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With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially be useful to construct target-oriented chassis organisms. Engineering the complicated metabolic systems of chassis organisms to biosynthesize target molecules from inexpensive biomass is the main goal of cell factory design. The process of data-driven cell factory design could be divided into several parts: (1) target molecule selection; (2) metabolic reaction and pathway design; (3) prediction of novel enzymes based on protein domain and structure transformation of biosynthetic reactions; (4) construction of large-scale DNA for metabolic pathways; and (5) DNA assembly methods and visualization tools. The construction of a one-stop cell factory system could achieve automated design from the molecule level to the chassis level. In this article, we outline data-driven rational biosynthesis design steps and provide an overview of related tools in individual steps.<\/jats:p>","DOI":"10.1093\/bib\/bbz065","type":"journal-article","created":{"date-parts":[[2019,5,10]],"date-time":"2019-05-10T11:15:24Z","timestamp":1557486924000},"page":"1238-1248","source":"Crossref","is-referenced-by-count":9,"title":["Data-driven rational biosynthesis design: from molecules to cell factories"],"prefix":"10.1093","volume":"21","author":[{"given":"Fu","family":"Chen","sequence":"first","affiliation":[{"name":"College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People\u2019s Republic of China"},{"name":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People\u2019s Republic of China"},{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological 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