Regulatory Networks
[back to TOC]
Structure [back to TOC]
Xiao, Y., and E. R. Dougherty, “ The
Impact of Function Perturbations in Boolean Networks,” Bioinformatics
Vol. 23, No. 10, 1265-1273, May, 2007. [pdf]
Brun, M., Kim, S., Choi, W., and E. R. Dougherty, “Comparison
of Network Models via Steady-State Trajectories,” EURASIP
Journal on Bioinformatics and Systems Biology Vol. 2007, Article
ID 82702, 11 pages, May, 2007. [pdf]
Ivanov,I., Pal, R., and E. R. Dougherty, “Dynamics Preserving Size Reduction Mappings
for Probabilistic Boolean Networks,” IEEE Transactions on Signal Processing, Vol. 55, No. 5, 2310-2322, May, 2007. [pdf]
Ivanov, I., and E. R. Dougherty, “Modeling
Genetic Regulatory Networks: Continuous or
Discrete?” Biological Systems, Vol. 14, No. 2,
219-229, June, 2006. [pdf]
Brun, M., Dougherty, E. R., and I. Shmulevich, “Steady-State
Probabilities for Attractors in Probabilistic Boolean Networks,”
Signal Processing, Vol. 85, No. 10,
1993-2013, October, 2005. [pdf]
Ivanov, I., and Dougherty, E. R., “Reduction
Mappings Between Probabilistic Boolean
Networks,” Applied Signal Processing, Vol. 4, No.
1, 125-131, January, 2004.[PDF]
Shmulevich, I., Gluhovsky, I., Hashimoto, R.,
Dougherty, E. R., and W. Zhang, “Steady-
State Analysis of Genetic Regulatory Networks Modeled by Probabilistic
Boolean
Networks,” Comparative Functional Genomics, Vol. 4,
601-608, December, 2003.[PDF]
Shmulevich, I., Lahdesmaki, H., Dougherty, E. R.,
Astola, J., and W. Zhang, “The Role of Certain
Post Classes in Boolean Network Models of Genetic Networks,” Proceedings
of
the National Academy of Science, Vol. 100, No. 19, 10734-10739,
2003.[PDF]
Dougherty, E. R., and I. Shmulevich, "Mappings
Between Probabilistic Boolean Networks," Signal Processing,
Vol. 83, No. 4, 799-809, 2003. [PDF]
Kim, S., Li, H., Dougherty, E. R., Chao, N., Chen,
Y., Bittner, M. L., and E. B. Suh, “Can Markov Chain Models
Mimic Biological Regulation,” Biological Systems,
Vol. 10, No. 4, 447-458, 2002. [PDF]
I. Shmulevich, E. R. Dougherty, W. Zhang,"From
Boolean to Probabilistic Boolean Networks as Models of Genetic
Regulatory Networks", Proceedings of IEEE, Vol. 90,
No. 11, pp. 1778-1792, 2002. [PDF]
I. Shmulevich, E. R. Dougherty, S. Kim, W. Zhang,"Probabilistic
Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory
Networks", Bioinformatics, Vol. 18, No. 2, pp.
261-274, 2002. [PDF]
Inference
[back to TOC]
E. R. Dougherty, "Validation of Inference
Procedures for Gene Regulatory Networks," Current Genomics,
Vol. 8, No. 6, 351-359, September, 2007. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, "Inferring
Connectivity of Genetic Networks Using Information Theoretic Criteria,"
to appear in IEEE/ACM Transactions on Computational Biology and
Bioinformatics.
S. Marshall, L. Yu, Y. Xiao and E. R. Dougherty, "Inference
of Probabilistic Boolean Networks from a Single Observed Temporal
Sequence," EURASIP Journal on Bioinformatics and Systems
Biology., Vol. 2007, Article ID 32454, 15 pages, May, 2007. [pdf]
Xiao, Y., and E. R. Dougherty, "Optimizing
Consistency-Based Design of Context- Sensitive Gene Regulatory Networks,"
IEEE Transactions on Circuits and Systems I,
Vol. 53, No. 11, 2431-2437, November, 2006. [pdf]
Zhao, W., Serpedin, E., and E. R. Dougherty, “Inferring
Gene Regulatory Networks from Time Series Data Using the Minimum
Description Length Principle,” Bioinformatics, Vol.
