Barrick Lab :: Publications

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Barrick Lab members *Equal contributions ^corresponding author(s)

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 Epub Oct 18. 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. 24:467-477. 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. 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
  • 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
  •  
    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. PMID: 26465114
  • Commentary: Metabolism: Evolution retraces its steps to advance
  • 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. 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
  • 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. Colin, R., 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. PubMed:24838886
    46. Renda, B.A.*, Hammerling, M.J.*, Barrick, J.E. (2014) Engineering reduced evolutionary potential for synthetic biology. Mol. Biosyst. 10:1668-1678. 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
  • 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. «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»

    Online Contributions

    Wikipedia molecular biology stubs
    Rfam: RNA families database
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