Epistemology of the Cell: A Systems Perspective on Biological Knowledge

Epistemology of the Cell: A Systems Perspective on Biological Knowledge

Volumn , Issue , 2011, Pages

  Dougherty, Edward R ^a   Bittner, Michael L ^a   Akay, Metin ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84891583594     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118104866     Document Type: Book

References (138)

1. Aristotle, Physics, Great Books of the Western World, Vol. 8, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952.
2. Ayala, F. J., From Paley to Darwin: Design to Natural Selection, Back to Darwin, ed. J. B. Cobb, William B. Eerdmans Publishing Co., Grand Rapids, MI, 2008.
3. Bacon, F., Novum Organum, Great Books of the Western World, Vol. 35, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952 (originally published 1620).
4. Barrett, W., The Illusion of Technique, Anchor Books, New York, 1979.
5. Barrett, W., Death of the Soul, Anchor Books, New York, 1986.
6. Batt, G., Ropers, D., de Jong, H., Geiselmann, J., Mateescu, R., Page, M., and D. Schneider, "Validation of Qualitative Models of Genetic Regulatory Networks by Model Checking: Analysis of the Nutritional Stress Response in Escherichia coli," Bioinformatics, 21 (suppl. 1), 19-28, 2005.
7. Bertsekas, D. P., Dynamic Programming and Optimal Control, Vols. 1 and 2, Athena Scientific, Nashua, NH, 1995.
8. Bittner, M., Meltzer, P., Khan, J., Chen, Y., Jiang, Y., Seftor, E., et al., "Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling," Nature, 406 (3), 536-540, 2000.
9. Boulesteix, A. L., "Over-optimism in Bioinformatics Research," Bioinformatics, 26, 437-439, 2010.
10. Boulesteix, A.-L., and C. Strobl, "Optimal Classifier Selection and Negative Bias in Error Rate Estimation: An Empirical Study on High-dimensional Prediction," BMC Medical Research Methodology, 9, 85, 2009.
11. Braga-Neto, U. M., "Fads and Fallacies in the Name of Small-sample Microarray Classification," IEEE Signal Processing Magazine, 24 (1), 91-99, 2007.
12. Braga-Neto, U. M., and E. R. Dougherty, "Is Cross-Validation Valid for Small-sample Microarray Classification," Bioinformatics, 20 (3), 374-380, 2004.
13. Braga-Neto, U. M., and E. R. Dougherty, "Exact Performance of Error Estimators for Discrete Classifiers," Pattern Recognition, 38 (11), 1799-1814, 2005.
14. Braga-Neto, U. M., and E. R. Dougherty, "Exact Correlation Between Actual and Estimated Errors in Discrete Classification," Pattern Recognition Letters, 31, 407-413, 2010.
15. Bryant, R. J., Banks, P. M., and D. P. O'Malley, "Ki67 Staining Pattern as a Diagnostic Tool in the Evaluation of Lymphoproliferative Disorders," Histopathology, 48 (5), 505-515, 2006.
16. Callebaut, W., and M. D. Laubichler, "Biological Complexity as a Challenge for Biological Theory," Biological Theory, 2, 1-2, 2007.
17. Carroll, S. B., Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, 1st ed., Norton, New York, 2005.
18. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W., and D. C. Prasher, "Green Fluorescent Protein as a Marker for Gene Expression," Science, 263 (5148), 802-805, 1994.
19. Chang, L., and M. Marin, "Mammalian MAP Kinase Signaling Cascades," Nature, 410 (6824), 37-40, 2001.
20. Chen, S. J., Zhu, Y. J., Tong, J. H., Dong, S., Huang, W., Chen, Y., et al., "Rearrangements in the Second Intron of the RARA Gene Are Present in a Large Majority of Patients with Acute Promyelocytic Leukemia and Are Used as Molecular Marker for Retinoic Acid-induced Leukemic Cell Differentiation," Blood, 78 (10), 2696-2701, 1991.
21. Datta, A., and E. R. Dougherty, Introduction to Genomic Signal Processing with Control, CRC Press, New York, 2007.
22. de Jong, H., Geiselmann, J., Hernandez, C., and M. Page, "Genetic Network Analyzer: Qualitative Simulation of Genetic Regulatory Networks," Bioinformatics, 19 (3), 336-344, 2003.
