<!-- 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* ||| | 114. | *^Lariviere, P.J.*, *Ashraf, A.H.M.Z.*, *Leonard, S.P.*, __Miller, L.G.__, Moran, N.A. *^Barrick, J.E.* (2023) Single-step genome engineering in the bee gut symbiont _Snodgrassella alvi_. _bioRxiv_ [[https://doi.org/10.1101/2023.09.19.558440][DOI: 10.1101/2023.09.19.558440]] || | 113. | 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* ||| | 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. Comm._ In press. _bioRxiv_ [[https://doi.org/10.1101/2024.04.08.588465 ][DOI: 10.1101/2024.04.08.588465]] || | 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. 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[[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. 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[[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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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
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