Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. 2019. Single cell microscopy reveals that levels of cyclic di-GMP vary among Bacillus subtilis subpopulations. J Bacteriol In press.

Kaval KG, Gebbie M, Goodson JR, Cruz MR, Winkler WC, Garsin DA. 2019. Ethanolamine utilization and bacterial microcompartment formation are subject to carbon catabolite repression. J Bacteriol 201: pii: 200703-18. Doi: 10.1128/JB.00703-18

Orr MW, Weiss CA, Severin GB, Turdiev H, Kim SK, Turdiev A, Liu K, Tu BP, Waters CM, Winkler WC, Lee VT. 2018. A subset of exoribonucleases serves as degradative enzymes for pGpG in c-di-GMP signalling. J Bacteriol 200 pii: e00300-18. Doi: 10.1128/JB.00300-18

Kaval KG, Singh KV, Cruz MR, DebRoy S, Winkler WC, Murray BE, Garsin DA. 2018. Loss of ethanolamine utilization in Enterococcus faecalis increases gastrointestinal tract colonization. MBio 9(3) pii: e00790-18. Doi: 10.1128/mBio.00790-18.

Goodson JR, Winkler WC. 2018. Processive Antitermination. Microbiol Spectr 6(5) doi: 10.1128/microbiolspec.RWR-0031-2018

Goodson JR, Klupt S, Zhang C, Straight P, Winkler WC. 2017. LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens.. Nature Microbiology 2:170003 Discussed in an accompanying commentary article: Nodwell JR. 2017. Antimicrobials: Expressing antibiotic gene clusters. Nature Microbiology 2:17061

Winkler WC. 2017. RNA-mediated regulation in Bacillus subtilis. In: Bacillus: Cellular and Molecular Biology (3rd Edition; Editor: Peter Graumann) Caister Academic Press, U.K. (pp. 155-190)

Furukawa K+, Ramesh A+, Zhou Z+, Weinberg Z, Vallery T, Winkler WC, Breaker RR. 2015. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Molecular Cell 57:1088-1098 (+=equal contribution; *=co-corresponding authors) Discussed in the description of the cover art for the issue.

DebRoy, S+, Gebbie M+, Ramesh A, Goodson JR, Cruz MR, van Hoof A, Winkler WC, Garsin DA 2014. A Riboswitch-Containing sRNA Controls Gene Expression by Sequestration of a Response Regulator. Science. 345:937-40. (+=equal contribution; *=co-corresponding authors) Discussed in an accompanying commentary article: Chen J, Gottesman S. 2014. Riboswitch regulates RNA. Science 345:876-7.

Shin JH, Wakeman CA, Goodson JR, Rodionov DA, Freedman BG, Senger RS, Winkler WC. 2014. Transport of magnesium by a bacterial Nramp-like protein. PLoS Genetics. 10:e1004429.

Wakeman CA, Goodson JR, Zacharia VM, Winkler WC. 2014. An Assessment of the requirement for magnesium transporters in Bacillus subtilis. J Bacteriol 196:1206-1214

Ramesh A, Winkler WC. 2014. Metabolite-binding ribozymes. Biochim Biophys Acta: Gene Regulatory Mechanisms 1839:989-994

Dambach M, Irnov I, Goodson JR, Winkler WC. 2013. Association of RNAs with Bacillus subtilis Hfq. PLoS One. 8:e55156

Ramesh A+, DebRoy S+, Goodson JR, Fox KA, Faz H, Garsin DA, Winkler WC. 2012. The mechanism for RNA recognition by ANTAR regulators of gene expression. PLoS Genetics. 8:e1002666 (+=equal contribution; *=co-corresponding authors) Discussed in an accompanying commentary article: Stewart V, van Tilbeurgh H. 2012. Found: the elusive ANTAR transcription antiterminator. PLoS Genetics 8:e1002773.

McCown P, Winkler WC, Breaker RR. 2012. Mechanism and distribution of glmS ribozymes. Methods Mol Biol. 848:113-29.

Winkler WC. 2012. RNA-mediated regulation in Bacillus subtilis. In: Bacillus: Cellular and Molecular Biology (2nd Edition; Editor: Peter Graumann) Caister Academic Press, U.K. (pp. 151-186)

Ramesh A, Wakeman CA, Winkler WC. 2011. Insights into metalloregulation by M box riboswitches via structural analysis of manganese-bound complexes. J Mol Biol 407:556-570 (*=co-corresponding authors)

Ferré D’Amare A, Winkler WC. 2011. The roles of metal ions in regulation by riboswitches. In: Metal Ions in Life Sciences. (Eds. Helmut Sigel, Astrid Sigel, Roland Sigel). 9:141-173.