23. Devroye, L., Gyorfi, L., and G. Lugosi, A Probabilistic Theory of Pattern Recognition, Springer-Verlag, New York, 1996.
24. Dougherty, E. R., "Validation of Inference Procedures for Gene Regulatory Networks," Current Genomics, 8 (1), 351-359, 2007.
25. Dougherty, E. R., "On the Epistemological Crisis in Genomics," Current Genomics, 9 (2), 69-79, 2008.
26. Dougherty, E. R., "Translational Science: Epistemology and the Investigative Process," Current Genomics, 10 (2), 102-109, 2009a.
27. Dougherty, E. R., Epistemology and the Role of Mathematics in Translational Science, Festschrift in Honor of Jaakko Astola on the Occasion of His 60th Birthday, eds. I. Tabus, K. Egiazarian, and M. Gabbouj, Tampere International Center for Signal Processing, Tampere, TICSP Series #47, 2009b.
28. Dougherty, E. R., and M. L. Bittner, "Causality, Randomness, Intelligibility, and the Epistemology of the Cell," Current Genomics, 11 (4), 221-237, 2010.
29. Dougherty, E. R., and U. M. Braga-Neto, "Epistemology of Computational Biology: Mathematical Models and Experimental Prediction as the Basis of Their Validity," Biological Systems, 14, 65-90, 2006.
30. Dougherty, E. R., and M. Brun, "A Probabilistic Theory of Clustering," Pattern Recognition, 37 (5), 917-925, 2004.
31. Dougherty, E. R., Kim, S., and Y. Chen, "Coefficient of Determination in Nonlinear Signal Processing," EURASIP Journal on Applied Signal Processing, 80 (10), 2219-2235, 2000.
32. Dougherty, E. R., Brun, M., Trent, J. M., and M. L. Bittner, "A Conditioning-Based Model of Contextual Regulation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 310-320, 2009.
33. Dupuy, A., and R. M. Simon, "Critical Review of Published Microarray Studies for Cancer Outcome and Guidelines on Statistical Analysis and Reporting," Journal of the National Cancer Institute, 99, 147-157, 2007.
34. Einstein, A., The Meaning of Relativity, Princeton University Press, Princeton, NJ, 1922.
35. Einstein, A., Herbert Spencer Lecture, Oxford University Press, New York, 1933.
36. Einstein, A., In a letter to Robert A. Thornton, December, 1944a.
37. Einstein, A., Remarks on Bertrand Russell's Theory of Knowledge, The Philosophy of Bertrand Russell, The Library of Living Philosophers, Vol. 5, ed. P. A. Schilpp, Tudor Publishers, Greensboro, NC, 1944b.
38. Einstein, A., Einstein's Reply to Criticisms, Albert Einstein: Philosopher-Scientist, The Library of Living Philosophers Series, ed. P. A. Schilpp, Cambridge University Press, Cambridge, 1949.
39. Einstein, A., An Undated Letter to Maurice Solovine, Letters to Solovine, ed. M. Solovine, Carol Publishing Group, New York, 1993.
40. Einstein, A., and L. Infeld, The Evolution of Physics, Simon & Schuster, New York, 1967 (originally published 1938).
41. Evan, G. I., Wyllie, A. H., Gilbert, C. S., Littlewood, T. D., Land, H., Brooks, M., et al., "Induction of Apoptosis in Fibroblasts by c-myc Protein," Cell, 69 (1), 119-128, 1992.
42. Faryabi, B., Chamberland, J.-F., Vahedi, G., Datta, A., and E. R. Dougherty, "Optimal Intervention in Asynchronous Genetic Regulatory Networks," IEEE Journal of Selected Topics in Signal Processing, 2, 412-423, 2008.
43. Faure, A., Naldi, A., Chaaouiya, C., and D. Thieffry, "Dynamical Analysis of a Generic Boolean Model for the Control of the Mammalian Cell Cycle," Bioinformatics, 22 (14), 124-131, 2006.
