<!-- Preferences start here * Set PAGETITLE = Barrick Lab :: Publications Preferences end here --> <noautolink> ---+ Barrick Lab :: Publications %ICON{move}% [[http://scholar.google.com/citations?user=a59MTe0AAAAJ&sortby=pubdate][View Barrick Lab Publications on Google Scholar]] <!-- | *In Press / Epub* ||| --> <div align="left"> *Barrick Lab researchers* *Equal contributions ^Corresponding author(s) _Undergraduate researchers_ </div> %TABLE{tableborder="0" databg="#FFFFFF" tablerules="all,none" cellborder="1"}% | *Preprints* ||| | 116. | *Roots, C.R.*, *^Barrick, J.E.* CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria. _bioRxiv_ [[https://doi.org/10.1101/2024.09.05.611466][DOI: 10.1101/2024.09.05.611466]] || | 115. | **Gifford I.*, **Suárez G.A.*, *^Barrick, J.E.* Evolution recovers the fitness of _Acinetobacter baylyi_ strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators. _bioRxiv_ [[https://doi.org/10.1101/2024.05.20.594936 ][DOI: 10.1101/2024.05.20.594936 ]] || | 114. | Rodríguez‑Pastor, R. Knossow N., Shahar, N, Hasik, A.Z., *Deatherage, D.E.*, Gutiérrez, R., Harrus, S.,Zaman, L., Lenski, R.E., *^Barrick, J.E.*, ^Hawlena, H. (2023) Parasite contingency loci and the evolution of host specificity: Simple sequence repeats mediate _Bartonella_ adaptation to a wild rodent host. _bioRxiv_ [[https://doi.org/10.1101/2024.01.18.576196 ][DOI: 10.1101/2024.01.18.576196 ]] || | *2024* ||| | 113. | *^Lariviere, P.J.*, *Ashraf, A.H.M.Z.*, *Leonard, S.P.*, __Miller, L.G.__, Moran, N.A. *^Barrick, J.E.* (2024) One-step genome engineering in bee gut bacterial symbionts. _mBio_ Epub Aug 6 [[https://doi.org/10.1128/mbio.01392-24][DOI: 10.1128/mbio.01392-24]] || | 112. | __*Radde, N.__, __*Mortensen, G.A.__, __Bhat, D.__, __Shah, S.__, __Clements, J.J.__, *Leonard, S.P.*, *McGuffie, M.J.*, *Mishler, D.M.*, *^Barrick, J.E.* (2024) Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. _Nat. Commun._ *15*: 6242. [[https://doi.org/10.1038/s41467-024-50639-9 ][DOI: 10.1038/s41467-024-50639-9 ]] [[http://www.ncbi.nlm.nih.gov/pubmed/39048554][PMID: 39048554]] || | 111. | *McGuffie, M.J.*, *^Barrick, J.E.* (2023) Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences. _PLoS ONE_ *19*:e0304164. [[https://doi.org/10.1371/journal.pone.0304164][DOI: 10.1371/journal.pone.0304164]] [[http://www.ncbi.nlm.nih.gov/pubmed/38805426][PMID: 38805426]] || | 110. | uz-Zaman, Md. H., *D'Alton, S.*, *Barrick, J.E.*, ^Ochman H. (2024) Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with _Escherichia coli_. _PLoS Biol._ *22*:e3002418. [[https://doi.org/10.1371/journal.pbio.3002418 ][DOI: 10.1371/journal.pbio.3002418]] [[http://www.ncbi.nlm.nih.gov/pubmed/38713714][PMID: 38713714]] || | 109. | Diaz Lluberes, I.A., Ahmido, T., Fernando, P.U.A.I., Kosgei, G.K., Bayliff, K.W., *Dwenger IV, J.H.*, Dolocan, A., *Barrick, J.E.*, Smith, C.B. (2024) Exploring the extended spectral signature and remote sensing capabilities of lanthanide enriched arrays of brochosomes. In: W.M. Shensky III, I. Rau, O. Sugihara (eds.). _Organic Photonic Materials and Devices XXVI_ *12883*:1288304. [[https://doi.org/10.1117/12.3001089][DOI: 10.1117/12.3001089]] || | *2023* ||| | 108. | Thuronyi, B W., DeBenedictis, E.A., *^Barrick, J.E.* (2023) No assembly required: Time for stronger, simpler publishing standards for DNA sequences. _PLoS Bio._ *21*:e3002376. [[https://doi.org/10.1371/journal.pbio.3002376][DOI: 10.1371/journal.pbio.3002376]] [[http://www.ncbi.nlm.nih.gov/pubmed/37971964][PMID: 37971964]] %BR% <div align="center"><img height="260" alt="" src="%ATTACHURL%/Thuronyi_2023_PLoSBiology.png" /></div> || | 107. | Rodríguez-Pastor, R., Hasik, A.Z., Knossow, N., Bar-Shira, E., Shahar, N., Gutiérrez, R., Zaman, L., Harrus, S., Lenski, R.E., *Barrick, J.E.