22, No. 17, 2129-2135, 2006. [pdf]
Dougherty, E. R., and Y. Xiao, “Design of
Probabilistic Boolean Networks under the Requirement of Contextual Data
Consistency,” IEEE Transactions on Signal Processing, Vol.
54, No. 9, 3603- 3613, 2006. [pdf]
Pal, R., Ivanov, I., Datta, A., and E. R.
Dougherty, “Generating Boolean Networks with a Prescribed
Attractor Structure,” Bioinformatics, Vol. 21, No.
21, 4021-4025, November, 2005. [pdf]
Zhou, X., Wang, X., Pal, R., Ivanov, I., Bittner,
M. L., and E. R. Dougherty, “A Bayesian
Connectivity-Based Approach to Constructing Probabilistic Gene
Regulatory Networks,” Bioinformatics, Vol. 20. No. 17,
2918-2927 November, 2004. [pdf]
Hashimoto, R., Kim, S., Shmulevich, I., Zhang, W.,
Bittner, M. L., and Dougherty, E. R., “A Directed-Graph
Algorithm to Grow Genetic Regulatory Subnetworks from Seed Genes
Based on Strength of Connection,”Bioinformatics, Vol. 20, No.
8, 1241-1247, 2004. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, "Construction
of Genomic Networks Using Mutual-Information Clustering and
Reversible-Jump Markov-Chain-Monte-Carlo Predictor Design," Signal
Processing, Vol. 83, No. 4, 745-761, 2003. [PDF]
Prediction
[back to TOC]
Pal, R., Datta, A., Fornace, A. J., Bittner, M.
L., and Edward R. Dougherty, “Boolean
Relationships Among Genes Responsive to Ionizing Radiation in the NCI
60 ACDS,”
Bioinformatics, 21, No. 8, 1542-1549, 2005. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Gene
prediction Using Multinomial Probit
Regression with Bayesian Gene Selection,” Applied Signal
Processing, Vol. 4, No. 1, 115-124, January, 2004.[PDF]
S. Kim, E. R. Dougherty, Y. Chen, K Sivakumar, P.
Meltzer, J. M Trent, and M. Bittner, "Multivariate Measurement
of Gene Expression Relationships", Genomics, 67,
201-209, 2000. [PDF]
S. Kim, E. R. Dougherty, M. L. Bittner, Y. Chen,
K. Sivakumar, P. Meltzer, J. M. Trent, "General Nonlinear
Framework for the Analysis of Gene Interaction via Multivariate
Expression Arrays", Journal of Biomedical Optics
5(4), 411–424, 2000 . [PDF]
E. R. Dougherty, S. Kim, Y. Chen, "Coeffcient
of Determination in Nonlinear Signal Processing", Signal
Processing 80, 2219-2235, 2000. [PDF]
Dougherty, E. R., Bittner, M., Chen, Y., Kim, S.,
Sivakumar, K., Barrera, J., Meltzer, P., and J. Trent, "Nonlinear
Filters in Genomic Control," Proceedings of the
IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing,
Antalya, Turkey, June, 1999.[PDF]
Intervention
and Control [back to TOC]
B. Faryabi, G. Vahedi, J.F. Chamberland, A. Datta,
and E. R. Dougherty “
Optimal Constrained Stationary Intervention in Gene Regulatory
Networks”,
Accepted for publication in the EURASIP
Journal on Bioinformatics and Systems Biology.
G. Vahedi, B. Faryabi, J.F. Chamberland, A. Datta,
and E. R.
Dougherty “
Intervention in Gene Regulatory Networks via a Stationary
Mean-First-Passage-Time Control Policy”,
Accepted for
publication in the IEEE Transactions of Biomedical Engineering.
B. Faryabi, J.F. Chamberland, G. Vahedi, A. Datta,
and E. R. Dougherty “
Optimal Intervention in Asynchronous Genetic Regulatory Networks”,
Accepted for publication in the IEEE Journal of
Selected Topics in Signal Processing.
B. Faryabi, A. Datta, and E. R. Dougherty “On
Approximate Stochastic Control in Genetic Regulatory Networks”,
IET Systems Biology, Vol. 1, No. 6, 361-368,
2007. [pdf]
Datta,A., Pal, R., Choudhary, A. and E. R.
Dougherty “Control Approaches for Probabilistic Gene Regulatory
Networks”, IEEE Signal Processing Magazine, Vol.