44. Feynman, R., QED: The Strange Theory of Light and Matter, Princeton University Press, Princeton, NJ, 1985.
45. Feynman, R., The Meaning of It All: Thoughts of a Citizen Scientist, Addison-Wesley, Reading, MA, 1998.
46. Fisher, R. A., Statistical Methods for Research Workers, Oliver and Boyd, Edinburgh, 1925.
47. Frank, P., Modern Science and Its Philosophy, Collier Books, New York, 1961.
48. Galen, On the Natural Faculties, Great Books of the Western World, Vol. 10, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952.
49. Galileo, Dialogues Concerning Two New Sciences, Dover, New York, 1954 (originally published 1638).
50. Galileo, Dialogue Concerning the Two Chief World Systems, Modern Library, New York, 2001 (originally published 1632).
51. Glass, L., and S. A. Kauffman, "The Logical Analysis of Continuous Non-linear Biochemical Control Networks," Journal of Theoretical Biology, 39, 103-129, 1973.
52. Glick, N., "Additive Estimators for Probabilities of Correct Classification," Pattern Recognition, 10, 211-222, 1978.
53. Gomez-Lazaro, M., Fernandez-Gomez, F. J., and J. Jordan, "p53: Twenty-Five Years Understanding the Mechanism of Genome Protection," Journal of Physiology and Biochemistry, 60 (4), 287-307, 2004.
54. Goutsias, J., and S. Kim, "A Nonlinear Discrete Dynamical Model for Transcriptional Regulation: Construction and Properties'," Biophysical Journal, 86, 1922-1945, 2004.
55. Hanczar, B., Hua, J., Sima, C., Weinstein, J., Bittner, M. L., and E. R. Dougherty, "Small-sample Precision of ROC-related Estimates," Bioinformatics, 26 (6), 822-830, 2010.
56. Hsing, T., Attoor, S., and E. R. Dougherty, "Relation Between Permutation-test P Values and Classifier Error Estimates," Machine Learning, 52 (1-2), 11-30, 2003.
57. 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 (8), 1509-1515, 2005.
58. Hughes, G. F., "On the Mean Accuracy of Statistical Pattern Recognizers," IEEE Transactions on Information Theory, 14, 55-63, 1968.
59. Hume, D., A Treatise of Human Nature, Oxford University Press, Oxford, 1951 (originally published 1738).
60. Hume, D., An Enquiry Concerning Human Understanding, Great Books of the Western World, Vol. 35, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952 (originally published 1751).
61. Husmeier, D., "Sensitivity and Specificity of Inferring Genetic Regulatory Interactions from Microarray Experiments with Dynamic Bayesian Networks," Bioinformatics, 19 (17), 2271-2282, 2003.
62. Ivanov, I., and E. R. Dougherty, "Modeling Genetic Regulatory Networks: Continuous or Discrete?" Biological Systems, 14, 219-229, 2006.
63. James, W., Pragmatism and Other Essays, Washington Square Press, New York, 1963.
64. Jeans, J. H., The Mysterious Universe, Cambridge University Press, Cambridge, 1930.
65. Jelizarow, M., Guillemot, V., Tenenhaus, A., Strimmer, K., and A.-L. Boulesteix, "Over Optimism in Bioinformatics: An Illustration," Bioinformatics, 26 (16), 1990-1998, 2010.
66. Kaltenbach, L. S., Romero, E., Becklin, R. R., Chettier, R., Bell, R., Phansaldar, A., et al., "Huntingtin Interacting Proteins Are Genetic Modifiers of Neurodegeneration," PLoS Genetics, 3 (5), e82, 2007.
67. Kant, I., Critique of Pure Reason, Great Books of the Western World, 2nd ed., Vol. 42, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952 (originally published 1787).
68. Kant, I., Critique of Pure Reason, Henry G. Bohn, London, 1855 (originally published 1787).
69. Kant, I., Prolegomena to Any Future Metaphysics, Kant's Prolegomena and Metaphysical Foundations of Natural Science, George Bell and Sons, London, 1891 (originally published 1783).
