Bioinformatics in the Post-Genomic Era

Jeff Augen has a 20-year history in information technology and computational biology. Most recently, as President and CEO of the technical computing software company TurboWorx Inc., Jeff has focused on the design of parallel computing solutions for biomedical research and drug discovery. In his former position as the Director of Strategy for IBM's Life Sciences Division, Jeff was responsible for the company's entry into several new areas of the life sciences computing market including, most notably, information-based medicine. He is a frequent speaker at industry events, a member of several editorial boards, and an author of many recent review articles and editorials, in addition to a chapter on computational biology for Anti-Cancer Drug Development; Lippincott 2003.Augen's academic background includes graduate and undergraduate degrees in Biochemistry and Molecular Biology from the University of Texas and Rice University, respectively. His thesis research involved the development of algorithms for predicting protein tertiary structure. © Copyright Pearson Education. All rights reserved.

• Preface. 1. Introduction. Overview. Computationally Intense Problems: A Central Theme in Modern Biology. Building the Public Infrastructure. The Human Genome’s Several Layers of Complexity. Toward Personalized Medicine. Illnesses are Polygenic. New Science, New Infrastructure. The Proactive Future of Information-Based Medicine. 2. Introduction to Bioinformatics. Introduction. The Emergence of Bioinformatics. The Public Database Infrastructure. Building Database Infrastructure for Bioinformatics. Traditional Bioinformatic Tools and Algorithms. Summary. 3. Gene Structure. Introduction. The Central Dogma of Molecular Biology. The Genetic Code. Structure and Content of the Genome. Computational Techniques for the Identification of Genomic Features. High-Throughput Gene Sequencing. Summary. 4. Computational Techniques for Sequence Analysis. Introduction. Hidden Markov Models. Perceptrons and Neural Networks. Pattern Discovery, Single Nucleotide Polymorphisms, and Haplotype Identification. Summary. 5. Transcription. Introduction. The Transcriptome. Technologies for Transcriptional Profiling. Hierarchical Clustering. Summary. 6. Overview of the Proteome and the Protein Translation Process. Introduction. Ribosomal Structure and the Protein Translation Process. Special Features of the Eukaryotic-Translation Process. Summary. 7. Protein Structure Prediction. Introduction. Overview of Ab Initio and Database-Driven Approaches. Overview of   Protein Structure. Protein Structure Databases. Ab Initio Structure Prediction. Predicting Lead–Target Interactions. Summary. 8. Medical Informatics and Information-Based Medicine. Introduction. The Continuous Evolution in Understanding that Leads to Genomic Medicine. Electronic Medical Records. Grid Computing and Medical Informatics. Modeling and Predicting Disease. Summary. 9. New Themes in Bioinformatics. Introduction. Overview of Parallel Computing and Workflow Distribution in Bioinformatics. Workflow Computing. High-Performance Computing and Systems Biology. The Delineation of Metabolic Pathways. Systems Biology. Summary. Further Reading. Index.