List of works - Jeffrey E Barrick

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

scientific article

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

scientific article

A glycine-dependent riboswitch that uses cooperative binding to control gene expression

scientific article

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain

scientific article

A road map for in vivo evolution experiments with blood‐borne parasitic microbes

scientific article published in 2022

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

scientific article

Achieving Specificity in Selected and Wild-Type N Peptide−RNA Complexes: The Importance of Discrimination against Noncognate RNA Targets ⬇️

scientific article published on November 11, 2003

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

scientific article

An mRNA structure that controls gene expression by binding S-adenosylmethionine

scientific article (publication date: September 2003)

Arresting Evolution

scientific article

Bacterial Production of Gellan Gum as a Do-It-Yourself Alternative to Agar.

scientific article published on 29 June 2018

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

scientific article

Balancing robustness and evolvability

scientific article

Bioassay for Determining the Concentrations of Caffeine and Individual Methylxanthines in Complex Samples

scientific article published on 14 November 2019

Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5.

scientific article published on September 2013

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes

scientific article (publication date: 2004)

Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

scientific article

Correction to: The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5.

scientific article published on 22 March 2013

Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

scientific article

Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates

scientific article published on 01 September 2018

Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria

scientific article published on 11 January 2022

Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source

scientific article published on 11 June 2015

Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600.

scientific article

Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1.

scientific article published on 19 September 2016

Engineered symbionts activate honey bee immunity and limit pathogens

scientific article published on 30 January 2020

Engineering a Culturable Serratia symbiotica Strain for Aphid Paratransgenesis

scientific article published on 04 December 2020

Engineering reduced evolutionary potential for synthetic biology

scientific article

Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects

scientific article

Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria

scientific article published in August 2005

Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria

scientific article published on 20 December 2019

Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli

scientific article published on 9 May 2016

Experimental Evolution of Campylobacter jejuni Leads to Loss of Motility, rpoN (σ54) Deletion and Genome Reduction

scientific article published on 06 November 2020

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment.

scientific article

Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.

scientific article

Genome dynamics during experimental evolution

scientific article

Genome evolution and adaptation in a long-term experiment with Escherichia coli

scientific article

Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution

scientific article

Genomic analysis of a key innovation in an experimental Escherichia coli population

scientific article

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

scientific article published on 29 May 2020

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

scientific article

Identification of a large noncoding RNA in extremophilic eubacteria

scientific article

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

scientific article

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

scientific article

Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

scientific article published on 12 April 2018

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

scientific article published on 12 February 2021

Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

scientific article

Large libraries reveal diverse solutions to an RNA recognition problem ⬇️

scientific article published on October 23, 2001

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

scientific article

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

scholarly article published 30 April 2016

Metabolite-binding RNA domains are present in the genes of eukaryotes

scientific article

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

scientific article

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

scientific article (publication date: 2 January 2013)

Nanostructured hybrid transparent conductive films with antibacterial properties

scientific article published on 30 April 2012

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

scientific article

OSTIR: open source translation initiation rate prediction

scientific article published on 22 August 2021

One-step genome engineering in bee gut bacterial symbionts

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system ⬇️

scientific article published on 15 March 2013

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli

scientific article published on 12 December 2014

Predicting riboswitch regulation on a genomic scale

scientific article published in January 2009

Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator.

scientific article published on 22 June 2015

Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli.

scientific article published on 20 September 2016

Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

scientific article published on 30 March 2020

Rapid evolution of silver nanoparticle resistance in Escherichia coli

scientific article

Rates of gene conversions between Escherichia coli ribosomal operons

scientific article published in 2020

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

scientific article

Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx

scientific article published on 30 June 2017

Repeatability and contingency in the evolution of a key innovation in phage lambda

scientific article

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

scientific article (publication date: 30 May 2003)

Second-order selection for evolvability in a large Escherichia coli population

scientific article

Sequence analysis of an artificial family of RNA-binding peptides

scientific article

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

scientific article published on 15 February 2017

Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

scientific article

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture.

scientific article

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

scientific article

Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure

scientific article published on 15 February 2019

Tandem riboswitch architectures exhibit complex gene control functions

scientific article

Tempo and mode of genome evolution in a 50,000-generation experiment

scientific article

The E. coli molecular phenotype under different growth conditions

scientific article published on 18 April 2017

The Genomic Basis of Evolutionary Novelties in a Leafhopper

scientific article published in 2022

The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm

scientific article published on 26 June 2015

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

scientific article

The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts

scientific article

The distributions, mechanisms, and structures of metabolite-binding riboswitches

scientific article

The dynamics of molecular evolution over 60,000 generations.

scientific article

The power of riboswitches.

scientific article published in January 2007

TheE. colimolecular phenotype under different growth conditions

pLannotate: engineered plasmid annotation

scientific article published on 01 July 2021

List of works by Jeffrey E Barrick

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

A glycine-dependent riboswitch that uses cooperative binding to control gene expression

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain

A road map for in vivo evolution experiments with blood‐borne parasitic microbes

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

Achieving Specificity in Selected and Wild-Type N Peptide−RNA Complexes: The Importance of Discrimination against Noncognate RNA Targets ⬇️

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

An mRNA structure that controls gene expression by binding S-adenosylmethionine

Arresting Evolution

Bacterial Production of Gellan Gum as a Do-It-Yourself Alternative to Agar.

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Balancing robustness and evolvability

Bioassay for Determining the Concentrations of Caffeine and Individual Methylxanthines in Complex Samples

Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5.

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes

Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

Correction to: The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of <i>Drosophila</i>-colonizing <i>Orbaceae</i>

Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5.

Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates

Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria

Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source

Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600.

Emergence of a Competence-Reducing Filamentous Phage from the Genome of Acinetobacter baylyi ADP1.

Engineered symbionts activate honey bee immunity and limit pathogens

Engineering a Culturable <i>Serratia symbiotica</i> Strain for Aphid Paratransgenesis

Engineering reduced evolutionary potential for synthetic biology

Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects

Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria

Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria

Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli

Experimental Evolution of Campylobacter jejuni Leads to Loss of Motility, rpoN (σ54) Deletion and Genome Reduction

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment.

Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.

Genome dynamics during experimental evolution

Genome evolution and adaptation in a long-term experiment with Escherichia coli

Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution

Genomic analysis of a key innovation in an experimental Escherichia coli population

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

Identification of a large noncoding RNA in extremophilic eubacteria

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Large libraries reveal diverse solutions to an RNA recognition problem ⬇️

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Metabolite-binding RNA domains are present in the genes of eukaryotes

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

Nanostructured hybrid transparent conductive films with antibacterial properties

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

OSTIR: open source translation initiation rate prediction

One-step genome engineering in bee gut bacterial symbionts

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system ⬇️

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli

Predicting riboswitch regulation on a genomic scale

Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator.

Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli.

Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

Rapid evolution of silver nanoparticle resistance in Escherichia coli

Rates of gene conversions between <i>Escherichia coli</i> ribosomal operons

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx

Repeatability and contingency in the evolution of a key innovation in phage lambda

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

Second-order selection for evolvability in a large Escherichia coli population

Sequence analysis of an artificial family of RNA-binding peptides

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture.

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure

Tandem riboswitch architectures exhibit complex gene control functions

Tempo and mode of genome evolution in a 50,000-generation experiment