24, No. 1, 54-63, 2007.[pdf]
Pal, R., Datta, A. and E. R. Dougherty, “Optimal
Infinite Horizon Control for Probabilistic Boolean Networks”, IEEE
Transactions on Signal Processing, 2006, Vol. 54, no. 6,
2375:2387. [pdf]
Choudhary, A., Datta, A., Bittner, M. L., and E.
R. Dougherty, “Intervention in a Family of
Boolean Networks,”Bioinformatics, Vol. 22, No. 2,
226-232, January, 2006. [PDF]
Pal, R., Datta, A., Bittner, M. L., and E. R.
Dougherty, “Intervention in Context-Sensitive
Probabilistic Boolean Networks", Bioinformatics,
Vol. 21, No. 7, 1211-1218, April, 2005. [pdf]
Datta, A., Choudhary, A., Bittner, M. L., and
Dougherty, E. R., “External Control in Markovian Genetic
Regulatory Networks: The Imperfect Information Case,” Bioinformatics,
Vol. 20, No. 6, 924-930, 2004. [PDF]
Datta, A., Choudhary, A., M. L. Bittner, and E. R.
Dougherty, “External Control in Markovian Genetic Regulatory
Networks,” Machine Learning,Vol. 52, no. 1-2,
169-181,
2003.[PDF]
I. Shmulevich, E. R. Dougherty, W. Zhang, "Gene
Perturbation and Intervention in Probabilistic Boolean Networks",
Bioinformatics, Vol. 18, 1319-1331, 2002. [PDF]
I. Shmulevich, E.R. Dougherty, and W. Zhang, "Control
of stationary behavior in Probabilistic Boolean Networks by means of
structural intervention", Biological Systems, Vol.
10, No. 4, 431-446, 2002. [PDF]
Classification
[back to TOC]
Performance Analysis and Error Estimation
[back to TOC]
Hanczar, B., Hua, J., Dougherty, E. R., "Decorrelation
of the True and Estimated Classifier Errors in High-dimensional Settings,"
EURASIP Journal on
Bioinformatics and Systems Biology, Article ID 38473, 12 pages, October, 2007.
[pdf]
Xiao, Y., Hua, J., and E. R. Dougherty, "
Quantification of the Impact of Feature Selection on Cross-Validation
Error Estimation Precision," EURASIP Journal on
Bioinformatics and Systems Biology, Vol. 2007, Article ID 16354,
11 pages, February, 2007. [pdf]
Xu, Q., Hua, J., Braga-Neto, U. M. Xiong, Z., Suh,
E., 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, 579-590, December, 2006. [pdf]
Sima, C., and E. R. Dougherty, “Optimal
Convex Error Estimators for Classification,” Vol.
39, No. 6, 1763-1780, Pattern Recognition, September, 2006. [pdf]
Sima, C., Attoor, S., Braga-Neto, U., Lowey, J., Suh, E., and E. R.
Dougherty, "Impact of Error Estimation on Feature-Selection
Algorithms," Pattern Recognition, Vol. 38, No. 12,
2472-2482, December, 2005. [pdf]
Braga-Neto, U., and E. R. Dougherty, “Exact Performance
Measures and Distributions of Error Estimators for Discrete Classifiers,”
Pattern Recognition, Vol. 38, No. 11,
1799-1814, November, 2005. [pdf]
Sima, C., Braga-Neto, U., and E. R. Dougherty, “Superior
Feature-Set Ranking For Small
Samples Using Bolstered Error Estimation,” Bioinformatics,
Vol. 21, No. 7, 1046-1054,
April, 2005. [pdf]
Attoor, S. N., and Dougherty, E. R., “Classifier
Performance as a Function of Distributional Complexity,”
Pattern Recognition, Vol. 37, No. 8, 1629-1640, August, 2004. [pdf]
Braga-Neto, U. M., and Dougherty, E. R., “Bolstered
Error Estimation,” Pattern Recognition, Vol. 37, No.
6, 1267-1281, June 2004. [PDF]
Braga-Neto, U. M., and Dougherty, E. R., “Is
Cross-Validation Valid for Small-Sample
Microarray Classification,” Bioinformatics, Vol. 20,
No. 3, 374-380, 2004 [PDF]
Braga-Neto, U. M., Hashimoto, R., Dougherty, E.