70. Kauffman, S. A., The Origins of Order, Oxford University Press, Oxford, 1993.
71. Kauffman, S. A., Does Science Make Belief in God Obsolete? John Templeton Foundation, http://www.templeton.org/belief/, 2007.
72. Kauffman, S. A., Breaking the Galilean Spell, Edge, http://www.edge.org/, 2008.
73. Keller, E. F., "Revisiting Scale-free Networks," BioEssays, 27, 1060-1068, 2005.
74. Kierkegaard, S., Concluding Unscientific Postscript, Princeton University Press, Princeton, NJ, 1941.
75. Kim, S., Dougherty, E. R., Shmulevich, I., Hess, K. R., Hamilton, S. R., Trent, J. M., et al., "Identification of Combination Gene Sets for Glioma Classification," Molecular Cancer Therapeutics, 1 (13), 1229-1236, 2002.
76. Kline, M., Mathematics and the Search for Knowledge, Oxford University Press, Oxford, 1985.
77. Koken, M. H., Puvion-Dutilleul, F., Guillemin, M. C., Viron, A., Linares-Cruz, G., Stuurman, N., et al., "The t(15;17) Translocation Alters a Nuclear Body in a Retinoic Acid-reversible Fashion," The EMBO Journal, 13 (5), 1073-1083, 1994.
78. Kolmogorov, A., "On the Analytical Methods of Probability Theory," Mathematishe Anallen, 104, 415-458, 1931.
79. Kolmogorov, A., Stationary Sequences in Hilbert Space. Bulletin of the Mathematics University of Moscow, 2, 1941.
80. Kumar, P. R., and W. Lin, "Optimal Adaptive Controller for Unknown Markov Chains," IEEE Transactions on Automatic Control, 27, 765-774, 1982.
81. Laplace, P.-S., A Philosophical Essay on Probabilities, Dover, New York, 1953 (originally published 1814).
82. Liang, S., Fuhrman, S., and R. Somogyi, "REVEAL A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures," Pacific Symposium on Biocomputing, 3, 18-29, 1998.
83. Marbach, D., Prill, R. J., Schaffter, T., Mattiussi, C., Flreano, D., and G. Stolovitzky, "Revealing Strengths and Weaknesses of Methods for Gene Network Inference," Proceedings of the National Academy of Sciences of the United States of America, 107 (14), 6286-6291, 2010.
84. Martins, D., Braga-Neto, U., Hashimoto, R., Bittner, M. L., and E. R. Dougherty, "Intrinsically Multivariate Predictive Genes," IEEE Journal of Selected Topics in Signal Processing, 2 (3), 424-439, 2008.
85. Matheron, G., Random Sets and Integral Geometry, John Wiley, New York, 1975.
86. Maxwell, J. C., "On Faraday's Lines of Force," Transactions of the Cambridge Philosophical Society, 10, 155-229, 1855.
87. Mehta, T., Murat, T., and D. B. Allison, "Towards Sound Epistemological Foundations of Statistical Methods for High-dimensional Biology," Nature Genetics, 36, 943-947, 2004.
88. Mill, J. S., A System of Logic, Ratiocinative and Inductive, University Press of the Pacific, Honolulu, HI, 2002 (originally published 1843).
89. Moffat, J. W., Reinventing Gravity: A Physicist Goes Beyond Einstein, Smithsonian Books/Collins, New York, 2008.
90. Newton, I., Mathematical Principles of Natural Philosophy, Great Books of the Western World, Vol. 34, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952 (originally published 1687).
91. Nilim, A., and L. El Ghaoui, "Robust Control of Markov Decision Processes with Uncertain Transition Matrices," Operations Research, 53, 780-798, 2005.
92. Noguchi, T., Metz, R., Chen, L., Mattéi, M. G., Carrasco, D., and R. Bravo, "Structure, Mapping, and Expression of ERP, a Growth Factor-inducible Gene Encoding a Nontransmembrane Protein Tyrosine Phosphatase, and Effect of ERP on Cell Growth," Molecular and Cell Biology, 13 (9), 5195-5205, 1993.
93. Nowell, P. C., and D. A. Hungerford, "A Minute Chromosome in Human Chronic Granulocytic Leukemia," Science, 132 (3438), 1497, 1960.
