Publications

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»
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. «Full Text»
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. *equal contributions «PubMed» «Press Links» «Science Podcast» «Faculty of 1000»
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»
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. *equal contributions «PubMed» «News Story» «Faculty of 1000»
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» «Supplement»
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 structures, distributions, and mechanisms 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. January, 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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