boolean Regulatory Networks,"
Proceedings of IEEE International Workshop on Genomic Signal
Processing and Statistics (GENSIPS'2014), Atlanta, GA, December 2014.
X. Jiang and BragaNeto, "A NaiveBayes
Approach to Bolstered Error Estimation in HighDimensional Spaces,"
Proceedings of IEEE International Workshop on Genomic Signal
Processing and Statistics (GENSIPS'2014), Atlanta, GA, December 2014.
U.M. BragaNeto, "Particle Filtering
Approach to State Estimation in Boolean Dynamical Systems,"
Proceedings of the IEEE Global Conference on Signal & Image Processing (GlobalSIP'13), Austin, TX, December 2013.
[Preprint]
T. Chen and U.M. BragaNeto,
"Optimal Bayesian MMSE Estimation of the Coefficient of Determination for Discrete Prediction,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2013), Houston, TX,
November 2013.
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty,
"Effect of Mixing Probabilities on the Bias of CrossValidation Under Separate Sampling,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2013), Houston, TX,
November 2013.
E. AtashpazGargari, U.M. BragaNeto and E.R. Dougherty,
"Improved BranchandBound Algorithm for UCurve Optimization,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2013), Houston, TX,
November 2013.
T. Chen and U.M. BragaNeto,
"A Statistical Test for Intrinsically Multivariate Predictive Genes,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2012), Washington, DC,
December 2012.
U.M. BragaNeto, "Joint State and Parameter Estimation for Boolean Dynamical Systems,"
Proceedings of the IEEE Statistical Signal Processing Workshop (SSP'12),
Ann Arbor, MI, August 2012.
[Preprint]
T. Chen and U.M. BragaNeto,
"SampleBased Estimators for the Intrinsically Multivariate Prediction Score,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2011), San Antonio, TX,
December 2011.
S. Afra and U.M. BragaNeto,
"Peaking Phenomenon and Error Estimation for Support Vector Machines,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2011), San Antonio, TX,
December 2011.
Y. Sun, U.M. BragaNeto and E.R. Dougherty,
"Modeling and systematic analysis of LCMS proteomics pipeline,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2011), San Antonio, TX,
December 2011.
E. AtashpazGargari, U.M. BragaNeto and E.R. Dougherty,
"Multiple Reaction Monitoring: Modeling and Systematic Analysis."
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2011), San Antonio, TX,
December 2011.
E. AtashpazGargari, C. Sima, U.M. BragaNeto and E.R. Dougherty,
Relationship Between the Accuracy of Classifier Error Estimation and Distribution Complexity,"
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2011), San Antonio, TX,
December 2011.
Z. Zhang, Y. Sun, U.M. BragaNeto, E.R. Dougherty and J. Zhang,
"A parallel programming framework with Markovian messaging for LCMS
peptide peak detection."
Proceedings of IEEE International Conference on Bioinformatics and Biomedicine
(BIBM'2011), Atlanta, GA, November 2011.
U.M. BragaNeto, "Optimal State Estimation for Boolean Dynamical Systems,"
Proceedings of the 45th Asilomar Conference on Signals, Systems, and Computers,
Pacific Grove, CA, November 2011.
[Preprint]
T. Chen and U.M. BragaNeto,
"Maximum Likelihood Estimation of the Binary Coefficient of Determination,"
Proceedings of the 45th Asilomar Conference on Signals, Systems, and Computers,
Pacific Grove, CA, November 2011.
Y. Sun, J. Zhang, U.M. BragaNeto and E.R. Dougherty,
"BPDA2D  An improved Bayesian peptide detection algorithm for Mass Spectrometry,"
59th ASMS Conference on Mass Spectrometry and Allied Topics,
Denver, Colorado, June 2001.
T. Chen and Ulisses BragaNeto,
"Maximum Likelihood Estimation of the Binary Coefficient of Determination,"
Eighth Annual Conference of the MidSouth Computational Biology and
Bioinformatics Society (MCBIOS'2011), College Station, TX, April 2011.
Y. Sun, J. Zhang, U.M. BragaNeto and E.R. Dougherty,
"BPDA+  An improved Bayesian peptide detection algorithm for Mass Spectrometry,"
Eighth Annual Conference of the MidSouth Computational Biology and
Bioinformatics Society (MCBIOS'2011), College Station, TX, April 2011.
E. AtashpazGargari, C. Sima, U.M. BragaNeto and E.R. Dougherty,
Relationship Between the Accuracy of Classifier Error Estimation and Distribution Complexity,"
Eighth Annual Conference of the MidSouth Computational Biology and
Bioinformatics Society (MCBIOS'2011), College Station, TX, April 2011.
