Jeffrey E. Barrick

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 10	2023

Other Publications

Article	Year
Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. PloS one\| PubMed ID: 21283682	2011
Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology (Reading, England)\| PubMed ID: 21700661	2011
Nanostructured hybrid transparent conductive films with antibacterial properties. ACS nano\| PubMed ID: 22519712	2012
Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600. Journal of bacteriology\| PubMed ID: 23012285	2012
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23248287	2013
Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. Physical biology\| PubMed ID: 23492852	2013
Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5. ACS synthetic biology\| PubMed ID: 23654268	2013
Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5. Journal of bacteriology\| PubMed ID: 23813729	2013
Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24379390	2014
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature chemical biology\| PubMed ID: 24487692	2014
Engineering reduced evolutionary potential for synthetic biology. Molecular bioSystems\| PubMed ID: 24556867	2014
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 24838886	2014
Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. mBio\| PubMed ID: 25205090	2014
Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC genomics\| PubMed ID: 25432719	2014
Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. PloS one\| PubMed ID: 25502413	2014
Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution. Journal of bacteriology\| PubMed ID: 25512307	2015
The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts. Journal of biological engineering\| PubMed ID: 25525459	2014
Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Frontiers in genetics\| PubMed ID: 25653667	2014
Rapid evolution of silver nanoparticle resistance in Escherichia coli. Frontiers in genetics\| PubMed ID: 25741363	2015
Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli. Genetics\| PubMed ID: 25911659	2015
Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source. Genome announcements\| PubMed ID: 26067973	2015
Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator. ACS synthetic biology\| PubMed ID: 26096262	2015
The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm. PloS one\| PubMed ID: 26114300	2015
Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment. Molecular biology and evolution\| PubMed ID: 26199375	2015
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. PLoS computational biology\| PubMed ID: 26275208	2015
Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. eLife\| PubMed ID: 26465114	2015
Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli. Molecular biology and evolution\| PubMed ID: 27189550	2016
Tempo and mode of genome evolution in a 50,000-generation experiment. Nature\| PubMed ID: 27479321	2016
Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1. Journal of bacteriology\| PubMed ID: 27645387	2016
Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli. ACS synthetic biology\| PubMed ID: 27648665	2017
Specificity of genome evolution in experimental populations of evolved at different temperatures. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28202733	2017
Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC genomics\| PubMed ID: 28412930	2017
The E. coli molecular phenotype under different growth conditions. Scientific reports\| PubMed ID: 28417974	2017
Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx. Applied and environmental microbiology\| PubMed ID: 28667117	2017
Arresting Evolution. Trends in genetics : TIG\| PubMed ID: 29029851	2017
Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids. ACS synthetic biology\| PubMed ID: 29608282	2018
Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides. PLoS genetics\| PubMed ID: 29649242	2018
Bacterial Production of Gellan Gum as a Do-It-Yourself Alternative to Agar. Journal of microbiology & biology education\| PubMed ID: 29983852	2018
Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates. Nucleic acids research\| PubMed ID: 30137492	2018
Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure. ACS synthetic biology\| PubMed ID: 30703321	2019
Bioassay for Determining the Concentrations of Caffeine and Individual Methylxanthines in Complex Samples. Applied and environmental microbiology\| PubMed ID: 31540989	2019
Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria. Nature communications\| PubMed ID: 31863068	2019
Engineered symbionts activate honey bee immunity and limit pathogens. Science (New York, N.Y.)\| PubMed ID: 32001655	2020
Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. Nucleic acids research\| PubMed ID: 32232367	2020
Experimental Evolution of Leads to Loss of Motility, N (σ54) Deletion and Genome Reduction. Frontiers in microbiology\| PubMed ID: 33240235	2020
Engineering a Culturable Strain for Aphid Paratransgenesis. Applied and environmental microbiology\| PubMed ID: 33277267	2021
Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with . Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 33441451	2021
Global Transcriptional Response of to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition. Microorganisms\| PubMed ID: 33578755	2021
Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria. Nature communications\| PubMed ID: 33579917	2021
Rates of gene conversions between Escherichia coli ribosomal operons. G3 (Bethesda, Md.)\| PubMed ID: 33585862	2021
pLannotate: engineered plasmid annotation. Nucleic acids research\| PubMed ID: 34019636	2021
Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 34083444	2021
Engineering insects from the endosymbiont out. Trends in microbiology\| PubMed ID: 34103228	2022
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. Cell systems\| PubMed ID: 34536379	2021
The Genomic Basis of Evolutionary Novelties in a Leafhopper. Molecular biology and evolution\| PubMed ID: 36026509	2022
Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. Artificial life 13 : proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems. International Conference on the Simulation and Synthesis of Living Systems (13th : 2012 : East Lansing, Mich.)\| PubMed ID: 36129423	2013
OSTIR: open source translation initiation rate prediction. Journal of open source software\| PubMed ID: 36177308	2021
Honey bee functional genomics using symbiont-mediated RNAi. Nature protocols\| PubMed ID: 36460809	2023
Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes. Biomacromolecules\| PubMed ID: 36516996	2023
Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals. BMC biology\| PubMed ID: 36575413	2022
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of -colonizing . bioRxiv : the preprint server for biology\| PubMed ID: 36824770	2023
Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences. bioRxiv : the preprint server for biology\| PubMed ID: 37090600	2023
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae. ISME communications\| PubMed ID: 37225918	2023