ArticleNature communications2016
Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Machine-Learning-Assisted Pathway Optimization in Large Combinatorial Design Spaces: A p-Coumaric Acid Case Study.ACS synthetic biology · 2026Article
- Combinatorial Optimization of Protein Systems in Synthetic Cells.ACS synthetic biology · 2026Article
- Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli.Nucleic acids research · 2026Article
- Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles.Frontiers in bioengineering and biotechnology · 2026Article
- Article
- Fine-Tuning Genetic Circuits via Host Context and RBS Modulation.ACS synthetic biology · 2025Article
- Optimizing multicopy chromosomal integration for stable high-performing strains.Nature chemical biology · 2024Article
- Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes inSynthetic and systems biotechnology · 2024Article
- Delaying production with prokaryotic inducible expression systems.Microbial cell factories · 2024Review
- Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast.Nature communications · 2024Article
- Simulated Design-Build-Test-Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Engineering.ACS synthetic biology · 2023Article
- Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript.Nucleic acids research · 2023Article
- Highly efficient biosynthesis of spermidine from L-homoserine and putrescine using an engineered Escherichia coli with NADPH self-sufficient system.Applied microbiology and biotechnology · 2022Article
- Review
- Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site.ACS synthetic biology · 2022Article
- A universal approach to gene expression engineering.Synthetic biology (Oxford, England) · 2022Article
- GenoChemetic Strategy for Derivatization of the Violacein Natural Product Scaffold.ACS chemical biology · 2021Article
- Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast.Microbial biotechnology · 2021Article
- Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Biotechnological Activities and Applications of Bacterial Pigments Violacein and Prodigiosin.Journal of biological engineering · 2021Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.
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