(r223) Barrick Lab :: Publications

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<div align="left"> *Barrick Lab researchers* &nbsp;*Equal contributions&nbsp;&nbsp;^Corresponding author(s)&nbsp; _Undergraduate researchers_ </div>
%TABLE{tableborder="0" databg="#FFFFFF" tablerules="all,none" cellborder="1"}%
| *Preprints and In Press* |||
| 94. | Borin, J.M., Avrani, S., *Barrick, J.E.*, Petrie, K.L., Meyer, J.R. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. [[https://doi.org/10.1101/2020.11.02.365361][bioRxiv]] ||
| 93. | *^Perreau, J.*, Patel, D.J., Anderson, H., Maeda, G.P, *Elston, K.M.*, *Barrick, J.E.*, Moran, N.A. Vertical transmission at the pathogen-symbiont interface: _Serratia symbiotica_ and aphids. [[https://doi.org/10.1101/2020.09.01.279018][bioRxiv]] ||
| 92. | *Deatherage, D.E.*, *^Barrick, J.E.* Profiling the initial burst of beneficial genetic diversity to anticipate evolution of a cell population. [[https://doi.org/10.1101/2020.07.10.196832][bioRxiv]] ||
| *2021* |||
| 91. | *McGuffie, M.C.*, *^Barrick, J.E.* (2021) pLannotate: engineered plasmid annotation. Epub May 21;gkab374. [[https://doi.org/10.1093/nar/gkab374][DOI: 10.1093/nar/gkab374]] [[http://www.ncbi.nlm.nih.gov/pubmed/34019636][PMID: 34019636]] %BR%<li> Webserver: [[http://plannotate.barricklab.org][http://plannotate.barricklab.org]]</li><li> GitHub: [[https://github.com/barricklab/pLannotate][https://github.com/barricklab/pLannotate]]</li> <div align="center"><img height="200" alt="" src="%ATTACHURL%/McGuffie_2021_NAR.png" /></div>   ||
| 90. | Consuegra, J., Gaffé, J., Lenski, R. E., Hindré, T., *Barrick, J. E.*, Tenaillon, O., Schneider, D. (2021) Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria. _Nat. Commun._ *12*:980. [[https://doi.org/10.1038/s41467-021-21210-7][DOI: 10.1038/s41467-021-21210-7]] %BR%<li> _Nature Ecology & Evolution_ Behind the Paper Post: [[https://natureecoevocommunity.nature.com/posts/insertion-sequence-elements-can-promote-bacterial-adaptation-in-the-short-run-but-constrain-it-over-longer-time-scales?utm_source=user_mailer&utm_medium=email&utm_campaign=notify_contributor_about_creating_a_post][Insertion Sequence elements can promote bacterial adaptation in the short run but constrain it over longer time-scales]]</li> |
| 89. | &ast;Bazurto, J.V., &ast;Riazi, S., *D’Alton, S.*, *Deatherage, D.E.*, Bruger, E.L., *Barrick, J.E.*, ^Marx, C.J. (2021) Global transcriptional response of _Methylorubrum extorquens_ to formaldehyde stress expands the role of EfgA and is distinct from antibiotic translational inhibition. _Microorganisms_ Epub Feb 10 [[https://doi.org/10.3390/microorganisms9020347][DOI: 10.3390/microorganisms9020347]] ||
| 88. | ^Card, K.J., Thomas, M.D., Graves, J.L., *Barrick, J.E.*, Lenski, R.E. (2021) Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with _Escherichia coli_. _Proc. Natl. Acad. Sci. U.S.A._ *118*: e2016886118. [[https://doi.org/10.1073/pnas.2016886118][DOI: 10.1073/pnas.2016886118]] [[http://www.ncbi.nlm.nih.gov/pubmed/33441451][PMID: 33441451]] ||
| 87. | *&ast;Gifford, I.*, *&ast;Dasgupta, A.*, *^Barrick, J.E.* (2021) Rates of gene conversions between _Escherichia coli_ ribosomal operons. _G3_ *11*:jkaa002. [[https://doi.org/10.1093/g3journal/jkaa002][DOI: 10.1093/g3journal/jkaa002]] [[http://www.ncbi.nlm.nih.gov/pubmed/33585862][PMID: 33585862]]  ||
| 86. | *Elston, K.M.*, *Perreau, J.*, Maeda, G.P., Moran, N.A., *^Barrick, J.E.* (2021) Engineering a culturable _Serratia symbiotica_ strain for aphid paratransgenesis. _Appl. Env. Microbiol._ *87*:e02245-20. [[https://doi.org/10.1128/AEM.02245-20][DOI: 10.1128/AEM.02245-20]] [[http://www.ncbi.nlm.nih.gov/pubmed/33277267][PMID: 33277267]] %BR% <li>[[https://aem.asm.org/content/87/4/e02994-20][ AEM Spotlight Article]]</li> ||
| *2020* |||
| 85. | Sher, A.A., Jerome, J.P., Bell, J.A., Yu, J., Kim, H.Y., *Barrick, J.E.*, Mansfield, L.S. (2020) Experimental evolution of _Campylobacter jejuni_ leads to loss of motility, rpoN (&sigma;54) deletion and genome reduction. _Front. Microbiol._ *11*:579989 [[https://doi.org/10.3389/fmicb.2020.579989][DOI: 10.3389/fmicb.2020.579989]] ||
