<!-- 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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Topic revision: r143 - 2016-12-06 - JeffreyBarrick