Predictive Biomarker Sciences, Inc. Important Publications

Our scientific team has contributed significant watershed articles:

GENOMIC SIGNAL PROCESSING

  1. Hanczar, B., Hua, J., and E. R. Dougherty, "Decorrelation of the True and Estimated Classifier Errors in High-dimensional Settings," EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2007, Article ID 38473, 12 pages, doi:10.1155/2007/38473, October, 2007.
  2. Dougherty, E. R., Hua, J., and M. L. Bittner, "Validation of Computational Methods in Genomics," Current Genomics, Vol. 8, No. 1, 1-19, March, 2007.
  3. 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.
  4. Dougherty, E. R., and M. Brun, "On the Number of Close-to-Optimal Feature Sets," Cancer Informatics, Vol. 2, 189-196, September, 2006.
  5. 191. Sima, C., and E. R. Dougherty, "Optimal Convex Error Estimators for Classification," Vol. 39, No. 6, 1763-1780, Pattern Recognition, September, 2006.
  6. 188. 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, Article ID 43056, 13 pages, May, 2006.
  7. 187. 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.
  8. 186. Datta, A., Pal, R., and E. R. Dougherty, "Intervention in Probabilistic Gene Regulatory Networks," Current Bioinformatics, Vol. 1, No. 2, 167-184, May, 2006.
  9. 185. 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.
  10. 179. 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.
  11. 178. Dougherty, E. R., Datta, A., and C. Sima, "Research Issues in Genomic Signal Processing," IEEE Signal Processing Magazine, Vol. 22, No. 6, 46-68, November, 2005.
  12. 172. Chen, J., Dougherty, E. R., Demir, S., Friedman, C., Sheng Li, C., and S. Wong, "Grand Challenges for Multimodal Bio-Medical Systems," IEEE Circuits and Systems Magazine, Spring Quarter, 46-52, May, 2005.
  13. 170. 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, April, 2005.
  14. 169. Pal, R., Datta, A., Fornace, A. J., Bittner, M. L., and E. R. Dougherty, "Boolean Relationships Among Genes Responsive to Ionizing Radiation in the NCI 60 ACDS," Bioinformatics, 21, No. 8, 1542-1549, April, 2005.
  15. 167. 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.
  16. 165. 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.
  17. 163. Dougherty, E. R., and A. Datta, "Genomic Signal Processing: Diagnosis and Therapy," IEEE Signal Processing Magazine, 107-112, Vol. 22 No. 1, January, 2005.
  18. 162. 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.
  19. 160. 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.
  20. 155. 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, July, 2004.
  21. 147. 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.
  22. 145. Braga-Neto, U. M., and E. R. Dougherty, "Is Cross-Validation Valid for Small-Sample Microarray Classification," Bioinformatics, Vol. 20, No. 3, 374-380, February, 2004.
  23. 137. 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.
  24. 133. 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, September, 2003.
  25. 130. 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, 169-191, July, 2003.
  26. 127. 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, May, 2003.
  27. 121. 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, January, 2003.
  28. 117. 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, December, 2002.
  29. 115. 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, November, 2002.
  30. 112. Chen, Y., Kamat, V., Dougherty, E. R., Bittner, M. L. Meltzer, P. S., and J. M. Trent, "Ratio Statistics of Gene Expression Levels and Applications to Microarray Data Analysis," Bioinformatics, Vol. 18, 1207-1215, September, 2002.
  31. 104. Kim, S., Dougherty, E. R., Barrera, J., Chen, Y., Bittner, M., and J. M. Trent, "Strong Feature Sets From Small Samples," Computational Biology, Vol. 9, No. 1, 127-146, February, 2002.
  32. 103. 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, January, 2002.
  33. 94. Dougherty, E. R., "Small Sample Issues for Microarray-Based Classification," Comparative and Functional Genomics, Vol. 2, 28-34, February, 2001.
  34. 89. Kim, S., Dougherty, E. R., Bittner, M. L., Chen, Y., Sivakumar, K., Meltzer, P., and J. M. Trent, "A General Framework for the Analysis of Multivariate Gene Interaction via Expression Arrays," Biomedical Optics, Vol. 5, No. 4, 411-424, October, 2000.
  35. 85. Kim, S., Dougherty, E. R., Chen, Y., Sivakumar, K., Meltzer, P., Trent, J. M., and M. Bittner, "Multivariate Measurement of Gene-Expression Relationships," Genomics, Vol. 67, 201- 209, July, 2000.

