Discrete and Topological Models in Molecular Biology

Table of Contents

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   Book Overview
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   Chapter 1 Perspectives in Computational Genome Analysis
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   Chapter 2 The Sequence Reconstruction Problem
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   Chapter 3 Extracting Coevolving Characters from a Tree of Species
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   Chapter 4 When and How the Perfect Phylogeny Model Explains Evolution
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   Chapter 5 An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques
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   Chapter 6 Simplicial Models and Topological Inference in Biological Systems
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   Chapter 7 Combinatorial Insights into RNA Secondary Structure
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   Chapter 8 Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis
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    Chapter 9 Modeling Autonomous Supramolecular Assembly
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    Chapter 10 The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach
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    Chapter 11 Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs
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    Chapter 12 Programmed Genome Processing in Ciliates
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    Chapter 13 The Algebra of Gene Assembly in Ciliates
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    Chapter 14 Invariants of Graphs Modeling Nucleotide Rearrangements
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    Chapter 15 Introduction to DNA Topology
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    Chapter 16 Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations
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    Chapter 17 Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links
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    Chapter 18 Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination
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    Chapter 19 Understanding DNA Looping Through Cre-Recombination Kinetics
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    Chapter 20 The QSSA in Chemical Kinetics: As Taught and as Practiced
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    Chapter 21 Algebraic Models and Their Use in Systems Biology
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    Chapter 22 Deconstructing Complex Nonlinear Models in System Design Space
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    Chapter 23 IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology