Design and Analysis of Biomolecular Circuits

1. Continuous Time Markov Chain Models for Chemical Reaction Networks
David F. Anderson, Thomas G. Kurtz

2. Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell
Kevin Burrage, Pamela M. Burrage, André Leier, Tatiana Marquez-Lago, Dan V. Nicolau

3. Graph-Theoretic Analysis of Multistability and Monotonicity for Biochemical Reaction Networks
Gheorghe Craciun, Casian Pantea, Eduardo D. Sontag

4. From Structure to Dynamics in Biological Networks
Murad Banaji

5. Contraction Theory for Systems Biology
Giovanni Russo, Mario Bernardo, Jean Jacques Slotine

6. Toward Modularity in Synthetic Biology: Design Patterns and Fan-out
Kyung Hyuk Kim, Deepak Chandran, Herbert M. Sauro

7. Retroactivity as a Criterion to Define Modules in Signaling Networks
Julio Saez-Rodriguez, Holger Conzelmann, Michael Ederer, Ernst Dieter Gilles

8. The Impact of Retroactivity on the Behavior of Biomolecular Systems
Domitilla Vecchio

9. Modularity, Retroactivity, and Structural Identification
Eduardo D. Sontag

10. Computer-Aided Design for Synthetic Biology
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, Douglas Densmore

11. High-Level Programming Languages for Biomolecular Systems
Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai

12. Rational Design of Robust Biomolecular Circuits: from Specification to Parameters
Marc Hafner, Tatjana Petrov, James Lu, Heinz Koeppl

13. Data Model Standardization for Synthetic Biomolecular Circuits and Systems
Michal Galdzicki, Deepak Chandran, John H. Gennari, Herbert M. Sauro

14. DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems
Nathan J. Hillson

15. Gene Synthesis – Enabling Technologies for Synthetic Biology
Michael Liss, Ralf Wagner

16. On the Construction of Minimal Cell Models in Synthetic Biology and Origins of Life Studies
Pasquale Stano, Pier Luigi Luisi

17. Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells
Serge Pelet, Matthias Peter

Keywords: Engineering, Circuits and Systems, Computer-Aided Engineering (CAD, CAE) and Design