Publications

Barrick JE
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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. «PubMed»
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. «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. «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. «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. Discovering and defining metabolite-binding riboswitches and other structured regulatory RNA motifs in bacteria. «PDF»

Posters and Presentations

4. Barrick, J.E., Dover, J.A., and Lenski, R.E. 2008. Growth regulation and genome reduction in Escherichia coli adapted to an unnatural nutritional requirement. Presentation. Evolution Conference, Minneapolis, MN.
3. Barrick, J.E., Ofria, C., and Lenski, R.E. 2007. Examining trade-offs between genetic regulation efficiency and evolvability in bacteria and digital organisms. Poster. Microbial Population Genetics Gordon Conference, Andover, NH. «PDF»
2. Barrick, J.E., and Breaker, R.R. 2006. The structures, distributions, mechanisms, and evolution of metabolite-binding riboswitches and other complex cis-regulatory RNA motifs in bacteria. Presentation. RNA Society 2006 Annual Meeting, Seattle, WA.
1. Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. 2004. A glycine riboswitch uses cooperative binding to control transcription termination. Presentation. Post-Initiation Activities of RNA Polymerase Conference, Mountain Lake, VA.

Online Contributions

Wikipedia molecular biology stubs
Rfam: RNA families database

Reading

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