Computing optimal factories in metabolic networks with negative regulation | Zendy

Spencer Krieger | Zendy; John Kececioglu | Zendy

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Computing optimal factories in metabolic networks with negative regulation

Author(s) -

Spencer Krieger,

John Kececioglu

Publication year - 2022

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btac231

Subject(s) - computer science , factory (object oriented programming) , linear programming , source code , integer programming , mathematical optimization , order (exchange) , integer (computer science) , code (set theory) , metabolic engineering , distributed computing , algorithm , mathematics , chemistry , programming language , set (abstract data type) , biochemistry , enzyme , finance , economics

A factory in a metabolic network specifies how to produce target molecules from source compounds through biochemical reactions, properly accounting for reaction stoichiometry to conserve or not deplete intermediate metabolites. While finding factories is a fundamental problem in systems biology, available methods do not consider the number of reactions used, nor address negative regulation.

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