Genome Sequencing Technolog and Algorithms -- List of Contributors -- Contents -- Part I The New DNA Sequencing Technology -- 1 An Overview of New DNA Sequencing Technology -- 1.1 An Overview -- 1.2 Massively Parallel Sequencing by Synthesis Pyrosequencing -- 1.3 Massively Parallel Sequencing by Other Approaches -- 1.4 Survey of Future Massively Parallel Sequencing Methods -- 2 Array-Based Pyrosequencing Technology -- 2.1 Introduction -- 2.2 Pyrosequencing Chemistry -- 2.3 Array-Based Pyrosequencing -- 2.4 454 Sequencing Chemistry -- 2.5 Applications of 454 Sequencing Technology -- 2.6 Advantages and Challenges -- 2.7 Future of Pyrosequencing -- 3 The Role of Resequencing Arrays in RevolutionizingDNA Sequencing -- 3.1 Introduction -- 3.2 DNA Sequencing by Hybridization with ResequencingArrays -- 3.3 Resequencing Array Experimental Protocols -- 3.4 Analyzing Resequencing Array Data with ABACUS -- 3.5 Review of RA Applications -- 3.6 Further Challenges -- 4 Polony Sequencing -- 4.1 Introduction -- 4.2 Overview -- 4.3 Construction of Sequencing Libraries -- 4.4 Template Amplification with Emulsion PCR -- 4.5 Sequencing -- 4.6 Future Directions -- 5 Genome Sequencing: A Complex Path to PersonalizedMedicine -- 5.1 Introduction -- 5.2 Personalized Medicine -- 5.3 Heterogeneous Data Sources -- 5.4 Information Modeling -- 5.5 Ontologies and Terminologies -- 5.6 Applications -- 5.7 Conclusion -- Part II Genome Sequencing and Fragment Assembly -- 6 Overview of Genome Assembly Techniques -- 6.1 Genome Sequencing by Shotgun-Sequencing Strategy -- 6.2 Trimming Vector and Low-Quality Sequences -- 6.3 Fragment Assembly -- 6.4 Assembly Validation -- 6.5 Scaffold Generation -- 6.6 Finishing -- 6.7 Three Strategies for Whole-Genome Sequencing -- 6.8 Discussion -- 7 Fragment Assembly Algorithms -- 7.1 TIGR Assembler -- 7.2 Phrap -- 7.3 CAP3 -- 7.4 Celera Assembler.

7.5 Arachne -- 7.6 EULER -- 7.7 Other Approaches to Fragment Assembly -- 7.8 Incompleteness of the Survey -- 8 Assembly for Double-Ended Short-Read SequencingTechnologies -- 8.1 Introduction -- 8.2 Short-Read Sequencing Technologies -- 8.3 Assembly for Short-Read Sequencing -- 8.4 Developing a Short-Read-Pair Assembler -- Part III Beyond Conventional Genome Sequencing -- 9 Genome Characterization in the Post-Human GenomeProject Era -- 9.1 Genome Resequencing and Comparative Assembly -- 9.2 Genotyping Versus Haplotyping -- 9.3 Large-Scale Genome Variations -- 9.4 Epigenomics: Genetic Variations Beyond GenomeSequences -- 9.5 Conclusion -- 10 The Haplotyping Problem: An Overview ofComputational Models and Solutions -- 10.1 Introduction -- 10.2 Preliminary Definitions -- 10.3 Inferring Haplotypes in a Population -- 10.4 Inferring Haplotypes in Pedigrees -- 10.5 Inferring Haplotypes from Fragments -- 10.6 A Glimpse over Statistical Methods -- 10.7 Discussion -- 11 Analysis of Genomic Alterations in Cancer -- 11.1 Introduction -- 11.2 Analysis of ESP Data -- 11.3 Combination of Techniques -- 11.4 Future Directions -- 12 High-Throughput Assessments of Epigenomics inHuman Disease -- 12.1 Introduction -- 12.2 Epigenetic Phenomena That Regulate Gene Expression -- 12.3 Epigenetics and Disease -- 12.4 High-Throughput Analyses of Epigenetic Phenomena -- 12.5 Conclusions -- 13 Comparative Sequencing, Assembly, and Anchoring -- 13.1 Comparing an Assembled Genome with AnotherAssembled Genome -- 13.2 Mutual Comparison of Genome Fragments -- 13.3 Comparing an Assembled Genome with GenomeFragments -- 13.4 Anchoring by Seed-and-Extend Versus PositionalHashing Methods -- 13.5 The UD-CSD Benchmark for Anchoring -- 13.6 Conclusions -- About the Authors -- Index.