R., Nguyen, D. V., and R. J. Carroll, “Is Cross-validation
Better than Resubstitution for Ranking Genes,” Bioinformatics,
Vol. 20,
No. 2, 253-258, January, 2004.[PDF]
Brun, M., Sabbagh, D., Kim, S., and E. R. Dougherty, “Corrected
Small-Sample Estimation for the Error of the Optimal Binary Filter,”
Bioinformatics, Vol. 19, No. 8, 944-951,
2003.[PDF]
Hsing, T., Attoor, S., and E. R. Dougherty, “Relation
Between Permutation-test P Values and Classifier Error Estimates,”
Machine Learning,Vol. 52, No. 1-2, 11-30,
2003.[PDF]
Classifier Design [back to TOC]
Hua, J., Lowey, J., Xiong, Z., and E. R. Dougherty, “Noise-Injected
Neural Networks Show Promise for Use on Small-Sample Expression Data,”
BMC Bioinformatics, 7:274, May,
2006.[pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Multi-class
Cancer Classification Using Multinomial Probit Regression with Bayesian
Variable Selection," IEE Proceedings
System Biology, Vol. 153, No. 2, 70-78, March, 2006.[pdf]
Dougherty, E. R., Hua, J., Xiong, Z., and Y. Chen,
“Optimal Robust Classifiers,” Pattern Recognition,
Vol. 38, No. 10, 1520-1532, October, 2005. [pdf]
Fu, W. J., Dougherty, E. R., Mallick, B., and R.
J. Carroll, “How Many Samples Are
Needed to Build a Classifier: A General Sequential Approach,”
Bioinformatics, Vol. 21,
No. 1, 63-70, January, 2005. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “Nonlinear-Probit
Gene Classification Using
Mutual-Information and Wavelet Based Feature Selection,” Biological
Systems, Vol. 12, No. 3, 371-386, September, 2004. [pdf]
Zhou, X., Wang, X., and E. R. Dougherty, “A
Bayesian Approach to Nonlinear Probit Gene
Selection and Classification,” Franklin Institute, Vol. 341,
No. 1, 2, 137-156, 2004. [pdf]
Dougherty, E. R., and J. Barrera, "Pattern Recognition Theory
in Nonlinear Signal Processing", Mathematical Imaging and
Vision, Vol. 16, No. 3, 181-197, 2002.
Feature Selection [back to TOC]
Sima, C., and E. R. Dougherty, "What
Should Be Expected from Feature Selection in Small-Sample Settings,"
Bioinformatics, Vol. 22, No. 19, 2430-2436, October, 2006. [pdf]
Dougherty, E. R., and M. Brun, "On the
Number of Close-to-Optimal Feature Sets," Cancer
Informatics, Vol. 2, 189-196, 2006. [pdf]
Choudhary, A., Brun, M., Hua, J., Lowey, J., Suh,
E., and E. R. Dougherty, "Genetic Test
Bed for Feature Selection," Bioinformatics, Vol. 22,
No. 7, 837-842, April, 2006. [PDF]
Dougherty, E. R., “Feature-Selection
Overfitting with Small-Sample Classifier Design,” IEEE
Intelligent Systems Magazine, 64-66, December, 2005. [PDF]
Zhou, X., Wang, X., and E. R. Dougherty, "Gene
Selection Using Logistic Regressions Based on AIC, BIC, and MDL Criteria,"
New Mathematics and Natural Computation, Vol. 1, No. 1, 129-145, March,
2005. [pdf]
Hua, J., Xiong, Z., Lowey, J., Suh, E., and E. R.
Dougherty, “Optimal Number of Features as a Function of Sample
Size for Various Classification Rules,” Bioinformatics, 21,
No. 8, 1509-1515, 2005. [pdf]
Silva, P. J. S., Hashimoto, R. F., Kim, S.,
Barrera, J., Brandao, L. O., Suh, E., and E. R.
Dougherty, “Feature Selection Algorithms to Find Strong Genes,”
Pattern Recognition Letters, Vol. 26, No.
10, 1444-1453, July, 2005. [pdf]
Hsing, T., Liu, L-Y., Brun, M., and E. R.
