Title |
Optimizing complex phenotypes through model-guided multiplex genome engineering
|
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Published in |
Genome Biology, May 2017
|
DOI | 10.1186/s13059-017-1217-z |
Pubmed ID | |
Authors |
Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie, George M. Church |
Abstract |
We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.∆A. By introducing targeted combinations of changes in multiplex we generate rich genotypic and phenotypic diversity and characterize clones using whole-genome sequencing and doubling time measurements. Regularized multivariate linear regression accurately quantifies individual allelic effects and overcomes bias from hitchhiking mutations and context-dependence of genome editing efficiency that would confound other strategies. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 6 | 38% |
United Kingdom | 2 | 13% |
Unknown | 8 | 50% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 10 | 63% |
Scientists | 4 | 25% |
Science communicators (journalists, bloggers, editors) | 2 | 13% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 1 | <1% |
Unknown | 108 | 99% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 36 | 33% |
Researcher | 21 | 19% |
Student > Bachelor | 12 | 11% |
Student > Master | 11 | 10% |
Other | 7 | 6% |
Other | 12 | 11% |
Unknown | 10 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 41 | 38% |
Agricultural and Biological Sciences | 28 | 26% |
Chemical Engineering | 5 | 5% |
Engineering | 4 | 4% |
Medicine and Dentistry | 3 | 3% |
Other | 13 | 12% |
Unknown | 15 | 14% |