title: In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.
abstract: Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.
authors.affiliation: Centre of Biological Engineering, Universidade do Minho, Braga, Portugal SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal.
authors.forename: Paulo
authors.initials: P
authors.lastname: Maia
authors.affiliation: Centre of Biological Engineering, Universidade do Minho, Braga, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
authors.affiliation: Centre of Biological Engineering, Universidade do Minho, Braga, Portugal irocha@deb.uminho.pt.
authors.forename: Isabel
authors.initials: I
authors.lastname: Rocha
mesh_terms: D000465:Algorithms; D046969:Clostridium acetobutylicum / Q000235:genetics / Q000378:metabolism*; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D007218:Industrial Microbiology / Q000379:methods*; D060847:Metabolic Engineering / Q000379:methods; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*