*, ^Hawlena, H. (2023) _Bartonella_ infections are prevalent in rodents despite efficient immune responses. _Parasites Vectors_ *16*:315. [[https://doi.org/10.1186/s13071-023-05918-7][DOI: 10.1186/s13071-023-05918-7]] [[http://www.ncbi.nlm.nih.gov/pubmed/37667323][PMID: 37667323]] || | 106. | *^Barrick, J.E.*, ^Blount, Z.D., Lake, D.M., *Dwenger IV, J.H.*, *Chavarria-Palma, J.E.*, Izutsu, M., Wiser, M.J. (2023) Daily transfers, archiving populations, and measuring fitness in the long-term evolution experiment with _Escherichia coli_. _J. Vis. Exp._ *198*:e65342. [[https://doi.org/10.3791/65342][DOI: 10.3791/65342]] [[http://www.ncbi.nlm.nih.gov/pubmed/37607082][PMID: 37607082]] || | 105. | **Elston, K.M.*, *Phillips, L.E., *Leonard, S.P.*, *Young, E.*, Holley, J.C., _Ahsanullah, T._, __McReynolds, B.__, Moran, N.A., *^Barrick, J.E.* (2023) The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of <i>Drosophila</i>-colonizing _Orbaceae_. _ISME Commun._ *3*:9. [[https://doi.org/10.1038/s43705-023-00255-3][DOI: 10.1038/s43705-023-00255-3]] [[http://www.ncbi.nlm.nih.gov/pubmed/37225918][PMID: 37225918]] || | 104. | ^Banerjee, P., Burks, G.R., *Bialik, S.B.*, Bello, E., Alleyne, M., Freeman, B.D., *Barrick, J.E.*, Schroeder C.M., Milliron, D.J. (2023) Nanostructure-derived anti-reflectivity in leafhopper brochosomes. _Adv. Photonics Res._ 202200343. [[https://doi.org/10.1002/adpr.202200343][DOI: 10.1002/adpr.202200343]] [[https://doi.org/10.26434/chemrxiv-2022-g1h5x][ChemRxiv]] || | 103. | *Elston, K.M.*, Maeda, G.P., *Perreau, J.*, *^Barrick, J.E.* (2023) Addressing the challenges of symbiont-mediated RNAi in aphids. _PeerJ_ *11*:e14961. [[https://doi.org/10.7717/peerj.14961][DOI: 10.7717/peerj.14961]] [[http://www.ncbi.nlm.nih.gov/pubmed/36874963][PMID: 36874963]] || | 102. | Burks, G.R., Yao, L., Kalutantirige, F.C., _Gray, K.J._, Bello, E., Rajagopalan, S., *Bialik, S.B.*, *Barrick, J.E.*, Alleyne, M., Chen, Q., ^Schroeder C.M. (2023) Electron tomography and machine learning for understanding the highly ordered structure of leafhopper brochosomes. _Biomacromolecules_ *24*:190-200. [[https://doi.org/10.1021/acs.biomac.2c01035][DOI: 10.1021/acs.biomac.2c01035]] [[http://www.ncbi.nlm.nih.gov/pubmed/36516996][PMID: 36516996]] || | 101. | **Lariviere, P.J.*, **Leonard, S.P.*, _Horak, R.D._, Powell, J.E., *^Barrick, J.E.* (2023) Honey bee functional genomics using symbiont-mediated RNAi. _Nat. Protoc._ *18*:902-928. [[https://doi.org/10.1038/s41596-022-00778-4][DOI: 10.1038/s41596-022-00778-4]] [[http://www.ncbi.nlm.nih.gov/pubmed/36460809][PMID: 36460809]] [[https://doi.org/10.1101/2022.04.22.489157][Preprint]] || | *2022* ||| | 100. | Maritan, E., Gallo, M., Srutkova, D., Jelinkova, A., Benada, O., Kofronova, O., Silva-Soares, N.F., Hudcovic, T., *Gifford, I.*, *Barrick, J.E.*, Schwarzer, M, Martino, M. E. (2022) Gut microbe _Lactiplantibacillus plantarum_ undergoes different evolutionary trajectories between insects and mammals. _BMC Biol._ *20*:290. [[https://doi.org/10.1186/s12915-022-01477-y][DOI: 10.1186/s12915-022-01477-y ]] [[http://www.ncbi.nlm.nih.gov/pubmed/36575413][PMID: 36575413]] || | 99. | Li, Z., Li, Y, _Xue A.Z._, Dang V., Holmes, V.R., Johnston, J.S., *Barrick, J.E.*, ^Moran, N.A. (2022) The genomic basis of evolutionary novelties in a leafhopper. _Mol. Biol. Evol._ *39*:msac184. [[https://doi.org/10.1093/molbev/msac184][DOI: 10.1093/molbev/msac184]] [[http://www.ncbi.nlm.nih.gov/pubmed/36026509][PMID: 36026509]] || | 98. | Rodríguez-Pastor, R., Shafran, Y., Knossow, N., Gutiérrez, R. Harrus, S., Zaman, L., Lenski, R. E., *Barrick, J. E.