Computational Methods in Synthetic Biology

Part I: Component Design

1. Computational Protein Design Methods for Synthetic Biology

Pablo Carbonell and Jean-Yves Trosset

Denis Selnihhin and Ebbe Sloth Andersen

3. Computational Design Of RNA Parts, Devices, and Transcripts With Kinetic Folding Algorithms Implemented On Multiprocessor Clusters

Tim Thimmaiah, William E. Voje Jr., and James M. Carothers

4. Regulatory RNA Design Through Evolutionary Computation And Strand Displacement

William Rostain, Thomas E. Landrain, Guillermo Rodrigo, and Alfonso Jaramillo

Part II: Circuit Design

5. Programming Languages for Circuit Design

Michael Pedersen and Boyan Yordanov

6. Kappa Rule-Based Modelling in Synthetic Biology

7. Modular Design Of Synthetic Gene Circuits With Biological Parts and Pools

Mario Andrea Marchisio

8. Computationally Guided Design Of Robust Gene Circuits

Najaf A. Shah and Casim A. Sarkar

9. Chemical Master Equation Closure for Computer-Aided Synthetic Biology

Patrick Smadbeck and Yiannis N. Kaznessis

10. Feedback loops in biological networks

Elisa Franco and Kate E. Galloway

Part III: Circuit Analysis and Simulations

11. Efficient Analysis Methods in Synthetic Biology

Curtis Madsen, Chris Myers, Nicholas Roehner, Chris Winstead, and Zhen Zhang

12. Using Computational Modeling and Experimental Synthetic Perturbations to Probe Biological Circuits

Joshua R. Porter and Eric Batchelor

13. In Silico Control Of Biomolecular Processes

Jannis Uhlendorf, Agnès Miermont, Thierry Delaveau, Gilles Charvin, François Fages, Samuel Bottani, Pascal Hersen, and Gregory Batt

14. Stochastic Modular Analysis For Gene Circuits: Interplay Among Retroactivity, Nonlinearity, and Stochasticity

Kyung Hyuk Kim and Herbert M Sauro

Part IV: Distributed Systems and Automation

15. Distributed Model Construction with Virtual Parts

Michael T. Cooling and Tommy Yu

16. The Synthetic Biology Open Language

Chris Myers, Kevin Clancy, Goksel Misirli, Ernst Oberortner, Matthew Pocock,

Jacqueline Quinn, Nicholas Roehner, and Herbert Sauro

17. Computational Methods For The Construction, Editing, and Error Correction Of DNA Molecules And Their Libraries

Ofir Raz and Tuval Ben Yehezkel