IMAGING

  1. Dougherty, E. R., and J. Barrera, "Pattern Recognition Theory in Nonlinear Signal Processing," Mathematical Imaging and Vision, Vol. 16, No. 3, 181-197, May, 2002.
  2. 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.
  3. 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.
  4. Dougherty, E. R., Kim, S., and Y. Chen, "Coefficient of Determination in Nonlinear Signal Processing," EURASIP Journal on Signal Processing, Vol. 80, No. 10, 2219-2235, October, 2000.
  5. Hirata, R., Dougherty, E. R., and J. Barrera, "Aperture Filters," EURASIP Journal on Signal Processing, Vol. 80, No. 4, 697-721, April, 2000.
  6. Grygorian, A. M., and E. R. Dougherty, "Design and Analysis of Robust Optimal Binary Filters in the Context of a Prior Distribution for the States of Nature," Mathematical Imaging and Vision, Vol. 11, No. 3, 239-254, December, 1999.
  7. Dougherty, E. R., and Y. Chen, "Logical Structural Filters," Optical Engineering, Vol. 37, No. 6, 1668-1676, June, 1998.
  8. Sinha, D., Sinha, P., Dougherty, E. R., and S. Batman, "Design and Analysis of Fuzzy Morphological Algorithms for Image Processing," IEEE Trans. on Fuzzy Systems, Vol. 5, No. 4, November, 1997.
  9. Chen, Y., and E. R. Dougherty, "Optimal and Adaptive Reconstructive Granulometric Bandpass Filters," EURASIP Journal on Signal Processing, Vol. 61, 65-81, 1997.
  10. Dougherty, E. R., "Optimal Binary Morphological Bandpass Filters Induced by Granulometric Spectral Representation," Mathematical Imaging and Vision, Vol. 7, No. 2, 175-192, April, 1997.
  11. Barrera, J., Dougherty, E. R., and N. Tomita, "Automatic Programming of Binary Morphological Machines by Design of Statistically Optimal Operators in the Context of Computational Learning Theory," Electronic Imaging, Vol. 6, No. 1, 54-67, January, 1997.
  12. Dougherty, E. R., and R. P. Loce, "Optimal Binary Differencing Filters: Design, Logic Complexity, Precision Analysis, and Application to Digital Document Processing," Electronic Imaging, Vol. 5, No. 1, 66-86, January, 1996.
  13. Sinha, D., and E. R. Dougherty, "A General Axiomatic Theory of Intrinsically Fuzzy Mathematical Morphologies," IEEE Trans. on Fuzzy Systems, Vol. 3, No. 4, November, 1995.
  14. Dougherty, E. R., and D. Sinha, "Computational Mathematical Morphology," EURASIP Journal on Signal Processing, Vol. 38, 21-29, 1994.
  15. Chen, Y., and E. R. Dougherty, "Gray-Scale Morphological Granulometric Texture Classification," Optical Engineering, Vol. 33, No. 8, 2713-2722, August, 1994.
  16. Dougherty, E. R., and R. P. Loce, "Optimal Mean-Absolute-Error Hit-or-Miss Filters: Morphological Representation and Estimation of the Binary Conditional Expectation," Optical Engineering, Vol. 32, No. 4, 815-823, April, 1993.
  17. Loce, R. P., and E. R. Dougherty, "Optimal Morphological Restoration: The Morphological Filter Mean-Absolute-Error Theorem," Visual Communication and Image Representation, Vol. 3, No. 4, 412-432, December, 1992.
  18. Dougherty, E. R., Newell, J., and J. Pelz, "Morphological Texture-Based Maximum-Likelihood Pixel Classification Based On Local Granulometric Moments," Pattern Recognition, Vol. 25, No. 10, 1181-1198, November, 1992.
  19. Sinha, D., and E. R. Dougherty, "Fuzzy Mathematical Morphology," Visual Communication and Image Representation, Vol. 3, No. 3, 286-302, September, 1992.
  20. Sand, F., and E. R. Dougherty, "Asymptotic Normality of the Morphological Pattern-Spectrum Moments and Orthogonal Granulometric Generators," Visual Communication and Image Representation, Vol. 3, No. 2, 203-214, June, 1992.
  21. Dougherty, E. R., "Euclidean Gray-Scale Granulometries: Representation and Umbra Inducement," Mathematical Imaging and Vision, Vol. 1, No. 1, 7-21, March, 1992.
  22. Dougherty, E. R., "Optimal Mean-Square N-Observation Digital Morphological Filters — Part I: Optimal Binary Filters," Computer Vision, Graphics, and Image Processing —Image Understanding, Vol. 55, No. 1, 36-54, January, 1992.
  23. Dougherty, E. R., "Optimal Mean-Square N-Observation Digital Morphological Filters — Part II: Optimal Gray-Scale Filters," Computer Vision, Graphics, and Image Processing — Image Understanding, Vol. 55, No. 1, 55-72, January, 1992.