| 84. | *^Barrick, J.E.* (2020) Limits to predicting evolution: Insights from a long-term experiment with _Escherichia coli_. In: W. Banzhaf, B.H.C. Cheng, K. Deb, K.E. Holekamp, R.E. Lenski, C. Ofria, R.T. Pennock, W.F. Punch, D.J. Whittaker (eds.). _Evolution in Action: Past, Present and Future: A Festschrift in Honor of Erik D. Goodman._ pp 63-76. Springer Series on Genetic and Evolutionary Computation. Cham, Switzerland: Springer. [[https://link.springer.com/chapter/10.1007/978-3-030-39831-6_7][Full Text]] [[https://doi.org/10.1007/978-3-030-39831-6_7][DOI: 10.1007/978-3-030-39831-6_7]] ||
| 83. | *^Barrick, J.E.*, *Deatherage D.E.*, ^Lenski, R.E. (2020) A test of the repeatability of measurements of relative fitness in the long-term evolution experiment with _Escherichia coli_. In: W. Banzhaf, B.H.C. Cheng, K. Deb, K.E. Holekamp, R.E. Lenski, C. Ofria, R.T. Pennock, W.F. Punch, D.J. Whittaker (eds.). _Evolution in Action: Past, Present and Future: A Festschrift in Honor of Erik D. Goodman._ pp 77-89. Springer Series on Genetic and Evolutionary Computation. Cham, Switzerland: Springer. [[https://link.springer.com/chapter/10.1007/978-3-030-39831-6_8][Full Text]] [[https://doi.org/10.1007/978-3-030-39831-6_8][DOI: 10.1007/978-3-030-39831-6_8]] <div align="center"><img height="280" alt="" src="%ATTACHURL%/Barrick_2020_Festshrift.png" /></div> ||
| 82. | ^*Blount, Z.D., ^*Maddamsetti, R., &ast;Grant, N.A., Ahmed, S.T., Jagdish, T., _Sommerfeld, B.A._, _Tillman, A._, _Moore, J.P._, Slonczewski, J.L., *Barrick, J.E.*, Lenski, R.E. (2020) Genomic and phenotypic evolution of _Escherichia coli_ in a novel citrate-only resource environment. _eLife_ *9*:e55414. [[https://elifesciences.org/articles/55414][Full Text]] [[http://www.ncbi.nlm.nih.gov/pubmed/32469311][PMID: 32469311]] ||
| 81. | *Suárez, G.A.*, __Dugan, K.R.__, *Renda, B.A.*, *Leonard, S.P.*, __Gangavarapu, L.S.__, *^Barrick, J.E.* (2020) Rapid and assured genetic engineering methods applied to <i>Acinetobacter baylyi</i> ADP1 genome streamlining. _Nucleic Acids Res._ *48*:4585–4600. [[https://doi.org/10.1093/nar/gkaa204][Full Text]] [[http://www.ncbi.nlm.nih.gov/pubmed/32232367][PMID: 32232367]] ||
| 80. | *Leonard, S.P.*, Powell, J.E., Perutka, J., *Geng, P.*, _Heckmann, L.C._, _Horak, R.D._, Davies, B.W., Ellington, A.D., *^Barrick, J.E.*, and ^Moran, N.A. (2020) Engineered symbionts activate honey bee immunity and limit pathogens. _Science_ *367*:573–576. [[https://doi.org/10.1126/science.aax9039][DOI]], [[http://www.ncbi.nlm.nih.gov/pubmed/32001655][PMID: 32001655]] %BR% <li> _UT News_: [[https://news.utexas.edu/2020/01/30/bacteria-engineered-to-protect-bees-from-pests-and-pathogens/][Bacteria Engineered to Protect Bees from Pests and Pathogens]]</li><li> _NIH Research Matters_: [[https://www.nih.gov/news-events/nih-research-matters/engineered-bacteria-protect-honey-bee-health][Engineered bacteria protect honey bee health]]</li><div align="center"><img height="200" alt="" src="%ATTACHURL%/Leonard_2020_Science_Cover.gif" /> <img height="200" alt="" src="%ATTACHURL%/Leonard_2020_Science.png" /></div> ||
| *2019* |||
| 79. | *Zhang, X.*, *Deatherage, D.E.*, Zheng, H., __Georgoulis, S.J.__, *^Barrick, J.E.* (2019) Evolution of satellite plasmids can stabilize the maintenance of newly acquired accessory genes in bacteria. _Nat. Comm._  *10*:5809. [[https://www.nature.com/articles/s41467-019-13709-x][Full Text]], [[http://www.ncbi.nlm.nih.gov/pubmed/31863068][PMID: 31863068]]%BR%<li> _Nature Ecology & Evolution_ Behind the Paper Post: [[https://natureecoevocommunity.nature.com/channels/521-behind-the-paper/posts/58201-satellite-plasmids-evolutionary-stability-experiments-come-full-orbit][Satellite plasmids: evolutionary stability experiments come full orbit]]</li>%BR%<div align="center"><img width="400" alt="" src="%ATTACHURL%/Zhang_2019_Nat_Comm.png" /></div>  ||
| 78. | __Gutierrez, A.E.__, __Shah, P.__, __Rex, A.E.__, __Nguyen, T.C.__, __Kenkare, S.P.__, *^Barrick, J.E.*, *^Mishler, D.M.* (2019) Bioassay for determining the concentrations of caffeine and individual methylxanthines in complex samples. _Appl. Env. Microbiol._ *85*:e01965-19. [[http://www.ncbi.nlm.nih.gov/pubmed/31540989][PMID: 31540989]]%BR%<div align="center"><img width="400" height="259" alt="" src="%ATTACHURL%/Gutierrez_2019_Appl_Env_Microbiol.png" /></div> ||
