<!-- 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]] %TABLE{tableborder="0" tablerules="none"}% | *Preprints* || | 66. | *Brown, C.W.*, Sridhara, V., Boutz, D.R., Person, M.D., Marcotte, E.M. *Barrick, J.E.*, Wilke, C.O. (2016) Large-scale analysis of post-translational modifications in _E. coli_ under glucose-limiting conditions. [[http://biorxiv.org/content/early/2016/04/30/051185][bioRxiv]] | | *2016* || | 65. | <div style="float:right"><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/Monk_2016_ACS_Synth_Biol.png"></div> 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.^* Rapid and inexpensive evaluation of nonstandard amino acid incorporation in _Escherichia coli_. _ACS Synth. Biol._ Epub. [[http://www.ncbi.nlm.nih.gov/pubmed/27648665][PMID: 27648665]] | | 64. | <div style="float:right"><img style="border-color: black; border-style: solid; border-width: 1px;" width="411" height="100" src="%ATTACHURL%/Renda_2016_J_Bacteriol.png"></div> Renda, B.A., Chan, C., Parent, K.N., *Barrick, J.E.^* Emergence of a competence reducing filamentous phage from the genome of _Acinetobacter baylyi_ ADP1. _J. Bacteriol._ Epub. [[http://www.ncbi.nlm.nih.gov/pubmed/27645387][PMID: 27645387]] | | 63. | <div style="float:right"><img style="border-color: black; border-style: solid; border-width: 1px;" width="355" height="150" src="%ATTACHURL%/Tenaillon_2016_Nature.png"></div> 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. [[http://www.ncbi.nlm.nih.gov/pubmed/27479321][PMID: 27479321]]<li>News: [[https://cns.utexas.edu/news/bacteria-show-capacity-for-rapid-beneficial-mutations][Bacteria show capacity for rapid, beneficial mutations]]</li><li>News: [[http://msutoday.msu.edu/news/2016/still-changing-after-all-these-years/][Still changing after all these years]]</li>| | | 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. [[http://www.ncbi.nlm.nih.gov/pubmed/27189550][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. [[http://www.ncbi.nlm.nih.gov/pubmed/26465114][PMID: 26465114]] | | 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. [[http://www.ncbi.nlm.nih.gov/pubmed/26275208][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. [[http://www.ncbi.nlm.nih.gov/pubmed/26199375][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. [[http://www.ncbi.nlm.nih.gov/pubmed/26096262][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. [[http://www.ncbi.nlm.nih.gov/pubmed/26114300][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. [[http://www.ncbi.nlm.nih.gov/pubmed/26067973][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25911659][PMID:25911659]] <li>[[http://genestogenomes.org/centennial-awards-honor-outstanding-genetics-articles/][Awarded GSA 1st Centennial Award for Population and Evolutionary Genetics]]</li> | | 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. ^corresponding author [[http://www.ncbi.nlm.nih.gov/pubmed/25741363][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25512307][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25653667][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25502413][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. *equal contributions ^corresponding authors [[http://www.ncbi.nlm.nih.gov/pubmed/25525459][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25432719][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. [[http://www.ncbi.nlm.nih.gov/pubmed/25205090][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. [[http://www.ncbi.nlm.nih.gov/pubmed/24838886][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. *equal contributions [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24556867][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. [[http://www.ncbi.nlm.nih.gov/pubmed/24487692][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. [[http://www.ncbi.nlm.nih.gov/pubmed/24379390][PubMed:24379390]] [[http://www.pnas.org/content/111/6/2056][«Commentary»]] | | *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. [[http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_95:_Open_Sequence_Initiative:_a_part_submission_standard_to_complement_modern_DNA_assembly_techniques][«BioBricks Foundation»]] [[http://hdl.handle.net/1721.1/81334][«DSpace»]] | | 42. | *Barrick, J.E.