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Front Cover; Epigenetics and Systems Biology; Copyright Page; Contents; List of Contributors; I. Introduction; References; II. Where Am I? Genomic Features and DNA Sequence Principles Defining Sites of Epigenetic Regulation: Machine Learning; 1 Computational Identification of Polycomb/Trithorax Response Elements; Introduction to Polycomb/Trithorax Response Elements; 2003 Ad Hoc Approach to PRE Prediction, Together with its Particular Motivations; Evaluating Classification Performance; Results of 2003 PRE Prediction; New Motifs Discovered; Recasting PRE Prediction as a Machine Learning Problem.

Misclassification Costs and the Trade-off DimensionEvolutionary Analysis and Search-Space Reduction; Today: Genome-Wide Profiling Data; How Good is Our Method When Evaluated Under These Data?; Sensitivity and Specificity of Genome-Wide Profiling; Conclusion; References; Glossary; List of Acronyms and Abbreviations; 2 Modeling Chromatin States; The Purpose of Modeling Chromatin States; The Common Approach; What Have We Learned From those Models?; Static Versus Dynamical Models; Chromatin States are Attractors; References; Glossary; List of Acronyms and Abbreviations.

3 Crossing Borders: Modeling Approaches to Understand Chromatin Domains and Their BoundariesIntroduction; The Expanding Universe of Structural Domains; Experimental Techniques; Modeling Higher Order Chromatin Structure; Formalizing Compartment Calling and Boundary Prediction; Outlook; References; List of Acronyms and Abbreviations; 4 Inferring Chromatin Signaling From Genome-Wide ChIP-seq Data; Introduction; Experimental Techniques; Modeling; Perturbing the System; Outlook; References; Glossary; List of Acronyms and Abbreviations.

III. Everything's Moving: In Vivo Dynamics of Epigenetic Regulators: Kinetic Models Based on Ordinary Differential Equation ... 5 "In Vivo Biochemistry": Absolute Quantification and Kinetic Modeling Applied to Polycomb and Trithorax Regulation; Introduction; The Journey Begins: DNA Recombinases Yield Their Secrets to Mathematics; The Journey Continues: Epigenetics Meets Mathematics; Absolute Quantification In Vivo: A Technical Challenge; Fluorescent Tagging: A Powerful Tool for Live Imaging; Absolute Quantification of Molecule Numbers: Double Check!

Everything's Moving: Methods for Measuring Kinetic Parameters In VivoIn Vivo Biochemistry of an Epigenetic System: What Did We Learn?; Mathematical Modeling of the System: Defining What We Don't Know; Basic Principles of Kinetic Modeling; Kinetic Modeling of Polycomb and ASH1 Makes Mechanistic Predictions; Model 1: Wrong But Useful; Model 2: Still Wrong But More Useful; Model 3: This One Might Be Right!; Back to the Bench: Testing the Model by Perturbing the System; Outlook; Acknowledgments; References; Glossary; List of Acronyms and Abbreviations.

6 Modeling Distributive Histone Modification by Dot1 Methyltransferases: From Mechanism to Biological Insights.

Includes index.

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