| 77. | *Geng, P.*, *Leonard, S.P.*, *Mishler, D.M.*, *^Barrick, J.E.* (2019) Synthetic genome defenses against selfish DNA elements stabilize engineered bacteria against evolutionary failure. _ACS Synth. Biol._ *8*:521-531. [[https://pubs.acs.org/doi/10.1021/acssynbio.8b00426][Full Text]], [[https://doi.org/10.1101/419283][Preprint]], [[http://www.ncbi.nlm.nih.gov/pubmed/30703321][PMID: 30703321]]%BR%<div align="center"><img width="400" height="200" alt="" src="%ATTACHURL%/Geng_2018_ACS_Synth_Biol.png" /></div> ||
| *2018* |||
| 76. | *Deatherage, D.E.*, *Leon, D.*, *Rodriguez, Á.E.*, __Omar, S.__, *^Barrick, J.E.* (2018) Directed evolution of _Escherichia coli_ with lower-than-natural plasmid mutation rates. _Nucleic Acids Res._ *46*:9236-9250. [[https://doi.org/10.1093/nar/gky751][Full Text]], [[http://www.ncbi.nlm.nih.gov/pubmed/30137492][PMID: 30137492]] <div align="center"><img width="400" alt="" src="%ATTACHURL%/Deatherage_2018_Nucleic_Acids_Res.png" /></div> ||
| 75. | __*McGuffey, J.C.__, **Leon, D.*, __Dhanji, E.Z.__, *Mishler, D.M.*, *^Barrick, J.E.* (2018) Bacterial production of gellan gum as a do-it-yourself alternative to agar. _J. Microbiol. Biol. Educ._ *19*:182-184. [[http://asmscience.org/deliver/fulltext/jmbe/19/2/jmbe-19-74.pdf][Full Text]], [[http://www.ncbi.nlm.nih.gov/pubmed/29983852][PMID: 29983852]]%BR%<div align="center"><img height="150" alt="" src="%ATTACHURL%/McGuffey_2018_JMBE.png" /></div>   ||
| 74. | *Leonard, S.P.*, Perutka, J., Powell, J.E., *Geng, P.*, _Richhart, D._, Byrom, M., Kar, S., Davies, B.W., Ellington, A.D., ^Moran, N.A., *^Barrick, J.E.* (2018) Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. _ACS Synth. Biol._ *7*:1279-1290. [[http://www.ncbi.nlm.nih.gov/pubmed/29608282][PMID: 29608282]]<div align="center"><img width="400" alt="" src="%ATTACHURL%/Leonard_2018_ACS_Synth_Biol.gif" /></div> ||
| 73. | *Leon, D.*, *D’Alton, S.*, Quandt, E.M., *^Barrick, J.E.* (2018) Innovation in an _E. coli_ evolution experiment is contingent on maintaining adaptive potential until competition subsides. _PLoS Genet._ *14*:e1007348. [[http://www.ncbi.nlm.nih.gov/pubmed/29649242][PMID: 29649242]]%BR%<div align="center"><img width="500" height="200" alt="" src="%ATTACHURL%/Leon_2018.png" /></div>  ||
| *2017* |||
| 72. | Good, B.H.*, McDonald, M.J.*, *Barrick, J.E.*, Lenski R.E., Desai, M.M. (2017) The dynamics of molecular evolution over 60,000 generations. _Nature_ *551*:45-50. [[http://www.ncbi.nlm.nih.gov/pubmed/29045390][PMID: 29045390]]%BR%<div align="center"><img width="400" height="250" alt="" src="%ATTACHURL%/Good_Nature_2017.png" /></div> ||
| 71. | Bull, J.J.*, *Barrick, J.E.^** (2017) Arresting evolution. _Trends Genet._ *33*:910-920. [[http://www.ncbi.nlm.nih.gov/pubmed/29029851][PMID: 29029851]]%BR%<div align="center"><img width="400" height="250" alt="" src="%ATTACHURL%/Bull_TrendsInGen_2017.png" /></div>  ||
| 70. | *^Barrick, J.E.* (2017) In future (cell) generations. “Voices” piece in What is the role of circuit design in the advancement of synthetic biology? Part 2. _Cell Syst._ *24*:467-477. [[http://www.ncbi.nlm.nih.gov/pubmed/28544877][PMID: 28544877]] ||
| 69. | *Suarez, G.A.*, *Renda, B.A.*, *Dasgupta, A.*, *Barrick, J.E.^* (2017) Reduced mutation rate and increased transformability of transposon-free _Acinetobacter baylyi_ ADP1-ISx. _Appl. Env. Microbiol._ *83*: e01025-17. [[http://www.ncbi.nlm.nih.gov/pubmed/28667117][PMID: 28667117]]%BR%<div align="center"><img width="300" height="250" alt="" src="%ATTACHURL%/Suarez_EnvMicrobiol_2017.png" /></div> ||
| 68. | *Brown, C.W.*, Sridhara, V., Boutz, D.R., Person, M.D., Marcotte, E.M. *Barrick, J.E.*, Wilke, C.O.^ (2017) Large-scale analysis of post-translational modifications in _E. coli_ under glucose-limiting conditions. _BMC Genomics_ *18*:301. [[http://www.ncbi.nlm.nih.gov/pubmed/28412930][PMID: 28412930]] ||
| 67. | Caglar, M.U., Houser, J.R., *Barnhart, C.S.*, Boutz, D.R., Carroll, S.M., __Dasgupta, A.__, _Lenoir, W.F._, Smith, B.L., Sridhara, V., Sydykova, D.K., Vander Wood, D., Marx, C.J., Marcotte, E.M.^, *Barrick, J.E.^*, Wilke, C.O.^ (2017) The _E. coli_ molecular phenotype under different growth conditions. _Sci. Rep._ *7*:45303. [[http://www.ncbi.nlm.nih.gov/pubmed/28417974][PMID: 28417974]]%BR%<div align="center"><img width="400" height="200" alt="" src="%ATTACHURL%/Caglar_SciRep_2017.png" /></div> ||