94. Pal, R., Datta, A., and E. R. Dougherty, "Optimal Infinite Horizon Control for Probabilistic Boolean Networks," IEEE Transactions on Signal Processing, 54, 2375-2387, 2006.
95. Pal, R., Datta, A., and E. R. Dougherty, "Robust Intervention in Probabilistic Boolean Networks," IEEE Transactions on Signal Processing, 56, 1280-1294, 2008.
96. Pear, W. S., Miller, J. P., Xu, L., Pui, J. C., Soffer, B., Quackenbush, R. C., et al., "Efficient and Rapid Induction of a Chronic Myelogenous Leukemia-like Myeloproliferative Disease in Mice Receiving P210 bcr/abl-transduced Bone Marrow," Blood, 92 (10), 3780-3792, 1988.
97. Plato, Republic, Great Books of the Western World, Vol. 8, eds. R. M. Hutchins and M. J. Adler, Encyclopedia Britannica, Chicago, 1952.
98. Popper, K., The Logic of Scientific Discovery, Hutchinson, London, 1959.
99. Popper, K., Conjectures and Refutations, Routledge, London, 1963.
100. Pugachev, V. S., Theory of Random Functions and Its Application to Control Problems, Pergamon Press, Oxford, 1965.
101. Qian, X., and E. R. Dougherty, "Effect of Function Perturbation on the Steady-state Distribution of Genetic Regulatory Networks: Optimal Structural Intervention," IEEE Transactions on Signal Processing, 56, 4966-4975, 2008.
102. Qian, X., and E. R. Dougherty, "On the Long-run Sensitivity of Probabilistic Boolean Networks," Journal of Theoretical Biology, 257, 560-577, 2009.
103. Qian, X., Ivanov, I., Ghaffari, N., and E. R. Dougherty, "Intervention in Gene Regulatory Networks via Greedy Control Policies Based on Long-run Behavior," BMC Systems Biology, 3, 61, 2009.
104. Reichenbach, H., The Rise of Scientific Philosophy, University of California Press, Berkeley, 1971.
105. Rommens, J. M., Iannuzzi, M. C., Kerem, B., Drumm, M. L., Melmer, G., Dean, M., et al., "Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping," Science, 245 (4922), 1059-1065, 1989.
106. Rosenblueth, A., and N. Wiener, "The Role of Models in Science," Philosophy of Science, 12, 316-321, 1945.
107. Russell, B., "On the Notion of Cause," Proceedings of the Aristotelian Society, 13, 1-26, 1913.
108. Schrödinger, E., Science Theory and Man, Dover, New York, 1957.
109. Shmulevich, I., and E. R. Dougherty, Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks, SIAM Press, New York, 2010.
110. Simon, J. L., Resampling: The New Statistics, 2nd ed., Resampling Stats, 1997.
111. Slack, J. M. W., From Egg to Embryo: Determinative Events in Early Development, Cambridge University Press, Cambridge, 1983.
112. Smalley, K. S., "A Pivotal Role for ERK in the Oncogenic Behaviour of Malignant Melanoma?" International Journal of Cancer, 104 (5), 527-532, 2003.
113. St Johnston, D., and C. Nusslein-Volhard, "The Origin of Pattern and Polarity in the Drosophila Embryo," Cell, 68 (2), 201-219, 1992.
114. Tabin, C. J., and R. A. Weinberg, "Analysis of Viral and Somatic Activations of the cHa-ras Gene," Virology, 53 (1), 260-265, 1985.
115. The Huntington's Disease Collaborative Research Group, "A Novel Gene Containing a Trinucleotide Repeat That Is Expanded and Unstable on Huntington's Disease Chromosomes," Cell, 72 (6), 971-983, 1993.
116. Turing, A. M., "The Chemical Basis of Morphogenesis," Philosophical Transactions of the Royal Society of London, 237 (641), 37-72, 1952.
117. Vahedi, G., Faryabi, B., Chamberland, J.-F., Datta, A., and E. R. Dougherty, "Intervention in Gene Regulatory Networks via a Stationary Mean-first-passage-time Control Policy," IEEE Transactions on Biomedical Engineering, 15, 2319-2331, 2008.
