Discrete and Topological Models in Molecular Biology

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