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Items: 1 to 50 of 72

1.

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

Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE.

Nucleic Acids Res. 2018 Aug 22. doi: 10.1093/nar/gky751. [Epub ahead of print]

PMID:
30137492
2.

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

McGuffey JC, Leon D, Dhanji EZ, Mishler DM, Barrick JE.

J Microbiol Biol Educ. 2018 Jun 29;19(2). pii: 19.2.74. doi: 10.1128/jmbe.v19i2.1530. eCollection 2018. No abstract available.

3.

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

Leon D, D'Alton S, Quandt EM, Barrick JE.

PLoS Genet. 2018 Apr 12;14(4):e1007348. doi: 10.1371/journal.pgen.1007348. eCollection 2018 Apr.

4.

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

Leonard SP, Perutka J, Powell JE, Geng P, Richhart DD, Byrom M, Kar S, Davies BW, Ellington AD, Moran NA, Barrick JE.

ACS Synth Biol. 2018 May 18;7(5):1279-1290. doi: 10.1021/acssynbio.7b00399. Epub 2018 Apr 13.

5.

The dynamics of molecular evolution over 60,000 generations.

Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM.

Nature. 2017 Nov 2;551(7678):45-50. doi: 10.1038/nature24287. Epub 2017 Oct 18.

6.

Arresting Evolution.

Bull JJ, Barrick JE.

Trends Genet. 2017 Dec;33(12):910-920. doi: 10.1016/j.tig.2017.09.008. Epub 2017 Oct 10. Review.

7.

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

Suárez GA, Renda BA, Dasgupta A, Barrick JE.

Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e01025-17. doi: 10.1128/AEM.01025-17. Print 2017 Sep 1.

8.

The E. coli molecular phenotype under different growth conditions.

Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO.

Sci Rep. 2017 Apr 18;7:45303. doi: 10.1038/srep45303.

9.

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

Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO.

BMC Genomics. 2017 Apr 17;18(1):301. doi: 10.1186/s12864-017-3676-8.

10.

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

Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE.

Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1904-E1912. doi: 10.1073/pnas.1616132114. Epub 2017 Feb 15.

11.

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

Monk JW, Leonard SP, Brown CW, Hammerling MJ, Mortensen C, Gutierrez AE, Shin NY, Watkins E, Mishler DM, Barrick JE.

ACS Synth Biol. 2017 Jan 20;6(1):45-54. doi: 10.1021/acssynbio.6b00192. Epub 2016 Sep 26.

PMID:
27648665
12.

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

Renda BA, Chan C, Parent KN, Barrick JE.

J Bacteriol. 2016 Nov 4;198(23):3209-3219. Print 2016 Dec 1.

13.

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

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE.

Nature. 2016 Aug 11;536(7615):165-70. Epub 2016 Aug 1.

14.

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

Hammerling MJ, Gollihar J, Mortensen C, Alnahhas RN, Ellington AD, Barrick JE.

Mol Biol Evol. 2016 Aug;33(8):2054-63. doi: 10.1093/molbev/msw094. Epub 2016 May 9.

PMID:
27189550
15.

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

Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE.

Elife. 2015 Oct 14;4. pii: e09696. doi: 10.7554/eLife.09696.

16.

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

Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004400. doi: 10.1371/journal.pcbi.1004400. eCollection 2015 Aug.

17.

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

Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE.

Mol Biol Evol. 2015 Nov;32(11):2897-904. doi: 10.1093/molbev/msv161. Epub 2015 Jul 20.

18.

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

Perry EB, Barrick JE, Bohannan BJ.

PLoS One. 2015 Jun 26;10(6):e0130639. doi: 10.1371/journal.pone.0130639. eCollection 2015.

19.

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

Jack BR, Leonard SP, Mishler DM, Renda BA, Leon D, Suárez GA, Barrick JE.

ACS Synth Biol. 2015 Aug 21;4(8):939-43. doi: 10.1021/acssynbio.5b00068. Epub 2015 Jul 1.

PMID:
26096262
20.

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

Quandt EM, Summers RM, Subramanian MV, Barrick JE.

Genome Announc. 2015 Jun 11;3(3). pii: e00640-15. doi: 10.1128/genomeA.00640-15.

21.

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

Maddamsetti R, Lenski RE, Barrick JE.

Genetics. 2015 Jun;200(2):619-31. doi: 10.1534/genetics.115.176677. Epub 2015 Apr 24.

22.

Rapid evolution of silver nanoparticle resistance in Escherichia coli.

Graves JL Jr, Tajkarimi M, Cunningham Q, Campbell A, Nonga H, Harrison SH, Barrick JE.

Front Genet. 2015 Feb 17;6:42. doi: 10.3389/fgene.2015.00042. eCollection 2015.

23.

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

Deatherage DE, Traverse CC, Wolf LN, Barrick JE.

Front Genet. 2015 Jan 21;5:468. doi: 10.3389/fgene.2014.00468. eCollection 2014.

24.

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

Alnahhas RN, Slater B, Huang Y, Mortensen C, Monk JW, Okasheh Y, Howard MD, Gottel NR, Hammerling MJ, Barrick JE.

J Biol Eng. 2014 Dec 1;8(1):28. doi: 10.1186/1754-1611-8-28. eCollection 2014.