| 66. | *Deatherage, D.E.*, __Kepner, J.L.__, Bennett, A.F., Lenski, R.E.^, *Barrick, J.E.^* (2017) Specificity of genome evolution in experimental populations of _Escherichia coli_ evolved at different temperatures. _Proc. Natl. Acad. Sci. U.S.A._ *114*:E1904-E1912. [[http://www.ncbi.nlm.nih.gov/pubmed/28202733][PMID: 28202733]]%BR%<div align="center"><img width="300" height="200" alt="" src="%ATTACHURL%/Deatherage_PNAS_2017.png" /></div> <li>News: [[https://cns.utexas.edu/news/genetic-signatures-reveal-environment-where-bacteria-evolved#.WKTc_HQu-eQ.twitter][Genetic signatures reveal environment where bacteria evolved]]</li> |||
| 65. | __Monk, J.W.__, *Leonard, S.P.*, *Brown, C.W.*, *Hammerling, M.J.*, __Mortensen, C.__, __Gutierrez, A.E.__, __Shin, N.Y.__, __Watkins, E.__, *Mishler, D.M.^*, *Barrick, J.E.^* (2017) Rapid and inexpensive evaluation of nonstandard amino acid incorporation in _Escherichia coli_. _ACS Synth. Biol._ *6*:45-54. [[http://www.ncbi.nlm.nih.gov/pubmed/27648665][PMID: 27648665]]%BR%<div align="center"><img width="300" height="150" alt="" src="%ATTACHURL%/Monk_ACSSynthBio_2017.png" /></div> ||
| *2016* |||
| 64. | *Renda, B.A.*, __Chan, C.__, Parent, K.N., *Barrick, J.E.^* (2016) Emergence of a competence reducing filamentous phage from the genome of _Acinetobacter baylyi_ ADP1. _J. Bacteriol._ *198*:3209-3219. [[http://www.ncbi.nlm.nih.gov/pubmed/27645387][PMID: 27645387]] ||
| 63. | Tenaillon, O.*, *Barrick, J.E.**, Ribeck, N., *Deatherage, D.E.*, Blanchard, J.L, __Dasgupta, A.__, *Wu, G.C.*, Wielgoss, S., Cruveiller, S., Medigue, C., Schneider, D., Lenski, R.E.^ (2016) Tempo and mode of genome evolution in a 50,000-generation experiment. _Nature_ *536*:165-170. [[http://www.ncbi.nlm.nih.gov/pubmed/27479321][PMID: 27479321]]%BR%<div align="center"><img width="400" height="230" alt="" src="%ATTACHURL%/Tenaillon_Nature_2016.png" /></div><li>News: [[https://cns.utexas.edu/news/bacteria-show-capacity-for-rapid-beneficial-mutations][Bacteria show capacity for rapid, beneficial mutations]]</li><li>News: [[http://msutoday.msu.edu/news/2016/still-changing-after-all-these-years/][Still changing after all these years]]</li> | |
| 62. | *Hammerling, M.J.*, Gollihar, J., __Mortensen, C.__, __Alnahhas, R.N.__, Ellington, A.D., *Barrick, J.E.* (2016) Expanded genetic codes create new mutational routes to rifampicin resistance in _Escherichia coli_. _Mol. Biol. Evol._ *33*:2054-2063. [[http://www.ncbi.nlm.nih.gov/pubmed/27189550][PMID: 27189550]] ||
| *2015* |||
| 61. | Quandt, E.M., Gollihar, J., Blount, Z.D., Ellington, A.D., Georgiou, G., *Barrick, J.E.* (2015) Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. _eLife_ *4*:e09696. [[http://www.ncbi.nlm.nih.gov/pubmed/26465114][PMID: 26465114]]<li>Commentary: [[https://elifesciences.org/articles/12386][Metabolism: Evolution retraces its steps to advance]]</li>||
| 60. | Houser, J.R., *Barnhart, C.*, Boutz, D.R., Carroll, S.M., Dasgupta, A., Michener, J.K., Needham, B.D., Papoulas, O., Sridhara, V., Sydykova, D.K., Marx, C.J., Trent, S.M., *Barrick, J.E.^*, Marcotte, E.M.^, Wilke, C.O.^ (2015) Controlled measurement and comparative analysis of cellular components in _E. coli_ reveals broad regulatory changes in response to glucose starvation. _PLoS Comput. Biol._ *11*:e1004400. [[http://www.ncbi.nlm.nih.gov/pubmed/26275208][PMID:26275208]] ||
| 59. | Maddamsetti, R., Hatcher, P.J., Cruveiller, S., Médigue, C., *Barrick, J.E.*, Lenski, R.E. (2015) Synonymous genetic variation in natural isolates of _Escherichia coli_ does not predict where synonymous substitutions occur in a long-term experiment. _Mol. Biol. Evol._ *32*:2897-2904. [[http://www.ncbi.nlm.nih.gov/pubmed/26199375][PMID:26199375]] ||
| 58. | *Jack, B.R.*, *Leonard, S.P.*, *Mishler, D.M.*, *Renda, B.A.*, *Leon, D.*, *Suárez, G.A.*, *Barrick, J.E.* (2015) Predicting the genetic stability of engineered DNA sequences with the EFM Calculator. _ACS Synth. Biol._ *4*:939-943. [[http://www.ncbi.nlm.nih.gov/pubmed/26096262][PMID:26096262]] ||
| 57. | Perry, E.B.^, *Barrick, J.E.*, Bohannan, B.J.M. (2015) The molecular and genetic basis of repeatable coevolution between _Escherichia coli_ and bacteriophage T3 in a laboratory microcosm. _PLoS ONE_ *10*:e0130639. [[http://www.ncbi.nlm.nih.gov/pubmed/26114300][PMID:26114300]]. ||
