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Table of contents
Abstract
Résumé
Résumé français détaillé
0.1 Outils de conception assistée par ordinateur
0.2 Analyse et modélisation de circuits métaboliques: des données
à la connaissance
Remerciements
Introduction
Synthetic biology’s aims and advances
Design tools for metabolic circuits
Analysis and modeling tools for metabolic circuits
Thesis structure and contributions
I Computational design tools
1 Enzyme Selection and Pathway Design
1.1 Abstract
1.2 Introduction
1.3 Enzyme selection
1.4 Pathway Design
1.5 Summary and conclusion
2 Molecular structure enumeration
2.1 Introduction
2.2 Results and Discussion
2.3 Conclusions
2.4 Methods
2.5 Supplementary Data
3 RetroPath3.0: Similarity-guided Monte Carlo Tree Search for metabolic engineering
3.1 Abstract
3.2 Introduction
3.3 Theoretical background
3.4 Results and Discussion
3.5 Conclusion
3.6 Materials and methods
3.7 Supplementary Tables
3.8 Supplementary Note 1: Parameters’ Role and Effects
4 Detectable Compounds Dataset
4.1 Abstract
4.2 Data
4.3 Experimental design, materials and methods
5 Active learning for cell-free optimization
5.1 Abstract
5.2 Results and Discussion
5.3 Methods
5.4 Supplementary Data
II Analyzing and modeling metabolic circuits
6 Transcriptional Biosensors for Metabolic Engineering
6.1 Abstract
6.2 Introduction
6.3 Designing a transcriptional biosensor to detect a compound of interest
6.4 Computer-assisted fine-tuning of biosensor properties
6.5 Custom-made biosensors’ new application domain: cell-free metabolic engineering
6.6 Conclusion
7 Building a minimal and generalisable model of transcription factor-based biosensors: Showcasing flavonoids
7.1 Abstract
7.2 Introduction
7.3 Materials and methods
7.4 Results
7.5 Discussion
7.6 Supplementary Data
8 Models for Cell-free Synthetic Biology
8.1 Abstract
8.2 Introduction
8.3 Translation and transcription processes in cell-free
8.4 Resource competition in cell-free
8.5 Metabolism in cell-free
8.6 Conclusion
9 Plug-and-Play Metabolic Transducers
9.1 Abstract
9.2 Introduction
9.3 Results
9.4 Discussion
9.5 Methods
9.6 Mathematical Modeling of Cell-Free Biosensors
9.7 Mathematical model derivation
10 Metabolic Perceptrons for Neural Computing in Biological Systems
10.1 Abstract
10.2 Introduction
10.3 Results
10.4 Discussion
10.5 Methods
10.6 Supplementary data
Conclusion & perspectives
Design tools for metabolic circuits
Analysis and modeling tools for metabolic circuits
List of Symbols
List of Tables
List of Figures
Bibliography
