title: Retropath: automated pipeline for embedded metabolic circuits.
abstract: Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such as smart therapeutics, however, require circuits that enable sensing and regulation. Here, we present RetroPath, an automated pipeline for embedded metabolic circuits that explores the circuit design space from a given set of specifications and selects the best circuits to implement based on desired constraints. Synthetic biology circuits embedded in a chassis organism that are capable of controlling the production, processing, sensing, and the release of specific molecules were enumerated in the metabolic space through a standard procedure. In that way, design and implementation of applications such as therapeutic circuits that autonomously diagnose and treat disease, are enabled, and their optimization is streamlined.
authors.affiliation: Univ. Evry, CNRS, iSSB , F-91000 Evry, France.
authors.forename: Pablo
authors.initials: P
authors.lastname: Carbonell
authors.forename: Pierre
authors.initials: P
authors.lastname: Parutto
authors.forename: Claire
authors.initials: C
authors.lastname: Baudier
authors.forename: Christophe
authors.initials: C
authors.lastname: Junot
authors.forename: Jean-Loup
authors.initials: JL
authors.lastname: Faulon
mesh_terms: D000465:Algorithms; D000544:Alzheimer Disease / Q000378:metabolism; D015415:Biomarkers / Q000378:metabolism; D015374:Biosensing Techniques; D004827:Epilepsy / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D053858:Metabolic Networks and Pathways; D012984:Software; D058615:Synthetic Biology / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D015415:Biomarkers; D014157:Transcription Factors