Discrete and Topological Models in Molecular Biology

Part I. Discrete and Graph-Theoretic Models for Data Analysis

1. Perspectives in Computational Genome Analysis
Giuditta Franco

2. The Sequence Reconstruction Problem
Angela Angeleska, Sabrina Kleessen, Zoran Nikoloski

3. Extracting Coevolving Characters from a Tree of Species
Alessandra Carbone

4. When and How the Perfect Phylogeny Model Explains Evolution
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi, Teresa M. Przytycka

5. An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques
Mark Daley

6. Simplicial Models and Topological Inference in Biological Systems
Vidit Nanda, Radmila Sazdanović

Part II. Molecular Arrangements and Structures

7. Combinatorial Insights into RNA Secondary Structure
Christine Heitsch, Svetlana Poznanović

8. Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis
Naomi Fox, Ileana Streinu

9. Modeling Autonomous Supramolecular Assembly
Meera Sitharam

10. The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach
Paolo Cermelli, Giuliana Indelicato, Reidun Twarock

11. Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs
Joanna Ellis-Monaghan, Greta Pangborn, Laura Beaudin, David Miller, Nick Bruno, Akie Hashimoto

Part III. Gene Rearrangements

12. Programmed Genome Processing in Ciliates
Aaron David Goldman, Elizabeth M. Stein, John R. Bracht, Laura F. Landweber

13. The Algebra of Gene Assembly in Ciliates
Robert Brijder, Hendrik Jan Hoogeboom

14. Invariants of Graphs Modeling Nucleotide Rearrangements
Egor Dolzhenko, Karin Valencia

Part IV. Topological Models and Spatial DNA Embeddings

15. Introduction to DNA Topology
Isabel K. Darcy, Stephen D. Levene, Robert G. Scharein

16. Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations
Dorothy Buck

17. Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links
Kenneth L. Baker

18. Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination
Kai Ishihara, Koya Shimokawa, Mariel Vazquez

Part V. Dynamics and Kinetics of Molecular Interactions

19. Understanding DNA Looping Through Cre-Recombination Kinetics
Massa J. Shoura, Stephen D. Levene

20. The QSSA in Chemical Kinetics: As Taught and as Practiced
Casian Pantea, Ankur Gupta, James B. Rawlings, Gheorghe Craciun

21. Algebraic Models and Their Use in Systems Biology
Reinhard Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba

22. Deconstructing Complex Nonlinear Models in System Design Space
Michael A. Savageau, Jason G. Lomnitz

23. IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology
Katarzyna A. Rejniak

Keywords: Computer Science, Theory of Computation, Mathematical and Computational Biology, Evolutionary Biology, Systems Biology, Cell Biology, Biological Networks, Systems Biology