Dougherty, “The Coefficient of Intrinsic Dependence (Feature
Selection Using el CID),”Pattern Recognition, Vol. 38, No. 5,
623-
636, May, 2005. [pdf]
Hua, J., Xiong, Z., and E. R. Dougherty, “Determination
of the Optimal Number of Features for Quadratic Discriminant Analysis
Via the Normal Approximation to the Discriminant Distribution,”
Pattern Recognition, Vol. 38, No. 3,
403-421, March, 2005. [pdf]
Hashimoto, R., Dougherty, E. R., Brun, M., Zhou, Z., Bittner, M. L.,
and J. M. Trent," Efficient Selection of Feature Sets
Possessing High Coefficients of Determination Based on Incremental
Determinations," Signal Processing, Vol. 83, No. 4,
695-712, February, 2003. [PDF]
Lee, K. E., Sha, N., Dougherty, E. R., Vannucci,
M., and B. K. Mallick, "Gene Selection: A
Bayesian Variable Selection Approach," Bioinformatics,
Vol. 19, 90-97, 2003. [PDF]
S. Kim, E. R. Dougherty, J. Barrera, Y. Chen, M.
L. Bittner, J.M. Trent, "Strong Feature Sets from Small Samples",
Journal of Computational Biology, Vol.9,
No.1, 127-146, 2002. [PDF]
Clustering [back to TOC]
Brun, M., Sima, C., Hua, J., Lowey, J., Carroll,
B., Suh, E., and E. R. Dougherty, “Model-Based Evaluation of
Clustering Validation Measures,” Pattern Recognition,
Vol. 40, No. 3, 807-824, March, 2007. [PDF]
Zhou, X., Wang, X., Dougherty, E. R., Russ, D.,
and Su, E., “Gene Clustering Based on Clusterwide Mutual
Information,” Journal of Computational Biology, Vol.
11, No. 1, 147-161, 2004. [PDF]
Dougherty, E. R., and Brun, M., “A
Probabilistic Theory of Clustering,” Pattern Recognition,
Vol. 37, No. 5, 917-925, May 2004. [PDF]
E. R. Dougherty, J. Barrera, M. Brun, S. Kim, R.
M. Cesar, Y. Chen, M. Bittner, J. M. Trent, "Inference from
Clustering with Application to Gene-Expression Microarrays", Journal
of Computational Biology, Vol.9 No.1, 105-126, 2002. [PDF]
Microarrays [back to TOC]
Hua, J., Craig, D. W., Brun, M., Webster, J.,
Zismann, V., Tembe, W., Joshipura, K., Huentelman, M. J., Dougherty, E.
R., and D. A. Stephan, "SNiPer-HD: Improved Genotype Calling
Accuracy by an Expectation-Maximization Algorithm for High-Density SNP
Arrays," Bioinformatics, Vol. 23, 57-63, January,
2007. [pdf]
Hua, J., Balagurunathan, Y. Chen, Y., Lowey, J.,
Bittner, M., Xiong, Z., Suh, E., and E. R.
Dougherty, “Normalization Benefits Microarray-Based
Classification,” EURASIP Journal on Bioinformatics and
Systems Biology, Vol. 2006, 2006 [pdf]
Attoor, S., Dougherty, E. R., Chen, Y., Bittner,
M. L., and J. M. Trent, “Which is Better for
cDNA-Microarray-Based Classification: Ratios or Direct Intensities,”
Bioinformatics,
Vol. 20, No. 16, 2513-2520, November, 2004. [pdf]
Balagurunathan, Y., Wang, N., Dougherty, E. R.,
Nguyen, D. V., Chen, Y., Bittner, M. L., Trent, J. M., and R. J.