| 56. | Quandt, E.M., Summers, R.M., Subramanian, M.V., *Barrick, J.E.^* (2015) Draft genome sequence of the bacterium _Pseudomonas putida_ CBB5, which can utilize caffeine as a sole carbon and nitrogen source. _Genome Announc._ *3*:e00640-15. [[http://www.ncbi.nlm.nih.gov/pubmed/26067973][PMID:26067973]] ||
| 55. | Maddamsetti, R., Lenski, R.E., *Barrick, J.E.* (2015) Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with _Escherichia coli_. _Genetics_ *200*:619-631. [[http://www.ncbi.nlm.nih.gov/pubmed/25911659][PMID:25911659]] <li>Award: [[http://genestogenomes.org/centennial-awards-honor-outstanding-genetics-articles/][GSA 1st Centennial Award for Population and Evolutionary Genetics]]</li> ||
| 54. | Graves, J.L.^, Tajkarimi, M., Cunningham, Q., Campbell, A., Nonga, H., Harrison, S.H., *Barrick, J.E.* (2015) Rapid evolution of silver nanoparticle resistance in _Escherichia coli_. _Front. Genet._ *6*:42. [[http://www.ncbi.nlm.nih.gov/pubmed/25741363][PMID:25741363]] ||
| 53. | *Renda, B.A.*, __Dasgupta, A.__, *Leon, D.*, *Barrick, J.E.* (2015) Genome instability mediates the loss of key traits by _Acinetobacter baylyi_ ADP1 during laboratory evolution. _J. Bacteriol._ *197*:872-881. [[http://www.ncbi.nlm.nih.gov/pubmed/25512307][PMID:25512307]] ||
| 52. | *Deatherage, D.E.*, *Traverse, C.C.*, *Wolf, L.N.*, *Barrick, J.E.* (2015) Detecting rare structural variation in evolving microbial populations from new sequence junctions using _breseq_. _Front. Genet._ *5*:468. [[http://www.ncbi.nlm.nih.gov/pubmed/25653667][PMID:25653667]] ||
| *2014* |||
| 51. | Sridhara, V., Meyer, A.G., Rai, P., *Barrick, J.E.*, Ravikumar, P., Ségre, D., Wilke, C.O. (2014) Predicting growth conditions from internal metabolic fluxes in an _in-silico_ model of _E. coli_. _PLoS ONE_ *9*:e114608. [[http://www.ncbi.nlm.nih.gov/pubmed/25502413][PMID:25502413]] ||
| 50. | __Alnahhas, R.N.*__, __Slater, B.*__, __Huang, Y.__, __Mortensen, C.__, __Monk, J.W.__, __Okasheh, Y.__, __Howard, M.D.__, *Gottel, N.R.*, *Hammerling, M.J.^*, *Barrick, J.E.^* (2014) The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts. _J. Biol. Eng._ *8*:28. [[http://www.ncbi.nlm.nih.gov/pubmed/25525459][PMID:25525459]] ||
| 49. | *Barrick, J.E.*, *Colburn, G.*, *Deatherage D.E.*, *Traverse, C.C.*, *Strand, M.D.*, __Borges, J.J.__, Knoester, D.B., *Reba, A.*, *Meyer, A.G.* (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using _breseq_. _BMC Genomics_ *15*:1039. [[http://www.ncbi.nlm.nih.gov/pubmed/25432719][PMID:25432719]]  ||
| 48. | Raeside, C., Gaffé, J., *Deatherage, D.E.*, Tenaillon, O., Briska, A.M., Ptashkin, R.N., Cruveiller, S., Médigue, C., Lenski, R.E., *Barrick, J.E.*, Schneider, D. (2014) Large chromosomal rearrangements during a long-term evolution experiment with _Escherichia coli_. _mBio_ *5*:e01377-14. [[http://www.ncbi.nlm.nih.gov/pubmed/25205090][PubMed:25205090]] ||
| 47. | *Deatherage, D.E.*, *Barrick, J.E.* (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using _breseq_. _Methods Mol. Biol._ *1151*:165-188. [[http://www.ncbi.nlm.nih.gov/pubmed/24838886][PubMed:24838886]] ||
| 46. | *Renda, B.A.**, *Hammerling, M.J.**, *Barrick, J.E.* (2014) Engineering reduced evolutionary potential for synthetic biology. _Mol. Biosyst._ *10*:1668-1678. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24556867][PubMed:24556867]] ||
| 45. | *Hammerling, M.J.*, Ellefson, J.W., Boutz, D.R., Marcotte, E.M., Ellington, A.D., *Barrick, J.E.* (2014) Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. _Nat. Chem. Biol._ *10*:178-180. [[http://www.ncbi.nlm.nih.gov/pubmed/24487692][PubMed:24487692]] ||
| 44. | *Quandt, E.M.*, *Deatherage, D.E.*, Ellington, A.D., Georgiou, G., *Barrick, J.E.* (2014) Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in _Escherichia coli_. _Proc. Natl. Acad. Sci. U.S.A._ *111*:2217-2222. [[http://www.ncbi.nlm.nih.gov/pubmed/24379390][PubMed:24379390]] <li>Commentary: [[http://www.pnas.org/content/111/6/2056][Refining a key metabolic innovation in Escherichia coli]]</li> ||
| *2013* |||
| 43. | *Hammerling, M.J.*, *Gottel, N.R.*, __Alnahhas, R.N.__, __Slater, B.__, __Huang, Y.__, __Okasheh, Y.__, __Howard, M.__, __Mortensen, C.__, __Monk, J.__, __Detelich, M.__, __Lannan, R.S.__, __Pitaktong, A.__, __Weaver, E.__, __Das, S.__, *Barrick, J.E.* (2013) BBF RFC95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques. [[http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_95:_Open_Sequence_Initiative:_a_part_submission_standard_to_complement_modern_DNA_assembly_techniques][«BioBricks Foundation»]] [[http://hdl.handle.net/1721.1/81334][«DSpace»]] ||