25.

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

Renda BA, Dasgupta A, Leon D, Barrick JE.

J Bacteriol. 2015 Mar;197(5):872-81. doi: 10.1128/JB.02263-14. Epub 2014 Dec 15.

26.

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

Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO.

PLoS One. 2014 Dec 12;9(12):e114608. doi: 10.1371/journal.pone.0114608. eCollection 2014.

27.

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

Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG.

BMC Genomics. 2014 Nov 29;15:1039. doi: 10.1186/1471-2164-15-1039.

28.

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

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D.

MBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14.

29.

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

Deatherage DE, Barrick JE.

Methods Mol Biol. 2014;1151:165-88. doi: 10.1007/978-1-4939-0554-6_12.

30.

Engineering reduced evolutionary potential for synthetic biology.

Renda BA, Hammerling MJ, Barrick JE.

Mol Biosyst. 2014 Jul;10(7):1668-78. doi: 10.1039/c3mb70606k. Epub 2014 Feb 21. Review.

31.

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

Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE.

Nat Chem Biol. 2014 Mar;10(3):178-80. doi: 10.1038/nchembio.1450. Epub 2014 Feb 2.

32.

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

Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2217-22. doi: 10.1073/pnas.1314561111. Epub 2013 Dec 30.

33.

Genome dynamics during experimental evolution.

Barrick JE, Lenski RE.

Nat Rev Genet. 2013 Dec;14(12):827-39. doi: 10.1038/nrg3564. Epub 2013 Oct 29. Review.

34.

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

Summers RM, Seffernick JL, Quandt EM, Yu CL, Barrick JE, Subramanian MV.

J Bacteriol. 2013 Sep;195(17):3933-9.

35.

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

Quandt EM, Hammerling MJ, Summers RM, Otoupal PB, Slater B, Alnahhas RN, Dasgupta A, Bachman JL, Subramanian MV, Barrick JE.

ACS Synth Biol. 2013 Jun 21;2(6):301-7. doi: 10.1021/sb4000146. Epub 2013 Mar 22.

PMID:
23654268
36.

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

Han P, Niestemski LR, Barrick JE, Deem MW.

Phys Biol. 2013 Apr;10(2):025004. doi: 10.1088/1478-3975/10/2/025004. Epub 2013 Mar 15.

37.

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

Wielgoss S, Barrick JE, Tenaillon O, Wiser MJ, Dittmar WJ, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):222-7. doi: 10.1073/pnas.1219574110. Epub 2012 Dec 17.

38.

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

Jerome JP, Klahn BD, Bell JA, Barrick JE, Brown CT, Mansfield LS.

J Bacteriol. 2012 Oct;194(20):5707-8.

39.

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

Blount ZD, Barrick JE, Davidson CJ, Lenski RE.

Nature. 2012 Sep 27;489(7417):513-8. doi: 10.1038/nature11514. Epub 2012 Sep 19.

40.

Nanostructured hybrid transparent conductive films with antibacterial properties.

Kholmanov IN, Stoller MD, Edgeworth J, Lee WH, Li H, Lee J, Barnhart C, Potts JR, Piner R, Akinwande D, Barrick JE, Ruoff RS.

ACS Nano. 2012 Jun 26;6(6):5157-63. doi: 10.1021/nn300852f. Epub 2012 Apr 30.

PMID:
22519712
41.

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

Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE.

Science. 2012 Jan 27;335(6067):428-32. doi: 10.1126/science.1214449.

42.

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

Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

G3 (Bethesda). 2011 Aug 1;1(3):183-186.

43.

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

Nahku R, Peebo K, Valgepea K, Barrick JE, Adamberg K, Vilu R.

Microbiology. 2011 Sep;157(Pt 9):2604-10. doi: 10.1099/mic.0.050658-0. Epub 2011 Jun 23.

44.

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

Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE.

Science. 2011 Mar 18;331(6023):1433-6. doi: 10.1126/science.1198914.

45.

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

Jerome JP, Bell JA, Plovanich-Jones AE, Barrick JE, Brown CT, Mansfield LS.

PLoS One. 2011 Jan 24;6(1):e16399. doi: 10.1371/journal.pone.0016399.

46.

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

Barrick JE, Kauth MR, Strelioff CC, Lenski RE.

Mol Biol Evol. 2010 Jun;27(6):1338-47. doi: 10.1093/molbev/msq024. Epub 2010 Jan 27.

47.

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

Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF.

Nature. 2009 Oct 29;461(7268):1243-7. doi: 10.1038/nature08480. Epub 2009 Oct 18.

PMID:
19838166
48.

Genome-wide mutational diversity in an evolving population of Escherichia coli.

Barrick JE, Lenski RE.

Cold Spring Harb Symp Quant Biol. 2009;74:119-29. doi: 10.1101/sqb.2009.74.018. Epub 2009 Sep 23.

49.

Predicting riboswitch regulation on a genomic scale.

Barrick JE.

Methods Mol Biol. 2009;540:1-13. doi: 10.1007/978-1-59745-558-9_1.

PMID:
19381548
50.

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

Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR.

RNA. 2008 May;14(5):822-8. doi: 10.1261/rna.988608. Epub 2008 Mar 27.

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