Carroll, “Noise Factor Analysis for cDNA Microarrays,”Biomedical
Optics, Vol. 9, No. 4, 663-845, 2004. [pdf]
Mousses, S., Caplen, N. J., Cornelison, R.,
Weaver, D., Basik, M., Hautaniemi, S., Elkahloun, A. G., Lotufo, R. A.,
Choudary, A., Dougherty, E. R., Suh, E., and O. Kallioniemi, “RNAi
Microarray Analysis in Cultured Mammalian Cells,” Genome
Research, Vol. 13, 2341-2347, October, 2003.[PDF]
Zhou, X., Wang, X., and E. R. Dougherty, “Binarization
of Microarray Data Based on a Mixture Model,” Molecular
Cancer Therapeutics, Vol. 2, No. 7, 679-684, 2003. [PDF]
Zhou, X., Wang, X., and E. R. Dougherty, “Missing
Value Estimation using Linear and
Nonlinear Regression with Bayesian Gene Selection,” Bioinformatics,
Vol. 19, No. 17, 2302-2307, November, 2003.[PDF]
Y. Chen, V. Kamat, E. R. Dougherty, M. L. Bittner,
Paul S. Meltzer, and J. M. Trent, "Ratio Statistics of Gene
Expression Levels and Applications to Microarray Data Analysis",
Bioinformatics, Vol.18, No.9, p.1207-1215,
2002. [PDF]
Balagurunathan, Y., Dougherty, E. R., Chen, Y.,
Bittner, M. L., and J. M. Trent, "Simulation of cDNA
Microarrays via a Parameterized Random Signal Model," Biomedical
Optics, Vol. 7, No. 3, 507-523, 2002. [PDF]
Y. Chen, E. R. Dougherty, and M. L. Bittner, " Ratio-Based
Decisions and the Quantitative Analysis of cDNA Microarray Images",
Journal Of Biomedical Optics 2(4), 364–374,
1997. [PDF]
Genomic Applications [back to TOC]
Johnson,
C. D., Balagurunathan, Y., Dougherty, E. R., Afshari, C. A., He, Q.,
and K. S. Ramos, “Insight Into Redox-regulatory Gene Networks in
Vascular Cells,” Bioinformation, Vol. 1, No. 10, 379-383,
April, 2007.[pdf]
Davidson, L. A., Nguyen, D. V., Hokanson, R. M.,
Callaway, E. S., Isett, R., Turner, N. D.,
Dougherty, E. R., Lupton, J. R., Carroll, R. J., and R. S. Chapkin, “Chemopreventive
n-3 Polyunsaturated Fatty Acids Reprogram Genetic Signatures During
Colon Cancer Initiation and Progression in the Rat,” Cancer
Research, Vol. 64, 6797-6804, September, 2004. [pdf]
Johnson, C. D., Balagurunathan, Y., Tadesse, M.
G., Falahatpishch, Marcel Brun, M. H., Walker, M. K., Dougherty, E. R.,
and K. S. Ramos, “Unraveling Gene-Gene Interactions Regulated
by Ligands of the Aril Hydrocarbon Receptor,” Environmental
Health Perspectives, Vol. 112, No. 4, 403-412, March 2004. [PDF]
Morikawa, J., Li, H., Kim, S., Nishii, K., Ueno,
S., Suh, E., Dougherty, E. R., Shmulevich, I.,
Shiku, H., Zhang, W., and T. Kobayashi., “Identification of
Signature Genes by
Microarray for Acute Myeloid Leukemia Without Maturation (FAB-M1) and
AML with
t(15;17)(q22;q12)(PML/RARa),” International Journal of
Oncology, Vol. 23, No. 3, 617-
625, 2003 [PDF]
Johnson, C. D., Balagurunathan, Y., Lu, K. P.,
Tadesse, M., Falahatpisheh, M. H.,
Balagurunathan, Y., Carroll, R. A., Dougherty, E. R., Afshari, C. A.,
and K. S. Ramos, Genomic Profiles and Predictive Biological
Networks in Oxidant-Induced Atherogenesis,” Physiological
Genomics, Vol. 13, 263-275, 2003. [PDF]
Kobayashi, T., Yamaguchi, M., Kim, S., Morikawa,
J., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., and
W. Zhang, "Gene Expression Profiling Identifies Strong
Feature Genes that Classify de novo CD5+ and CD5 Diffuse Large B-cell
Lymphoma and Mantle Cell Lymphoma," Cancer Research,
Vol. 63, 60-66, 2003. [PDF]
Kim, S., Dougherty, E. R., Shmulevich, I., Hess,
K. R., Hamilton, S. R., Trent, J. M., Fuller, G. N., and W. Zhang, "Identification
of Combination Gene Sets for Glioma Classification," Molecular
Cancer Therapeutics, Vol. 1, No. 13, 1229-1236, 2002. [PDF]
I. Hedenfalk, D. Duggan, Y. Chen, M. Radmacher, M.
L. Bittner, R. Simon, P. Meltzer, B. usterson, M. Esteller, M. Raffeld,
Z. Yakhini, A. Ben-Dor, E. R. Dougherty, J.a Kononen, L. Bubendorf, W.
Fehrle, S. Pittaluga, S. Gruvberger, N. Loman, O. Johannsson, H.
Olsson, B. Wilfond, G. Sauter, O.-P. Kallioniemi, Å. Borg and J.