| 42. | *Barrick, J.E.*, Lenski, R.E. (2013) Genome dynamics during experimental evolution. _Nat. Rev. Genet._ *14*:827-834. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24166031][«PubMed»]] ||
| 41. | Summers, R.M., Seffernick, J.L., *Quandt, E.M.*, Yu, C.L., *Barrick, J.E.*, Subramanian, M.V. (2013) Caffeine Junkie: an unprecedented GST-dependent oxygenase required for caffeine degradation by _P. putida_ CBB5. _J. Bacteriol._ *195*:3933-3939. [[http://www.ncbi.nlm.nih.gov/pubmed/23813729][«PubMed»]] ||
| 40. | *Quandt, E.M.*, *Hammerling, M.J.*, Summers, R.M., __Otoupal, P.B.__, __Slater, B.__, __Alnahhas, R.N.__, __Dasgupta, A.__, __Bachman, J.L.__, Subramanian, M.V., *Barrick, J.E.* (2013) Decaffeination and measurement of caffeine content by addicted _Escherichia coli_ with a refactored <em>N</em>-demethylation operon from _Pseudomonas putida_ CBB5. _ACS Synth. Biol._ *2*:301-307. [[http://www.ncbi.nlm.nih.gov/pubmed/23654268][«PubMed»]] ||
| 39. | Han, P., Niestemski, L.R., *Barrick, J.E.*, Deem, M.W. (2013) Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. _Phys. Biol._ *10*:025004. [[http://www.ncbi.nlm.nih.gov/pubmed/23492852][«PubMed»]] ||
| 38. | Wielgoss, S.*, *Barrick, J.E.**,Tenaillon, O.*, Wiser, M.J., _Dittmar, W.J._, Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R.E., Schneider, D. (2013) Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. _Proc. Natl. Acad. Sci. U.S.A._ *110*:222-227.  [[http://www.ncbi.nlm.nih.gov/pubmed/23248287][«PubMed»]] ||
| *2012* |||
| 37. | Blount, Z.D., *Barrick, J.E.*, Davidson, C.J., Lenski, R.E. (2012) Genomic analysis of a key innovation in an experimental _E. coli_ population. _Nature_ *489*:513-518. [[http://www.ncbi.nlm.nih.gov/pubmed/22992527][«PubMed»]] ||
| 36. | Jerome, J.P., Klahn, B., Bell, J.A., *Barrick, J.E.*, Brown, C.T., Mansfield, L.S. (2012) Draft genome sequences of two _Campylobacter jejuni_ clinical isolates, NW and D2600. _J.Bact._ *194*:5707-5708. ||
| 35. | *Reba, A.*, *Meyer, A.G.*, *Barrick, J.E.* (2012) Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. In: C. Adami et al. (eds.). _Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems._ pp 473-480. Cambridge, MA: MIT Press. *Awarded Best Synthetic Biology Paper.* [[http://dx.doi.org/10.7551/978-0-262-31050-5-ch062][«Full Text»]] ||
| 34. | Kholmanov, I.N., Stoller, M.D., Edgeworth, J., Lee, W.H., Li, H., Lee, J., *Barnhart, C.*, Potts, J.R., Piner, R., Akinwande, D., *Barrick, J.E.*, Ruoff, R.S. (2012) Nanostructured hybrid transparent conductive films with antibacterial properties. _ACS Nano_ *6*:5157-5163. [[http://www.ncbi.nlm.nih.gov/pubmed/22519712][«PubMed»]] ||
| 33. | *Wolf, L.N.*, *Barrick, J.E.* (2012) Tracking winners and losers in _E. coli_ evolution experiments. _Microbe Magazine_ *2* (3):124-128. [[http://www.microbemagazine.org/index.php?option=com_content&view=article&id=4544:tracking-winners-and-losers-in-e-coli-evolution-experiments&catid=939:07-2011-features&Itemid=1210][«Article»]] ||
| 32. | Meyer, J.R., Dobias, D.T., Weitz, J.S., *Barrick, J.E.*, Quick, R.T., Lenski, R.E. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. _Science_ *335*:428-432. [[http://www.ncbi.nlm.nih.gov/pubmed/22282803][«PubMed»]] ||
| *2011* |||
| 31. | Nahku, R., Peebo, K., Valgepea, K., *Barrick, J.E.*, Adamberg, K., Vilu, R. (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_ *157*:2604-2610. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=21700661][«PubMed»]]  ||
| 30. | Wielgoss, S., *Barrick, J.E.*, Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R.E., Schneider, D. (2011) Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with _Escherichia coli_. _G3: Genes, Genomes, Genetics_ *1*:183-186. [[http://www.ncbi.nlm.nih.gov/pubmed/22207905][«PubMed»]] <li>[[SupplementLongTermMutationRates][Supplementary data and scripts]]</li> ||