118. van de Vijver, M. J., He, Y. D., van't Veer, L. J., Dai, H., Hart, A. A., Voskuil, D. W., et al., "Gene Expression Signature as a Predictor of Survival in Breast Cancer," The New England Journal of Medicine, 347, 1999-2009, 2002.
119. van't Veer, L. J., Dai, H., van de Vijver, M. J., He, Y. D., Hart, A. A. M., Mao, M., et al., "Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer," Nature, 415, 530-536, 2002.
120. Vapnik, V. N., and A. Chervonenkis, Theory of Pattern Recognition, Nauka, Moscow, 1974.
121. Varmus, H., "Ten Years On-The Human Genome and Medicine," The New England Journal of Medicine, 362 (21), 2028-2029, 2010.
122. Vennstrom, B., Sheiness, D., Zabielski, J., and J. M. Bishop, "Isolation and Characterization of c-myc, a Cellular Homolog of the Oncogene (v-myc) of Avian Myelocytomatosis Virus Strain 29," Virology, 42 (3), 773-779, 1982.
123. Waddington, C. H., How Animals Develop, Allen & Unwin, London, 1935.
124. Waddington, C. H., "Canalization of Development and the Inheritance of Acquired Characters," Nature, 150, 563-565, 1942.
125. Waddington, C. H., Principles of Development and Differentiation, Macmillian, New York, 1966.
126. Webster's New Twentieth Century Dictionary, Unabridged, 2nd ed., Collins, New York, 1978.
127. Weeraratna, A. T., Jiang, Y., Hostetter, G., Rosenblatt, K., Duray, P., Bittner, M. L., and J. M. Trent, "Wnt5a Signaling Directly Affects Cell Motility and Invasion of Metastatic Melanoma," Cancer Cell, 1, 279-288, 2002.
128. Werhli, A. V., Grzegorczyk, M., and D. Husmeier, "Comparative Evaluation of Reverse Engineering Gene Regulatory Networks with Relevance Networks, Graphical Gaussian Models and Bayesian Networks," Bioinformatics, 22 (20), 2523-2531, 2006.
129. Wiener, N., Cybernetics: or Control and Communication in the Animal and Machine, MIT Press, Cambridge, MA, 1948.
130. Wiener, N., Extrapolation, Interpolation, and Smoothing of Stationary Time Series, MIT Press, Cambridge, MA, 1949.
131. Wiener, N., and A. Rosenblueth, "The Mathematical Formation of the Problem of Conduction of Impulses in a Network of Connected Excitable Elements, Specifically in Cardiac Muscle," Archives of the Institute of Cardiology, Mexico, 16, 204-265, 1946.
132. Windelband, W., A History of Philosophy, Harper and Brothers, New York, 1958.
133. Wu, X., Wakefield, J. K., Liu, H., Xiao, H., Kralovics, R., Prchal, J. T., and J. C. Kappes, "Development of a Novel Trans-lentiviral Vector That Affords Predictable Safety," Molecular Therapeutics, 2 (1), 47-55, 2000.
134. 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, 5 (6), 579-590, 2006.
135. Yousefi, M. R., Hua, J., Sima, C., and E. R. Dougherty, "Reporting Bias When Using Real Data Sets to Analyze Classification Performance," Bioinformatics, 26 (1), 68-76, 2010.
136. Zhao, W., Serpedin, E., and E. R. Dougherty, "Inferring Gene Regulatory Networks from Time Series Data Using the Minimum Description Length Principle," Bioinformatics, 22 (17), 2129-2135, 2006.
137. Zhao, C., Bittner, M. L., Chapkin, R., and E. R. Dougherty, "Characterization of the Effectiveness of Reporting Lists of Small Feature Sets Relative to the Accuracy of the Prior Biological Knowledge," Cancer Informatics, 9, 49-60, 2010.
138. Zollanvari, A., Braga-Neto, U. M., and E. R. Dougherty, "On the Joint Sampling Distribution Between the Actual Classification Error and the Resubstitution and Leave-one-out Error Estimators for Linear Classifiers," IEEE Transactions on Information Theory, 56 (2), 784-804, 2010.