ArticleNature biotechnology2015
Multiplexed tracking of combinatorial genomic mutations in engineered cell populations.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A self-iterative orthogonal base-editing platform enables multiplex N-to-N diversification and genome-scale functional screening in Escherichia coli.Nucleic acids research · 2026Article
- D-LIM: A neural network for interpretable gene-gene interactions.PLoS computational biology · 2026Article
- Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation.Microbial cell factories · 2020Article
- Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network.Cell systems · 2020Article
- Recent insights into the genotype-phenotype relationship from massively parallel genetic assays.Evolutionary applications · 2019Review
- A versatile platform strain for high-fidelity multiplex genome editing.Nucleic acids research · 2019Article
- Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to the Antimalarial Drug Fosmidomycin in E. coli.ACS synthetic biology · 2018Article
- Synthetic biology advances and applications in the biotechnology industry: a perspective.Journal of industrial microbiology & biotechnology · 2018Article
- Efficient Genome Editing ofFrontiers in microbiology · 2018Article
- Genome-wide analysis of E. coli cell-gene interactions.BMC systems biology · 2017Article
- Optimizing complex phenotypes through model-guided multiplex genome engineering.Genome biology · 2017Article
- Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences.Nucleic acids research · 2017Article
- Article
- A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome.Scientific reports · 2016Article
- High-throughput evaluation of synthetic metabolic pathways.Technology · 2016Article
- The LASER database: Formalizing design rules for metabolic engineering.Metabolic engineering communications · 2015Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiplexed genome engineering approaches can be used to generate targeted genetic diversity in cell populations on laboratory timescales, but methods to track mutations and link them to phenotypes have been lacking. We present an approach for tracking combinatorial engineered libraries (TRACE) through the simultaneous mapping of millions of combinatorially engineered genomes at single-cell resolution. Distal genomic sites are assembled into individual DNA constructs that are compatible with next-generation sequencing strategies. We used TRACE to map growth selection dynamics for Escherichia coli combinatorial libraries created by recursive multiplex recombineering at a depth 10(4)-fold greater than before. TRACE was used to identify genotype-to-phenotype correlations and to map the evolutionary trajectory of two individual combinatorial mutants in E. coli. Combinatorial mutations in the human ES2 ovarian carcinoma cell line were also assessed with TRACE. TRACE completes the combinatorial engineering cycle and enables more sophisticated approaches to genome engineering in both bacteria and eukaryotic cells than are currently possible.
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