Barrick Lab :: Publications

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Barrick Lab researchers  *Equal contributions  ^Corresponding author(s)  Undergraduate researchers
Preprints
119. VanDieren A.J., *^Barrick, J.E. (2024) Evolution in response to prophage activation attenuates the virulence of culturable Serratia symbiotica relatives of aphid endosymbionts. bioRxiv DOI: 10.1101/2024.12.04.626866
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 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 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 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. DOI: 10.1371/journal.ppat.1012591 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. DOI: 10.1371/journal.pgen.1011306 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. DOI: 10.1128/mbio.01392-24 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. DOI: 10.1038/s41467-024-50639-9 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. DOI: 10.1371/journal.pone.0304164 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. DOI: 10.1371/journal.pbio.3002418 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. 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. DOI: 10.1371/journal.pbio.3002376 PMID: 37971964
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. DOI: 10.1186/s13071-023-05918-7 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. DOI: 10.3791/65342 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 Drosophila-colonizing Orbaceae. ISME Commun. 3:9. DOI: 10.1038/s43705-023-00255-3 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. DOI: 10.1002/adpr.202200343 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. DOI: 10.7717/peerj.14961 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. DOI: 10.1021/acs.biomac.2c01035 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. DOI: 10.1038/s41596-022-00778-4 PMID: 36460809 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. DOI: 10.1186/s12915-022-01477-y 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. DOI: 10.1093/molbev/msac184 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. DOI: 10.1111/1755-0998.13649 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. DOI: 10.1128/mbio.03512-21 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. DOI: 10.1016/j.tim.2021.05.004 PMID: 34103228
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. DOI: 10.1016/j.cels.2021.08.011 PMID: 34536379 bioRxiv
94. Roots, C.T., Lukasiewicz, A., ^Barrick, J.E. (2021) OSTIR: open source translation initiation rate prediction. J. Open Source Softw. 6:3362. 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. DOI: 10.1073/pnas.2104592118 PMID: 34083444
92. McGuffie, M.C., ^Barrick, J.E. (2021) pLannotate: engineered plasmid annotation. Nucleic Acids Res. 49:W516-W522. DOI: 10.1093/nar/gkab374 PMID: 34019636
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. DOI: 10.1128/mBio.00359-21 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. DOI: 10.1038/s41467-021-21210-7 PMID: 33579917
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. DOI: 10.3390/microorganisms9020347 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. DOI: 10.1073/pnas.2016886118 PMID: 33441451
87. *Gifford, I., *Dasgupta, A., ^Barrick, J.E. (2021) Rates of gene conversions between Escherichia coli ribosomal operons. G3 11:jkaa002. DOI: 10.1093/g3journal/jkaa002 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. DOI: 10.1128/AEM.02245-20 PMID: 33277267
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 DOI: 10.3389/fmicb.2020.579989 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. Full Text 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. Full Text DOI: 10.1007/978-3-030-39831-6_8
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. Full Text 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 Acinetobacter baylyi ADP1 genome streamlining. Nucleic Acids Res. 48:4585–4600. Full Text 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. DOI: 10.1126/science.aax9039 PMID: 32001655
  • UT News: Bacteria Engineered to Protect Bees from Pests and Pathogens
  • NIH Research Matters: Engineered bacteria protect honey bee health
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    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. DOI: 10.1038/s41467-019-13709-x Full Text, PMID: 31863068
  • Nature Ecology & Evolution Behind the Paper Post: Satellite plasmids: evolutionary stability experiments come full orbit

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    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. PMID: 31540989
    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. DOI: 10.1021/acssynbio.8b00426, Preprint, PMID: 30703321
    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. DOI: 10.1093/nar/gky751, PMID: 30137492
    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. Full Text, PMID: 29983852
    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. DOI: 10.1021/acssynbio.7b00399 PMID: 29608282
    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. DOI: 10.1371/journal.pgen.1007348 PMID: 29649242
    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. DOI: 10.1038/nature24287 PMID: 29045390
    71. Bull, J.J.*, Barrick, J.E.^* (2017) Arresting evolution. Trends Genet. 33:910-920. PMID: 29029851
    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. 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. DOI: 10.1128/AEM.01025-17 PMID: 28667117
    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. 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. PMID: 28417974
    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. PMID: 28202733
  • News: Genetic signatures reveal environment where bacteria evolved
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    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. PMID: 27648665
    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. 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. PMID: 27479321
  • News: Bacteria show capacity for rapid, beneficial mutations
  • News: Still changing after all these years
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    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. 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. DOI: 10.7554/eLife.09696 PMID: 26465114
  • Commentary: Metabolism: Evolution retraces its steps to advance
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    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. 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. 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. DOI: 10.1021/acssynbio.5b00068 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. 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. 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. PMID:25911659
  • Award: GSA 1st Centennial Award for Population and Evolutionary Genetics
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    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. 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. 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. 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. 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. 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. 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. 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. DOI: 10.1007/978-1-4939-0554-6_12 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. DOI: 10.1039/c3mb70606k 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. 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. PubMed:24379390
  • Commentary: Refining a key metabolic innovation in Escherichia coli
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    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. «BioBricks Foundation» «DSpace»
    42. Barrick, J.E., Lenski, R.E. (2013) Genome dynamics during experimental evolution. Nat. Rev. Genet. 14:827-834. «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. «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 N-demethylation operon from Pseudomonas putida CBB5. ACS Synth. Biol. 2:301-307. «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. «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. DOI: 10.1073/pnas.1219574110 «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. «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. «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. «PubMed»
    33. Wolf, L.N., Barrick, J.E. (2012) Tracking winners and losers in E. coli evolution experiments. Microbe Magazine 2 (3):124-128. «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. «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. «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. «PubMed»
  • Supplementary data and scripts
    		•
    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. «PubMed» «Press Links» «Science Podcast» «Faculty of 1000» «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. «PubMed» «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. «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. «PubMed»«Faculty of 1000»
  • News: Time In A Bottle: Scientists Watch Evolution Unfold
    		•
    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. «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. «PubMed»
  • Perl scripts accompanying book chapter
    		•
    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. «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. «PubMed»
    21. Barrick, J.E. and Breaker R.R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biology 8:R239. «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 «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 cis-regulatory noncoding RNA in prokaryotes. PLOS Comput. Biol. 3:e126. «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 preQ1 contains an unusually small aptamer domain. Nat. Struct. Mol. Biol. 14 (4):308-317. «PubMed»
    17. Barrick, J.E. and Breaker R.R. (2007) The Power of Riboswitches. Scientific American 296 (1):50-57. «PubMed»
    16. Lenski, R.E., Barrick, J.E., and Ofria, C. (2006) Balancing Robustness and Evolvability. PLoS Biology 4:e428. «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. «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. «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 S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol. 6: R70. «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. «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. «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. «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. «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. «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. «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. «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. «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. «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. «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. «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. «PubMed»

    Ph.D Thesis

    Barrick JE. (2006) Advisor: Ronald R. Breaker. Discovering and defining metabolite-binding riboswitches and other structured regulatory RNA motifs in bacteria. «PDF»
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    Topic revision: r298 - 2024-12-06 - 02:23:52 - Main.JeffreyBarrick
     
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