| 29. | Woods, R.J.*, *Barrick, J.E.*^*, Cooper, T.F., Shrestha, U., Kauth, M.R., Lenski, R.E.^ (2011) Second-order selection for evolvability in a large _Escherichia coli_ population. _Science_ *331*:1433-1436. [[http://www.ncbi.nlm.nih.gov/pubmed/21415350][«PubMed»]] [[http://www.santafe.edu/news/item/science-lenski-slow-evolution-is-better/][«Press Links»]] [[http://www.sciencemag.org/content/331/6023/1455.2.full][«Science Podcast»]] [[http://f1000.com/9422956][«Faculty of 1000»]] [[ErratumScience2011][«Erratum»]] ||
| 28. | Jerome, J.P., Bell, J.A., Plovanich-Jones, A.E., *Barrick, J.E.*, Brown, C.T., Mansfield, L.S. (2011) Standing genetic variation in contingency loci drives the rapid adaptation of _Campylobacter jejuni_ to a novel host. _PLoS ONE_ *6*:e16399. [[http://www.ncbi.nlm.nih.gov/pubmed/21283682][«PubMed»]] [[http://zoonotica.wordpress.com/2011/07/06/254campylobacter-adaptation/][«Blog Article»]] ||
| *2010 and earlier* |||
| 27. | *Barrick, J.E.*, Kauth, M.R., Strelioff, C.C., and Lenski, R.E. (2010) _Escherichia coli_ _rpoB_ mutants have increased evolvability in proportion to their fitness defects. _Mol. Biol. Evol._ *27*:1338-1347. [[http://www.ncbi.nlm.nih.gov/pubmed/20106907][«PubMed»]] ||
| 26. | *Barrick, J.E.**, Yu, D.S.*, Yoon, S.H., Jeong, H, Oh, T.K., Schneider, D., Lenski, R.E., and Kim, J.F. (2009) Genome evolution and adaptation in a long-term experiment with _Escherichia coli_. _Nature._ *461*:1243-1247. [[http://www.ncbi.nlm.nih.gov/pubmed/19838166][«PubMed»]][[http://f1000biology.com/article/id/1166598][«Faculty of 1000»]] <li>News: [[https://www.sciencedaily.com/releases/2009/10/091018141716.htm][Time In A Bottle: Scientists Watch Evolution Unfold]]</li> ||
| 25. | *Barrick, J.E.* and Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of _Escherichia coli_. _Cold Spring Harbor Symp. Quant. Biol._ *74*:119-129. [[http://www.ncbi.nlm.nih.gov/pubmed/19776167][«PubMed»]] ||
| 24. | *Barrick, J.E.* (2009) Predicting riboswitch regulation on a genomic scale. In _Riboswitches: Methods and Protocols_. (ed. A. Serganov), pp. 1-13. Humana Press, New York. [[http://www.ncbi.nlm.nih.gov/pubmed/19381548][«PubMed»]] <li>[[SupplementRiboswitchPrediction][Perl scripts accompanying book chapter]]</li> | <img alt="" src="http://barricklab.org/twiki/pub/Lab/PublicationList/riboswitch_methods_cover.jpg" style="border-color: black; border-style: solid; border-width: 1px" /> |
| 23. | Regulski, E.E., Moy, R.H., Weinberg, Z., *Barrick, J.E.*, Yao, Z., Ruzzo, W.L., and Breaker, R.R. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. _Mol. Microbiol._ *68*:918-932. [[http://www.ncbi.nlm.nih.gov/pubmed/18363797][«PubMed»]] ||
| 22. | Weinberg, Z., Regulski, E.E., Hammond, M.C., *Barrick, J.E.*, Yao, Z., Ruzzo, W.L., and Breaker, R.R. (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. _RNA_ *14*:822-828. [[http://www.ncbi.nlm.nih.gov/pubmed/18369181][«PubMed»]] ||
| 21. | *Barrick, J.E.* and Breaker R.R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. _Genome Biology_ *8*:R239. [[http://www.ncbi.nlm.nih.gov/pubmed/17997835][«PubMed»]] ||
| 20. | Weinberg, Z., *Barrick, J.E.*, Yao, Z., Roth, A., Kim, J.N., Gore, J., Wang, J.X., Lee, E.R., Block, K.F., Sudarsan, N, Neph, S., Tompa, M., Ruzzo, W.L., Breaker, R.R. (2007) Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. _Nucleic Acids Res._ *35*:4809-4819 [[http://www.ncbi.nlm.nih.gov/pubmed/17621584][«PubMed»]] ||
| 19. | Yao, Z., *Barrick, J.E.*, Weinberg, Z., Neph, S., Breaker, R.R., Tompa, M., Ruzzo, W.L. (2007) A computational pipeline for high-throughput discovery of <em>cis</em>-regulatory noncoding RNA in prokaryotes. _PLOS Comput. Biol._ *3*:e126. [[http://www.ncbi.nlm.nih.gov/pubmed/17616982][«PubMed»]] ||
| 18. | Roth, A., Winkler, W.C., Regulski, E.E., Lee, B.W., Lim, J., Jona, I., *Barrick, J.E.*, Ritwik, A., Kim, J.N., Welz, R., Iwata-Reuyl D., Breaker R.R. (2007) A riboswitch selective for the queuosine precursor preQ<sub>1</sub> contains an unusually small aptamer domain. _Nat. Struct. Mol. Biol._ *14* (4):308-317. [[http://www.ncbi.nlm.nih.gov/pubmed/17384645][«PubMed»]] ||
| 17. | *Barrick, J.E.* and Breaker R.R. (2007) The Power of Riboswitches. _Scientific American_ *296* (1):50-57. [[http://www.ncbi.nlm.nih.gov/pubmed/17186833][«PubMed»]] ||
| 16. | Lenski, R.E., *Barrick, J.E.*, and Ofria, C. (2006) Balancing Robustness and Evolvability. _PLoS Biology_ *4*:e428. [[http://www.ncbi.nlm.nih.gov/pubmed/17238277][«PubMed»]] ||