Trent, "Gene Expression Profiles in Hereditary Breast Cancer",
New England Journal of Medicine,
244:539-548. 2001. [PDF]
[Supplemental Information]
M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E.
Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, A. Ben-Dor, E.
Dougherty, E. Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter,
P. Pollock, E. Gillanders, D. Leja, K. Dietrich, C., M. Berens, D.
Alberts, V. Sondak, N. Hayward, and J. Trent, "Molecular
Classification of Cutaneous Malignant Melanoma by Gene Expression
Profiling", Nature 406: 536-540, 2000, [PDF]
[Supplemental Information]
Biomedical Image Processing
[back to TOC]
Leyk, M., Nguyen, D. V., Attoor, S. N., Dougherty,
E. R., Turner, N. D., Bancroft, L. K.,
Chapkin, R. S., Lupton, J. R., and R. J. Carroll, “Comparing
Automatic and Manual
Image Processing in FLARE Assay Analysis for Colon Carcinogenesis,”
Statistical
Applications in Genetics and Molecular Biology, Vol. 4, No. 1,
March, 2005. [pdf]
Grigoryan, A. M., Hostetter, G., Kallioniemi, O.,
and E. R. Dougherty, "Simulation Toolbox
for 3D-FISH Spot Counting Algorithms," Real-Time Imaging,
Vol. 8, No. 3, 203-212, 2002.
Grigoryan, A., Dougherty, E. R., Kononen, J., Bubendorf, L., Hostetter,
G., and O. Kallioniemi, "Morphological Spot Counting from
Stacked Images for Automated Analysis of Gene Copy Numbers by
Fluorescence In Situ Hybridization," Biomedical Optics,
Vol. 7, No. 1, 109-122, 2002. [PDF]
Morphological Granulometric Analysis
[back to TOC]
Franciškovic-Bilinski, S., Bilinski, H., Vdovic,
N., Balagurunathan, Y., and E. R. Dougherty, “Application of
Image-based Granulometry to Siliceous and Calcareous Estuarine and
Marine Sediments,” Estuarine, Coastal, and Shelf Science,
Vol. 58, No. 2, 227-239, October, 2003
Balagurunathan, Y., and E. R. Dougherty, “Morphological
Quantification of Surface Roughness,” Optical Engineering,
Vol. 42, No. 6, 1795-1804, June, 2003.
McKenzie, J., Marshall, S., Gray, A. J., and E. R.
Dougherty, “Morphological Texture Analysis Using the Texture
Evolution Function,” International Journal of Pattern
Recognition and Artificial Intelligence, Vol. 17, No. 2, 167-185,
March, 2003.
Balagurunathan, Y. and E. R. Dougherty, “Granulometric
Parametric Estimation for the Random Boolean Model Using Optimal Linear
Filters and Optimal Structuring Elements,” Pattern
Recognition Letters, Vol. 24, No. 2, 283-293, January, 2003.
Dougherty, E. R., “Granulometric Size
Density for Segmented Random-Disk Models,” Mathematical
Imaging and Vision, Vol. 17, No. 3, 267-276, November, 2002.
Balagurunathan, Y., and E. R. Dougherty, "Optimal
Linear Granulometric Estimation for Random Sets,” Pattern
Recognition, Vol. 35, No. 6, 1315-1325, June, 2002
Sivakumar, K., Balagurunathan, Y., and E. R.
Dougherty, "Asymptotic Joint Normality of the Granulometric
Moments," Pattern Recognition Letters, Vol. 22, No.
14, 1537-1543, December, 2001.
Theera-Umpon, N., Dougherty, E.R., and P. Gader, "Non-Homothetic
Granulometric Mixing Theory," Pattern Recognition,
Vol. 34, No. 12, 2547-2560, December, 2001.
Dougherty, E. R., and Y. Chen, "Robust
Optimal Granulometric Bandpass Filters," Signal Processing,
Vol. 81, 1357-1372, July, 2001.
Dougherty, E. R., and Y. Chen, "Robust
Optimal Granulometric Bandpass Filters," Signal Processing,
Vol. 81, 1357-1372, July, 2001.
Balagurunathan, Y., Dougherty, E. R.,
Franciskovic-Bilinski, S., Bilinski, H., and N. Vdovi, "Morphological
Granulometric Analysis of Sediment Images," Image
Analysis and Stereology, Vol. 20, No. 2, 87-99, June, 2001.
