Open AccessComputing 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 , integer (computer science) , order (exchange) , code (set theory) , metabolic engineering , algorithm , mathematics , chemistry , programming language , set (abstract data type) , finance , economics , biochemistry , enzyme
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.