Y. Wang, N. Ghaffari, C.D. Johnson, U.M. BragaNeto, H. Wang, R. Chen and H. Zhou,
"Evaluation of Coverage and Depth of Transcriptome by RNASEQ In Chickens,"
Eighth Annual Conference of the MidSouth Computational Biology and
Bioinformatics Society (MCBIOS'2011), College Station, TX, April 2011.
T. Chen and U.M. BragaNeto,
"Approximate expressions for the variances of nonrandomized
error estimators and CoD estimators for the discrete histogram
rule."
Proceedings of the IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2010), Cold Spring Harbor, NY,
November 2010.
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty,
"RMS bounds and sample size considerations for error estimation
in linear discriminant analysis."
Proceedings of the IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2010), Cold Spring Harbor, NY,
November 2010.
C.C. Allen, X. Li, L.O. Tedeschi, H. Zhou, J.A. Paschal,
T.E. Spencer, U.M. BragaNeto, D.H. Keisler, M. Amstalden,
and G.L. Williams,
"Dietary Treatments that Facilitate Early Onset of
Puberty in Heifers Alter Gene Expression in the Arcuate Nucleus."
Proceedings of the 42nd SSR Annual Meeting, Pittsburgh, PA, July 2009.
C. Sima, T.T. Vu, U.M. BragaNeto and E.R. Dougherty,
"Bolstered Error Estimation with Feature Selection."
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2009), Minneapolis, MN,
May 2009.
A. Zollanvari, U.M. BragaNeto and E.R. Dougherty,
"Sample Size Calculation from Specified RMS of the Resubstitution
Error for Linear Classifiers."
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2009), Minneapolis, MN,
May 2009.
E. Nascimento, U.M. BragaNeto, C. CalzavaraSilva, A. Gomes
F. Abath, C Brito, M.Cordeiro, A. Silva, C. Magalhaes, R. Andrade,
L. Gil and E.T.A. Marques, Jr.,
"Gene expression profiling during acute stage of dengue infection can predict patient outcome."
Proceedings of First Pan American Dengue Research Network Meeting,
Recife, Brazil, July 2008.
E. Nascimento, A. Silva, B. AcioliSilva, C. CalzavaraSilva, U.M. BragaNeto, M. Cordeiro, C. Brito, M. Magalhaes, L. Gil and E.T.A. Marques, Jr.,
"Analysis of Complement System Reveals That Increased Alternative Pathway Activation Is correlated With Dengue Severity."
Proceedings of First Pan American Dengue Research Network Meeting,
Recife, Brazil, July 2008.
B. AcioliSilva, E. Nascimento, F. Pastor, C. CalzavaraSilva, A. Gomes, A. Silva, M. Cordeiro, U.M. BragaNeto, S. Crovella and E.T.A. Marques, Jr.,
"Complement Factor H (CFH) Promoter Polymorphism C257T is Correlated with High Levels
of CFH mRNA and Protein Expression and Resistance to Dengue Hemorrhagic Fever."
Proceedings of First Pan American Dengue Research Network Meeting,
Recife, Brazil, July 2008.
E. Nascimento, U.M. BragaNeto, M. Magalhaes, C. Brito,
M. Cordeiro, A. Silva and E.T.A. Marques, Jr.,
"HLAC alleles are associated with resistance to sequential dengue infection
and clinical outcomes."
Proceedings of First Pan American Dengue Research Network Meeting,
Recife, Brazil, July 2008.
U.M. BragaNeto,
"An AsymptoticallyExact Expression for the Variance of Classification
Error for the Discrete Histogram Rule."
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2008), Phoenix, AZ,
June 2008.
D.C. Martins, Jr., U.M. BragaNeto, M.L. Bittner and
E.R. Dougherty, "Network Properties of Intrinsically Multivariate
Predictive Genes." Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2008), Phoenix, AZ,
June 2008.
T.T. Vu, U.M. BragaNeto and E.R. Dougherty,
"Preliminary Study on Bolstered Error Estimation in HighDimensional Spaces."
Proceedings of IEEE International Workshop on
Genomic Signal Processing and Statistics (GENSIPS'2008), Phoenix, AZ,
June 2008.
U.M. BragaNeto, Error Estimation Critically Impacts
"Feature Selection in Genomics and Proteomics Applications." Presented at The Fifth
Annual Conference of the MidSouth Computational Biology and
Bioinformatics Society (MCBIOS 2008), Oklahoma City, OK, February 2008.
