Synthetic Gene Circuits: Methods and Protocols

1. Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits Madalena Chaves and Hidde de Jong 2. Stochastic Differential Equations for Practical Simulation of Gene Circuits Jesus Pico, Alejandro Vignoni, and Yadira Boada 3. Using Models To (Re-)Design Synthetic Circuits Giselle McCallum and Laurent Potvin-Trottier 4. Automated bio-circuit design with SYNBADm Irene Otero-Muras and Julio R. Banga 5. Setting up an Automated Biomanufacturing Laboratory Marilene Pavan 6. Computer-aided Design and Pre-validation of Large Batches of DNA Assemblies Valentin Zulkower 7. Computer-aided Planning for the Verification of Large Batches of DNA Constructs Valentin Zulkower 8. Characterizing Genetic Parts and Devices using RNA Sequencing Deepti Vipin, Zoya Ignatova, and Thomas E. Gorochowski 9. Steady-State Cell-Free Gene Expression with Microfluidic Chemostats Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, and Sebastian J. Maerkl 10. A Microfluidic/Microscopy-Based Platform for On-Chip Controlled Gene Expression in Mammalian Cells Mahmoud Khazim, Elisa Pedone, Lorena Postiglione, Diego di Bernardo, and Lucia Marucci 11. Optimal Experimental Design for Systems and Synthetic Biology Using Amigo2 Eva Balsa-Canto, Lucia Bandiera, and Filippo Menolaschina 12. A Cyber-Physical Platform for Model Calibration Lucia Bandiera, David Gomez Cabeza, Eva Balsa-Canto, and Filippo Menolascina 13. Prediction of cellular burden with host-circuit models Evangelos-Marios Nikolados, Andrea Y. Weisse, and Diego A. Oyarzun 14. A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks Andras Gyorgy 15. Engineering Sensors for Gene Expression Burden Alice Boo and Francesca Ceroni 16. Engineering Protein-based Parts for Genetic Devices in Mammalian Cells Giuliano Bonfa, Federica Cella, and Velia Siciliano