<!-- 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* ||| | 118. | **Roots, C.T.*, *Hill, A.M., Wilke, C.O., *^Barrick, J.E.* (2024) Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria. _bioRxiv_ [[https://doi.org/10.1101/2024.11.28.625058][DOI: 10.1101/2024.11.28.625058 ]] || | 117. | *^Lariviere, P.J.*, *Ashraf, A H M Z.*, *Gifford, I.*, _Tanguma, S.L._, *Barrick, J.E.*, ^Moran, N.A. (2024) Virulence-linked adhesin drives mutualist colonization of the bee gut via biofilm formation. _bioRxiv_ [[https://doi.org/10.1101/2024.10.14.618124][DOI: 10.1101/2024.10.14.618124]] || | 116. | *Roots, C.T.*, *^Barrick, J.E.* (2024) 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]] || | *2024* ||| | 115. | 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. (2024) Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate _Bartonella_ adaptation to a wild rodent host. _PLoS Pathogens_ *20*:e1012591. [[https://doi.org/10.1371/journal.ppat.1012591][DOI: 10.1371/journal.ppat.1012591]] [[http://www.ncbi.nlm.nih.gov/pubmed/39348417][PMID: 39348417]] || | 114. | **Gifford, I.*, **Suárez G.A.*, *^Barrick, J.E.* (2024) Evolution recovers the fitness of _Acinetobacter baylyi_ strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators. _PLoS Genetics_ *20*:e1011306. [[https://doi.org/10.1371/journal.pgen.1011306][DOI: 10.1371/journal.pgen.1011306]] [[http://www.ncbi.nlm.nih.gov/pubmed/39283914][PMID: 39283914]] || | 113. | *^Lariviere, P.J.*, *Ashraf, A H M Z.*, *Navarro-Escalante, L.*, *Leonard, S.P.*, __Miller, L.G.__, Moran, N.A. *^Barrick, J.E.* (2024) One-step genome engineering in bee gut bacterial symbionts. _mBio_ *15*:e0139224. [[https://doi.org/10.1128/mbio.01392-24][DOI: 10.1128/mbio.01392-24]] [[http://www.ncbi.nlm.nih.gov/pubmed/39105596][PMID: 39105596]] || | 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.* (2024) 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. 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[[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" /> |
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