Genomics and Proteomics Engineering in Medicine and Biology

METIN AKAY, PHD, is the Interim Chair and Professor of Bioengineering for the Harrington Department of Bioengineering at the Arizona State University. Dr. Akay is the founding Series Editor of the IEEE Press Series on Biomedical Engineering. In 1997, he received the prestigious Early Career Achievement Award from the IEEE Engineering in Medicine and Biology Society (EMBS). He was the program chair of both the annual IEEE EMBS Conference and Summer School for 2001. Dr. Akay has published several papers in the field and authored, coauthored, or edited fourteen books. He is also the editor in chief of the Wiley Encyclopedia of Biomedical Engineering.

• Preface xiContributors xiii1. Qualitative Knowledge Models in Functional Genomics and Proteomics 1Mor Peleg, Irene S. Gabashvili, and Russ B. Altman1.1. Introduction 11.2. Methods and Tools 31.3. Modeling Approach and Results 61.4. Discussion 191.5. Conclusion 20References 212. Interpreting Microarray Data and Related Applications Using Nonlinear System Identification 25Michael Korenberg2.1. Introduction 252.2. Background 252.3. Parallel Cascade Identification 302.4. Constructing Class Predictors 342.5. Prediction Based on Gene Expression Profiling 352.6. Comparing Different Predictors Over the Same Data Set 462.7. Concluding Remarks 48References 493. Gene Regulation Bioinformatics of Microarray Data 55Gert Thijs, Frank De Smet, Yves Moreau, Kathleen Marchal, and Bart De Moor3.1. Introduction 553.2. Introduction to Transcriptional Regulation 573.3. Measuring Gene Expression Profiles 593.4. Preprocessing of Data 613.5. Clustering of Gene Expression Profiles 633.6. Cluster Validation 703.7. Searching for Common Binding Sites of Coregulated Genes 763.8. Inclusive: Online Integrated Analysis of Microarray Data 873.9. Further Integrative Steps 893.10. Conclusion 90References 914. Robust Methods for Microarray Analysis 99George S. Davidson, Shawn Martin, Kevin W. Boyack, Brian N. Wylie, Juanita Martinez, Anthony Aragon, Margaret Werner-Washburne, Mónica Mosquera-Caro, and Cheryl Willman4.1. Introduction 994.2. Microarray Experiments and Analysis Methods 1004.3. Unsupervised Methods 1034.4. Supervised Methods 1174.5. Conclusion 127References 1285. In Silico Radiation Oncology: A Platform for Understanding Cancer Behavior and Optimizing Radiation Therapy Treatment 131G. Stamatakos, D. Dionysiou, and N. Uzunoglu5.1. Philosophiae Tumoralis Principia Algorithmica: Algorithmic Principles of Simulating Cancer on Computer 1315.2. Brief Literature Review 1335.3. Paradigm of Four-Dimensional Simulation of Tumor Growth and Response to Radiation Therapy In Vivo 1355.4. Discussion 1485.5. Future Trends 150References 1506. Genomewide Motif Identification Using a Dictionary Model 157Chiara Sabatti and Kenneth Lange6.1. Introduction 1576.2. Unified Model 1606.3. Algorithms for Likelihood Evaluation 1646.4. Parameter Estimation via Minorization–Maximization Algorithm 1676.5. Examples 1706.6. Discussion and Conclusion 171References 1727. Error Control Codes and the Genome 173Elebeoba E. May7.1. Error Control and Communication: A Review 1737.2. Central Dogma as Communication System 1807.3. Reverse Engineering the Genetic Error Control System 1847.4. Applications of Biological Coding Theory 203References 2058. Complex Life Science Multidatabase Queries 209Zina Ben Miled, Nianhua Li, Yue He, Malika Mahoui, and Omran Bukhres8.1. Introduction 2098.2. Architecture 2128.3. Query Execution Plans 2148.4. Related Work 2198.5. Future Trends 222References 2239. Computational Analysis of Proteins 227Dimitrios I. Fotiadis, Yorgos Goletsis, Christos Lampros, and Costas Papaloukas9.1. Introduction: Definitions 2279.2. Databases 2299.3. Sequence Motifs and Domains 2329.4. Sequence Alignment 2359.5. Modeling 2419.6. Classification and Prediction 2429.7. Natural Language Processing 2489.8. Future Trends 252References 25210. Computational Analysis of Interactions Between Tumor and Tumor Suppressor Proteins 257E. Pirogova, M. Akay, and I. Cosic10.1. Introduction 25710.2. Methodology: Resonant Recognition Model 26110.3. Results and Discussions 26510.4. Conclusion 284References 285Index 289About the Editor 299

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