*, ^Hawlena, H. (2022) A road map for in vivo evolution experiments with blood-borne parasitic microbes. _Mol. Ecol. Resour._ *22*:2843-2859. [[https://doi.org/10.1111/1755-0998.13649][DOI: 10.1111/1755-0998.13649]] [[http://www.ncbi.nlm.nih.gov/pubmed/35599628][PMID: 35599628]] || | 97. | Gómez-Garzón, C, *Barrick, J.E.*, ^Payne, S.M. (2022) Disentangling the evolutionary history of Feo, the major ferrous iron transport system in bacteria. _mBio_ *13*:e03512-21. [[https://doi.org/10.1128/mbio.03512-21][DOI: 10.1128/mbio.03512-21]] [[http://www.ncbi.nlm.nih.gov/pubmed/35012344][PMID: 35012344]] || | 96. | *Elston, K.M.*, Leonard, S.P., *Geng, P.*, *Bialik, S.B.*, __Robinson, E.__, *^Barrick, J.E.* (2022) Engineering insects from the endosymbiont out. _Trends Microbiol._ *30*:79-96. [[https://doi.org/10.1016/j.tim.2021.05.004][DOI: 10.1016/j.tim.2021.05.004]] [[http://www.ncbi.nlm.nih.gov/pubmed/34103228][PMID: 34103228]] <div align="center"><img height="200" alt="" src="%ATTACHURL%/Elston_2021_TiM.png" /></div>|| | *2021* ||| | 95. | *Deatherage, D.E.*, *^Barrick, J.E.* (2021) High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. _Cell_ _Syst._ *12*:79-96. [[https://doi.org/10.1016/j.cels.2021.08.011][DOI: 10.1016/j.cels.2021.08.011]] [[http://www.ncbi.nlm.nih.gov/pubmed/34536379][PMID: 34536379]] [[https://doi.org/10.1101/2020.07.10.196832][bioRxiv]] %BR% <div align="center"><img height="260" alt="" src="%ATTACHURL%/Deatherage_2022_CellSystems.png" /></div>|| | 94. | *Roots, C.T.*, Lukasiewicz, A., *^Barrick, J.E.* (2021) OSTIR: open source translation initiation rate prediction. _J. Open Source Softw._ *6*:3362. [[https://doi.org/10.21105/joss.03362][DOI: 10.21105/joss.03362]] || | 93. | Borin, J.M., Avrani, S., *Barrick, J.E.*, Petrie, K.L., ^Meyer, J.R. (2021) Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. _Proc. Natl. Acad. Sci. U.S.A._ *118*:e2104592118. [[https://doi.org/10.1073/pnas.2104592118][DOI: 10.1073/pnas.2104592118]] [[http://www.ncbi.nlm.nih.gov/pubmed/34083444][PMID: 34083444]] || | 92. | *McGuffie, M.C.*, *^Barrick, J.E.* (2021) pLannotate: engineered plasmid annotation. _Nucleic Acids Res._ *49*:W516-W522. [[https://doi.org/10.1093/nar/gkab374][DOI: 10.1093/nar/gkab374]] [[http://www.ncbi.nlm.nih.gov/pubmed/34019636][PMID: 34019636]] %BR%<ul><li> Webserver: [[http://plannotate.barricklab.org][http://plannotate.barricklab.org]]</li><li> GitHub: [[https://github.com/barricklab/pLannotate][https://github.com/barricklab/pLannotate]]</li></ul> <div align="center"><img height="200" alt="" src="%ATTACHURL%/McGuffie_2021_NAR.png" /></div> || | 91. | *^Perreau, J.*, Patel, D.J., Anderson, H., Maeda, G.P, *Elston, K.M.*, *Barrick, J.E.*, Moran, N.A. (2021) Vertical transmission at the pathogen-symbiont interface: _Serratia symbiotica_ and aphids. _mBio_ *12*:e00359-21. [[https://doi.org/10.1128/mBio.00359-21][DOI: 10.1128/mBio.00359-21]] [[http://www.ncbi.nlm.nih.gov/pubmed/33879583][PMID: 33879583]] || | 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]] [[http://www.ncbi.nlm.nih.gov/pubmed/33579917][PMID: 33579917]] %BR%<ul><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></ul> | | 89. | *Bazurto, J.V., *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_ *9*:347. [[https://doi.org/10.3390/microorganisms9020347][DOI: 10.3390/microorganisms9020347]] [[http://www.ncbi.nlm.nih.gov/pubmed/33578755][PMID: 33578755]] || | 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. | **Gifford, I.