| 15. | Puerta-Fernandez, E., *Barrick, J.E.*, Roth, A., and Breaker, R.R. (2006) Identification of a new, non-coding RNA in extremophilic eubacteria. _Proc. Natl. Acad. Sci U.S.A_ *103*:19490-19495. [[http://www.ncbi.nlm.nih.gov/pubmed/17164334][«PubMed»]] ||
| 14. | Sudarsan N., Hammond M.C., Block K.F., Welz R., *Barrick J.E.*, Roth A., Breaker R.R. (2006) Tandem riboswitch architectures exhibit complex gene control functions. _Science_ *314*:300-304. [[http://www.ncbi.nlm.nih.gov/pubmed/17038623][«PubMed»]] ||
| 13. | Corbino, K.A., *Barrick, J.E.*, Lim, J., Welz, R., Tucker, B.J., Puskarz, I., Mandal, M., Rudnick, N.D., and Breaker, R.R. (2005) Evidence for a second class of <em>S</em>-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. _Genome Biol._ *6*: R70. [[http://www.ncbi.nlm.nih.gov/pubmed/16086852][«PubMed»]] ||
| 12. | *Barrick, J.E.*, Sudarsan, N., Weinberg, Z., Ruzzo, W.L., and Breaker, R.R. (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. _RNA_ *11*:774-784. [[http://www.ncbi.nlm.nih.gov/pubmed/15811922][«PubMed»]] ||
| 11. | Mandal, M., Lee, M., *Barrick, J.E.*, Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. _Science_ *306*:275-279. [[http://www.ncbi.nlm.nih.gov/pubmed/15472076][«PubMed»]] ||
| 10. | *Barrick, J.E.*, Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J.K., and Breaker, R.R. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. _Proc. Natl. Acad. Sci. U.S.A._ *101*:6421-6426. [[http://www.ncbi.nlm.nih.gov/pubmed/15096624][«PubMed»]] ||
| 9. | Nahvi, A., *Barrick, J.E.*, and Breaker, R.R. (2004) Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. _Nucleic Acids Res._ *32*:143-150. [[http://www.ncbi.nlm.nih.gov/pubmed/14704351][«PubMed»]] ||
| 8. | Mandal, M., Boese, B., *Barrick, J.E.*, Winkler, W.C., and Breaker, R.R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. _Cell_ *113*:577-586. [[http://www.ncbi.nlm.nih.gov/pubmed/12787499][«PubMed»]] ||
| 7. | Sudarsan, N., *Barrick, J.E.*, and Breaker, R.R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. _RNA_ *9*:644-647. [[http://www.ncbi.nlm.nih.gov/pubmed/12756322][«PubMed»]] ||
| 6. | Winkler, W.C., Nahvi, A., Sudarsan, N., *Barrick, J.E.*, and Breaker, R.R. (2003) An mRNA structure that controls gene expression by binding S-adenosylmethionine. _Nat. Struct. Biol._ *10*:701-707. [[http://www.ncbi.nlm.nih.gov/pubmed/12910260][«PubMed»]] ||
| 5. | *Barrick, J.E.*, and Roberts, R.W. (2003) Achieving specificity in selected and wild-type N peptide&ndash;RNA complexes: The importance of discrimination against noncognate RNA targets. _Biochemistry_ *42*:12998-13007. [[http://www.ncbi.nlm.nih.gov/pubmed/14596615][«PubMed»]] ||
| 4. | *Barrick, J.E.*, and Roberts, R.W. (2002) Sequence analysis of an artificial family of RNA-binding peptides. Protein Sci. *11*:2688-2696. [[http://www.ncbi.nlm.nih.gov/pubmed/12381850][«PubMed»]] ||
| 3. | *Barrick, J.E.*, Takahashi, T.T., Ren, J.S., Xia, T.B., and Roberts, R.W. (2001) Large libraries reveal diverse solutions to an RNA recognition problem. _Proc. Natl. Acad. Sci. U.S.A._ *98*:12374-12378. [[http://www.ncbi.nlm.nih.gov/pubmed/11675487][«PubMed»]] ||
| 2. | *Barrick, J.E.*, Takahashi, T.T., Balakin, A., and Roberts, R.W. (2001) Selection of RNA-binding peptides using mRNA-peptide fusions. _Methods_ *23*:287-293. [[http://www.ncbi.nlm.nih.gov/pubmed/11243841][«PubMed»]] ||
| 1. | Liu, R.H., *Barrick, J.E.*, Szostak, J.W., and Roberts, R.W. (2000) Optimized synthesis of RNA-protein fusions for in vitro protein selection. _Methods Enzymol._ *318*:268-293. [[http://www.ncbi.nlm.nih.gov/pubmed/10889994][«PubMed»]] ||

---++ Ph.D Thesis

%TABLE{valign="top" cellspacing="0" tableframe ="void" cellborder="0" tableborder="0"}%
| *Barrick JE*. (2006) Advisor: [[http://breaker.sites.yale.edu/&lrm;][Ronald R. Breaker]]. Discovering and defining metabolite-binding riboswitches and other structured regulatory RNA motifs in bacteria. [[%ATTACHURL%/060818_thesis.pdf][«PDF»]] | <img alt="" src="http://barricklab.org/twiki/pub/Lab/PublicationList/Barrick_thesis.png" style="background-color: black; border-color: black; border-style: solid; border-width: 1px" /> |
Barrick Lab > PublicationList
Contributors to this topic
JeffreyBarrick, SarahBialik
Topic revision: r223 - 2021-05-27 - 13:42:46 - Main.JeffreyBarrick