Irnov I, Sharma CM, Vogel J, Winkler WC. 2010. Identification of noncoding and regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 38:6637-6651

Irnov I, Winkler WC. 2010. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide genes in Bacillales. Mol Microbiol 76:559-575 Discussed in an accompanying commentary article: Artsimovitch I. 2010. A processive riboantiterminator seeks a switch to make biofilms. Mol Microbiology 76:535-9

Ramesh A, Winkler WC. 2010. Magnesium-sensing riboswitches in bacteria. RNA Biology Jan 1; 7:77-83

Wakeman CA, Ramesh A, Winkler WC. 2009. Multiple metal binding sites are required for metalloregulation by M box riboswitch RNAs. J Mol Biol 392:723-35

Wakeman CA, Winkler WC. 2009. Analysis of the RNA backbone: Structural analysis of riboswitches by in-line probing and selective 2’-hydroxyl acylation and primer extension (SHAPE). Methods Mol Biol 540:173-91

Brautigam CA, Wakeman CA, Winkler WC. 2009. Methods for analysis of ligand-induced RNA conformational changes. Methods Mol Biol. 540:77-95

Wakeman CA, Winkler WC. 2009. Structural probing techniques for natural aptamers. Methods Mol Biol. 535:115-33

Dambach M, Winkler WC. 2009. Expanding roles for metabolite-sensing RNAs. Curr Opin Microbiol 12:161-9

Fox KA+, Ramesh A+, Stearns JE, Bourgogne A, Reyes A, Winkler WC, Garsin DA. 2008. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc Natl Acad Sci USA. 106:4435-4440. (+=equal contribution; *=co-corresponding authors)

Attia AS, Sedillo JL, Wang W, Liu W, Brautigam CA, Winkler W, Hansen EJ. 2008. Moraxella catarrhalis expresses an unusual Hfq protein. Infect Immun 76:2520-2530

Collins JA+, Irnov I+, Baker SC, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes & Dev 21(24): 3356-3368 (+=equal contribution)

Dann CE 3rd+, Wakeman CA+, Sieling, CL, Baker SC, Imov I, Winkler WC. 2007. Structure and mechanism of a metal-sensing regulatory RNA. Cell. 130:878-892 (+=equal contribution) Discussed in an accompanying commentary: Helmann JD. 2007. Measuring metals with RNA. Molecular Cell 27:859-60.

Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwick A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. 2007. A riboswitch selective for the queuosine precursor preQ(1) contains an unusually small aptamer domain. Nat Struct Mol Biol 14:308-317

Winkler WC. 2007. RNA-mediated regulation in Bacillus subtilis. In: Bacillus: Cellular and Molecular Biology (1st Edition; Editor: Peter Graumann) Caister Academic Press, U.K. (pp. 167-214)

Wakeman CA, Winkler WC, Dann CE 3rd. 2007. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci. 32:415-424

Irnov, Kertsburg A, Winkler WC. 2006. Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: General principles and prospects for discovery. Cold Spring Harb Quant Biol 71:239-249

Winkler WC, Dann CE 3rd#,. 2006. RNA allostery glimpsed. Nat Struct Mol Biol 13:569-571

Wickiser JK, Winkler WC, Breaker RR, Crothers D. 2005. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell 18:49-60

Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. 2005. Molecular-recognition characteristics of SAM-binding riboswitches. Agnew Chem Int Ed Engl. 45:964-968

Winkler WC, Breaker RR. 2005. Regulation of bacterial gene expression by riboswitches. Annual Review of Microbiology 59:487-517

Winkler WC. 2005. Metabolic monitoring by bacterial mRNAs. Archives in Microbiology 183:151-159

Winkler WC. 2005. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 9:594-602

Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. 2004. RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci USA. 101:6421-6426

Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. 2004. Control of bacterial gene expression by a natural metabolite-responsive ribozyme. Nature 428:281-286

Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nature Structural Biology 10:701-707

Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. 2003. Metabolite-sensing riboswitches control fundamental biochemical pathways in bacteria. Cell 113:577-586

Winkler WC, Breaker RR. 2003. Genetic control by metabolite-binding riboswitches. ChemBioChem. 4:1024-1032

Winkler WC, Cohen-Chalamish S, Breaker RR. 2002. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci USA 99:15908-15913

Winkler W, Nahvi A, Breaker RR. 2002. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956

Grundy FJ, Winkler WC, Henkin TM. 2002. tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome. Proc Natl Acad Sci USA. 99:11121-11126 Winkler WC, Grundy FJ, Murphy BA, Henkin TM. 2001. The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 7:1165-1172

Curnow AW, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin TM, Söll D. 1997. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc Natl Acad Sci USA 94:11819-11826

Winkler WC, Gonzalez G, Wittenberg JB, Hille R, Dakappagari N, Jacob A, Gonzalez LA, Gilles-Gonzalez MA. 1996. Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the Rhizobial heme-based oxygen sensor FixL. Chemistry and Biology 3:841-850

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