*, **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% <ul><li>[[https://aem.asm.org/content/87/4/e02994-20][ AEM Spotlight Article]]</li></ul> || | *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 (σ54) deletion and genome reduction. _Front. Microbiol._ *11*:579989 [[https://doi.org/10.3389/fmicb.2020.579989][DOI: 10.3389/fmicb.2020.579989]] [[http://www.ncbi.nlm.nih.gov/pubmed/33240235][PMID: 33240235]] || | 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., *Grant, N.A., Ahmed, S.T., Jagdish, T., _Sommerfeld, B.A._, _Tillman, A._, _Moore, J._, 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: 10.1126/science.aax9039]] [[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 prolong the maintenance of newly acquired accessory genes in bacteria. _Nat. Comm._ *10*:5809. [[https://doi.org/10.1038/s41467-019-13709-x ][DOI: 10.1038/s41467-019-13709-x]] [[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][DOI: 10.1021/acssynbio.8b00426]], [[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][DOI: 10.1093/nar/gky751]], [[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. [[https://doi.org/10.1021/acssynbio.7b00399][DOI: 10.1021/acssynbio.7b00399]] [[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. [[https://doi.org/10.1371/journal.pgen.1007348][DOI: 10.1371/journal.pgen.1007348]] [[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. [[https://doi.org/10.1038/nature24287 ][DOI: 10.1038/nature24287]] [[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._ *4*: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. [[https://doi.org/10.1128/AEM.01025-17 ][DOI: 10.1128/AEM.01025-17 ]] [[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. [[https://doi.org/10.7554/eLife.09696][DOI: 10.7554/eLife.09696 ]] [[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. [[https://doi.org/10.1021/acssynbio.5b00068][DOI: 10.1021/acssynbio.5b00068]] [[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. [[https://doi.org/10.1007/978-1-4939-0554-6_12][DOI: 10.1007/978-1-4939-0554-6_12]] [[http://www.ncbi.nlm.nih.gov/pubmed/24838886][PMID: 24838886]] || | 46. | *Renda, B.A.**, *Hammerling, M.J.**, *Barrick, J.E.* (2014) Engineering reduced evolutionary potential for synthetic biology. _Mol. Biosyst._ *10*:1668-1678. [[https://doi.org/10.1039/c3mb70606k][DOI: 10.1039/c3mb70606k]] [[https://pubmed.ncbi.nlm.nih.gov/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. [[https://doi.org/10.1073/pnas.1219574110 ][DOI: 10.1073/pnas.1219574110]] [[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–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/‎][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" /> |
Edit
|
Attach
|
Watch
|
P
rint version
|
H
istory
:
r301
|
r288
<
r287
<
r286
<
r285
|
B
acklinks
|
V
iew topic
|
More topic actions...
Barrick Lab
>
PublicationList
Contributors to this topic
JeffreyBarrick, SarahBialik
Topic revision: r286 - 2024-09-09 - 11:46:43 - Main.JeffreyBarrick
Barrick Lab
Contact
Research
Publications
Team
Protocols
Reference
Software
UT Austin
Mol Biosciences
ILS
Microbiology
EEB
CSSB
CBRS
The LTEE
iGEM team
SynBioCyc
SynBio course
NGS course
BEACON
Search
Log in
Copyright ©2025 Barrick Lab contributing authors. Ideas, requests, problems?
Send feedback
JeffreyBarrick, SarahBialik JeffreyBarrick, SarahBialik JeffreyBarrick, SarahBialik
Barrick Lab
Contact
Research
Team
Protocols
Reference
Software
UT Austin
Mol Biosciences
ILS
Microbiology
EEB
CSSB
CBRS
The LTEE
iGEM team
SynBioCyc
SynBio course
NGS course
BEACON
Search
Log in