Batman, S., and E. R. Dougherty, "Morphological
Granulometric Estimation of Random Patterns in the Context of
Parameterized Random Sets," Pattern Recognition,
Vol. 34, No. 6, June, 2001.
Dougherty, E. R., "Optimal Conjunctive
Granulometric Bandpass Filters," Mathematical Imaging and
Vision, Vol. 14, No. 1, 39-51, January, 2001.
Sivakumar, K., Patel, M. J., Kehtarnavaz, N.,
Balagurunathan, Y., and E. R. Dougherty, "A Constant-time
Algorithm for Erosions/Dilations with Applications to Morphological
Texture Feature Computation," Real-Time Imaging,
Vol. 6, 223-239, June, 2000.
Batman, S., Dougherty, E. R., and F. Sand "Heterogeneous
Morphological Granulometries," Pattern Recognition,
Vol. 33, No. 6, 1047-1057, June, 2000.
Optimal Filtering [back to TOC]
Dougherty, E. R., “Automatic Design of
Morphological Operators,” Electronic Imaging, Vol.
13, No. 3, 486-491, July, 2004.
Brun, M., Hirata, R., Barrera, J., and E. R.
Dougherty, “Nonlinear Filter Design Using Envelopes,” Mathematical
Imaging and Vision, Vol. 21, No. 1, 81-97, July, 2004.
Dougherty, E.R., “A Lattice-Based Minimal
Gray-Scale Switching Algorithm for Obtaining the Optimal Increasing
Filter from the Optimal Filter,” Mathematical Imaging and
Vision, Vol. 21, No. 1, 43-52, July, 2004.
Green, A., Dougherty, E. R., Marshall, S., and D.
Greenhalgh, “Optimal Filters with Multiresolution Apertures,”
Mathematical Imaging and Vision, Vol. 20,
No. 3, 237-250, May, 2004.
Green, A., Marshall, S., Greenhalgh, D., and E. R.
Dougherty, “Design of Multi-mask Apertures,” Signal
Processing, Vol. 83, No. 9, 1961-1971, September, 2003.
Brun, M., Dougherty, E. R., Hirata, R., and J. Barrera, “Design
of Optimal Binary Filters Under Joint Multiresolution-Envelope
Constraint,” Pattern Recognition Letters, Vol. 24,
No. 7, 937-945, April, 2003.
Hirata, R., Brun, M., Barrera, J., and E. R.
Dougherty, “Multiresolution Design of Aperture Filters,”
Mathematical Imaging and Vision, Vol. 16,
No. 3, 199-222, May 2002.
Grigoryan, A. M., and E. R. Dougherty, "Bayesian
Robust Optimal Linear Filters," Signal Processing,
Vol. 81, No. 12, 2503-2521, December, 2001.
Grigoryan, A. M., and E. R. Dougherty, "Optimization
of Linear Filters under Power-Spectral-Density Stabilization,"
IEEE Trans. on Signal Processing, Vol. 49,
No. 10, 1-8, October, 2001.
Dougherty, E. R., Barrera, J., Mozelle, G., Kim,
S., and M. Brun, "Multiresolution Analysis for Optimal Binary
Filters," Mathematical and Imaging and Vision, Vol.
14, No. 1, 53-72, January, 2001.
Hirata, N. T., Dougherty, E. R., and J. Barrera, "Iterative
Design of Morphological Binary Image Operators," Optical
Engineering, Vol. 39, No. 12, 3106-3123, December, 2000.
Barrera, J., Dougherty, E. R., and M. Brun, "Hybrid
Human-Machine Binary Morphological Operator Design: An Independent
Constraint Approach," Signal Processing, Vol. 80,
No. 8, 1469-1487, August, 2000.
Kamat, V. G., Dougherty, E. R., and J. Barrera, "Multiresolution
Bayesian Design of Binary Filters," Electronic Imaging,
Vol. 9, No., 3, 283-295, July, 2000
Hirata, N., Dougherty, E. R., and J. Barrera, "A
Switching Algorithm for Design of Optimal Increasing Binary Filters
over Large Windows," Pattern Recognition, Vol. 33,
No. 6, 1059-1081, June, 2000.
Hirata, R., Dougherty, E. R., and J. Barrera, "Aperture
Filters," Signal Processing, Vol. 80, No. 4,
697-721, April, 2000.