*, Lenski, R.L. (2013) Genome dynamics during experimental evolution. _Nat. Rev. Genet._ *14*:827-834. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=24166031][«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._ *175*:3933-3939. [[http://www.ncbi.nlm.nih.gov/pubmed/23813729][«PubMed»]] | | 40. | *Quandt, E.M.*, *Hammerling, M.J.*, Summers, R.J., *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 <i>N</i>-demethylation operon from _Pseudomonas putida_ CBB5. _ACS Synth. Biol._ *2*:301-307. [[http://www.ncbi.nlm.nih.gov/pubmed/23654268][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/23492852][«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. *equal contributions [[http://www.ncbi.nlm.nih.gov/pubmed/23248287][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/22992527][«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.* [[http://dx.doi.org/10.7551/978-0-262-31050-5-ch062][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/22519712][«PubMed»]] | | 33. | *Wolf, L.N.*, *Barrick, J.E.* (2012) Tracking winners and losers in _E. coli_ evolution experiments. _Microbe Magazine_ *2* (3):124-128. [[http://www.microbemagazine.org/index.php?option=com_content&view=article&id=4544:tracking-winners-and-losers-in-e-coli-evolution-experiments&catid=939:07-2011-features&Itemid=1210][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/22282803][«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. [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=21700661][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/22207905][«PubMed»]] <li>[[SupplementLongTermMutationRates][Supplementary data and scripts]]</li>| | 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 ^corresponding authors [[http://www.ncbi.nlm.nih.gov/pubmed/21415350][«PubMed»]] [[http://www.santafe.edu/news/item/science-lenski-slow-evolution-is-better/][«Press Links»]] [[http://www.sciencemag.org/content/331/6023/1455.2.full][«Science Podcast»]] [[http://f1000.com/9422956][«Faculty of 1000»]] [[ErratumScience2011][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/21283682][«PubMed»]] [[http://zoonotica.wordpress.com/2011/07/06/254campylobacter-adaptation/][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/20106907][«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 [[http://www.ncbi.nlm.nih.gov/pubmed/19838166][«PubMed»]] [[http://news.msu.edu/story/6993/][«News Story»]] [[http://f1000biology.com/article/id/1166598][«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. [[http://www.ncbi.nlm.nih.gov/pubmed/19776167][«PubMed»]] | | 24. | <div style="float:right"><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/riboswitch_methods_cover.jpg"></div> *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. [[http://www.ncbi.nlm.nih.gov/pubmed/19381548][«PubMed»]] <li>[[SupplementRiboswitchPrediction][Perl scripts accompanying book chapter]]</li> | | 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 structures, distributions, and mechanisms 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 <i>cis</i>-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 <i>S</i>-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 src="%ATTACHURL%/Barrick_thesis.png" style="background-color: black; border-color: black; border-style: solid; border-width: 1px;"> | ---++ Online Contributions %TABLE{valign="center" cellspacing="0" width="100%"}% | <img src="%ATTACHURL%/wikipedia.jpg" style="background-color: black; border-color: black; border-style: solid; border-width: 1px;" height=48 width=48> | [[http://en.wikipedia.org/wiki/Special:Contributions/JeffreyBarrick][Wikipedia]] _[[http://en.wikipedia.org/wiki/Category:Molecular_and_cellular_biology_stubs][molecular biology stubs]]_| | <img src="%ATTACHURL%/rfam.gif" style="background-color: black; border-color: black; border-style: solid; border-width: 1px;" height=32 width=48> | [[http://rfam.sanger.ac.uk/search/keyword?query=Barrick][Rfam: RNA families database]] |
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JeffreyBarrick, SarahBialik JeffreyBarrick, SarahBialik JeffreyBarrick, SarahBialik
Barrick Lab
Contact
Research
Team
Protocols
Reference
Computation
Software
UT Austin
Mol Biosciences
ILS
Microbiology
EEB
CSSB
CBRS
The LTEE
iGEM team
SynBioCyc
SynBio course
NGS course
BEACON
Search
Log in