M. Pereira, A. Pastor, B. AcioliSantos, L. Segat, R. Dhalia,
U.M. BragaNeto, E.T.A. Marques, Jr. and S. Crovella, "MBL2 gene
polymorphisms protect against severe dengue manifestation associated
with thrombocytopenia phenotype development." Proceedings of XVIII
Brazilian Virology Meeting, Buzios, Brazil, 2007.
L. Alencar, A. Barbosa, K. Barbosa, M. Tenorio, C. Brito, P. Chiklinkar,
E. Nascimento, R. Dhalia, U.M. BragaNeto, E.T.A. Marques, Jr.,
"Analysis of epitope mapping of the dengue3 envelope protein on dengue
patients: comparison between the enzymelinked immunospot (elispot)
and the multipred epitope predictive computational program."
Proceedings of XVII Brazilian Virology Meeting, Campos do Jordao, Brazil, 2006.
U.M. BragaNeto, "Why Error Estimation is Fundamental to
the Estimation of Regulatory Networks." Presented at the Models for Genetic Regulatory
Network Workshop, College Station, TX, November 2005.
U.M. BragaNeto,
SmallSample Error Estimation: Mythology Versus Mathematics.
Proceedings of SPIE Vol. 5916:
Mathematical Methods in Pattern and Image Analysis.
Edited by J.T. Astola, I. Tabus and J. Barrera,
San Diego, CA, August 2005.
U.M. BragaNeto,
Grayscale Level Multiconnectivity.
Proceedings of the 7th International Symposium
on Mathematical Morphology: 40 Years On  ISMM'05.
Edited by C. Ronse, L. Najman and E. Decencière,
pp. 129138, Paris, France, April 2005.
U.M. BragaNeto and John Goutsias,
On a General Theory of Connectivity in Image Analysis.
Proceedings of the IEEEEURASIP Workshop on Nonlinear Signal and Image Processing  NSIP'01.
Edited by K. Barner, G.Arce and C. Boncelet (CDROM), Baltimore, MD, June 2001.
X. Han, C. Xu, U.M. BragaNeto and J. L. Prince,
GraphBased Topology Correction for Brain Cortex Segmentation.
Proceedings of the XVIIth International Conference on Information Processing
in Medical Imaging  IPMI'01.
Edited by M.F. Insana and R.M. Leahy, pp 395401, Davis, CA, June 2001.
U.M. BragaNeto and John Goutsias,
Multiresolution Connectivity:
An Axiomatic Approach.
Proceedings of the 5th International Symposium
on Mathematical Morphology and Its Applications
to Image and Signal Processing  ISMM'2000.
Edited by J. Goutsias, L. Vincent and D. Bloomberg,
pp. 159168, Palo Alto, CA, June 2000.
U.M. BragaNeto and John Goutsias,
Automatic Target Detection and Tracking
in ForwardLooking Infrared Image Sequences
using Morphological Connected Operators.
Proceedings of the 33rd Annual Conference on Information
Sciences and Systems  CISS'99.
Vol. I, pp. 173178, Baltimore, MD, March 1999.
U.M. BragaNeto and John Goutsias,
On Detecting Mines and Minelike Objects
in Highly Cluttered Multispectral Aerial
Images by Means of Mathematical Morphology.
In Detection and Remediation Technologies
for Mines and Minelike Targets III,
Proceedings of SPIE 3392, pp. 987999, Orlando, FL, April 1998.
U.M. BragaNeto,
"Alternating Sequential Filters by
AdaptiveNeighborhood Structuring Functions."
Proceedings of the 3rd International Symposium
on Mathematical Morphology and Its Applications
to Image and Signal Processing  ISMM'96.
Edited by P. Maragos, R.W. Schafer and M.A. Butt,
pp. 139146, Atlanta, GA, May 1996.
U.M. BragaNeto, W.A. Siqueira Neto and A.F. Dias e Silva,
"Mammographic Calcification Detection by
Mathematical Morphology Methods."
Proceedings of the 3rd International Workshop on Digital Mammography.
Edited by K. Doi, M.L. Giger,
R.M. Nishikawa and R.A. Schmidt,
pp. 263266, Chicago, IL, June 1996.
U.M. BragaNeto and R.A. Lotufo,
"Mathematical Morphology tools for
3D image analysis of porous media."
In Neural, Morphological and Stochastic Methods in
Image and Signal Processing,
Proceedings of SPIE 2568.
Edited by E.R. Dougherty, F. PrĂȘteux and S.S. Shen,
pp. 139150, San Diego, CA, July 1995.
Return to main page

