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Wade C. Winkler, Ph.D. - Publications

Affiliations: 
Ohio State University, Columbus, Columbus, OH 
Area:
Regulation of gene expression
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60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kim SK, Orr MW, Turdiev H, Jenkins CC, Lormand JD, Myers TM, Burnim AA, Carter JA, Kung WC, Jiang X, Sondermann H, Winkler WC, Lee VT. Diribonuclease activity eliminates toxic diribonucleotide accumulation. Cell Reports. 43: 114759. PMID 39276351 DOI: 10.1016/j.celrep.2024.114759  0.461
2024 Elghondakly A, Jermain MD, Winkler WC, Ferré-D'Amaré AR. Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG. Structure (London, England : 1993). PMID 38959899 DOI: 10.1016/j.str.2024.06.001  0.562
2023 Myers TM, Ingle S, Weiss CA, Sondermann H, Lee VT, Bechhofer DH, Winkler WC. Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3'-5' exonuclease. Nucleic Acids Research. PMID 37650646 DOI: 10.1093/nar/gkad662  0.537
2022 Weiss CA, Myers TM, Wu CH, Jenkins C, Sondermann H, Lee VT, Winkler WC. NrnA is a 5'-3' exonuclease that processes short RNA substrates in vivo and in vitro. Nucleic Acids Research. PMID 36478094 DOI: 10.1093/nar/gkac1091  0.435
2022 Lee VT, Sondermann H, Winkler W. Nano-RNases: oligo- or dinucleases? Fems Microbiology Reviews. PMID 36026528 DOI: 10.1093/femsre/fuac038  0.332
2022 Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT. Correction: A dedicated diribonuclease resolves a key bottleneck for the terminal step of RNA degradation. Elife. 11. PMID 35088715 DOI: 10.7554/eLife.77091  0.467
2022 Papenfort K, Woodson SA, Schmitz RA, Winkler WC. Special Issue: Regulating with RNA in Microbes: In conjunction with the 6th Meeting on Regulating with RNA in Bacteria and Archaea. Molecular Microbiology. 117: 1-3. PMID 35040218 DOI: 10.1111/mmi.14867  0.499
2021 Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H. Structural characterization of NrnC identifies unifying features of dinucleotidases. Elife. 10. PMID 34533457 DOI: 10.7554/eLife.70146  0.417
2021 Elghondakly A, Hao Wu C, Klupt S, Goodson J, Winkler WC. A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity. Journal of Molecular Biology. 167100. PMID 34119489 DOI: 10.1016/j.jmb.2021.167100  0.591
2021 Weiss CA, Winkler WC. Riboswitch-Mediated Detection of Metabolite Fluctuations During Live Cell Imaging of Bacteria. Methods in Molecular Biology (Clifton, N.J.). 2323: 153-170. PMID 34086280 DOI: 10.1007/978-1-0716-1499-0_12  0.352
2020 Goodson JR, Zhang C, Trettel D, Ailinger HE, Lee PE, Spirito CM, Winkler WC. An Autoinhibitory Mechanism Controls RNA Binding Activity of the Nitrate-Sensing Protein NasR. Molecular Microbiology. PMID 32314426 DOI: 10.1111/Mmi.14517  0.588
2019 Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT. A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation. Elife. 8. PMID 31225796 DOI: 10.7554/Elife.46313  0.576
2019 Kaval KG, Gebbie M, Goodson JR, Cruz MR, Winkler WC, Garsin DA. Ethanolamine Utilization and Bacterial Microcompartment (BMC) Formation are Subject to Carbon Catabolite Repression (CCR). Journal of Bacteriology. PMID 30833356 DOI: 10.1128/Jb.00703-18  0.43
2019 Kim S, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT. Author response: A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation Elife. DOI: 10.7554/Elife.46313.053  0.536
2018 Orr MW, Weiss CA, Severin GB, Turdiev H, Kim SK, Turdiev A, Liu K, Tu BP, Waters CM, Winkler WC, Lee VT. A subset of exoribonucleases serve as degradative enzymes for pGpG in c-di-GMP signaling. Journal of Bacteriology. PMID 30249708 DOI: 10.1128/Jb.00300-18  0.399
2018 Goodson JR, Winkler WC. Processive Antitermination. Microbiology Spectrum. 6. PMID 30191803 DOI: 10.1128/microbiolspec.RWR-0031-2018  0.499
2017 Goodson JR, Klupt S, Zhang C, Straight P, Winkler WC. LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens. Nature Microbiology. 2: 17003. PMID 28191883 DOI: 10.1038/Nmicrobiol.2017.3  0.446
2015 Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Molecular Cell. 57: 1088-98. PMID 25794617 DOI: 10.1016/J.Molcel.2015.02.009  0.631
2014 DebRoy S, Gebbie M, Ramesh A, Goodson JR, Cruz MR, van Hoof A, Winkler WC, Garsin DA. Riboswitches. A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator. Science (New York, N.Y.). 345: 937-40. PMID 25146291 DOI: 10.1126/Science.1255091  0.676
2014 Shin JH, Wakeman CA, Goodson JR, Rodionov DA, Freedman BG, Senger RS, Winkler WC. Transport of magnesium by a bacterial Nramp-related gene. Plos Genetics. 10: e1004429. PMID 24968120 DOI: 10.1371/Journal.Pgen.1004429  0.732
2014 Ramesh A, Winkler WC. Metabolite-binding ribozymes. Biochimica Et Biophysica Acta. 1839: 989-994. PMID 24769284 DOI: 10.1016/J.Bbagrm.2014.04.015  0.666
2014 Wakeman CA, Goodson JR, Zacharia VM, Winkler WC. Assessment of the requirements for magnesium transporters in Bacillus subtilis. Journal of Bacteriology. 196: 1206-14. PMID 24415722 DOI: 10.1128/Jb.01238-13  0.713
2013 Dambach M, Irnov I, Winkler WC. Association of RNAs with Bacillus subtilis Hfq. Plos One. 8: e55156. PMID 23457461 DOI: 10.1371/Journal.Pone.0055156  0.83
2012 Ramesh A, DebRoy S, Goodson JR, Fox KA, Faz H, Garsin DA, Winkler WC. The mechanism for RNA recognition by ANTAR regulators of gene expression. Plos Genetics. 8: e1002666. PMID 22685413 DOI: 10.1371/Journal.Pgen.1002666  0.661
2012 McCown PJ, Winkler WC, Breaker RR. Mechanism and distribution of glmS ribozymes. Methods in Molecular Biology (Clifton, N.J.). 848: 113-29. PMID 22315066 DOI: 10.1007/978-1-61779-545-9_8  0.721
2012 Zacharia V, Lafontaine D, Winkler WC. RNA sensors of intracellular metabolites Regulatory Rnas in Prokaryotes. 195-220. DOI: 10.1007/978-3-7091-0218-3_11  0.381
2011 Ferré-D'Amaré AR, Winkler WC. The roles of metal ions in regulation by riboswitches. Metal Ions in Life Sciences. 9: 141-73. PMID 22010271 DOI: 10.1039/9781849732512-00141  0.35
2011 Ramesh A, Wakeman CA, Winkler WC. Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. Journal of Molecular Biology. 407: 556-70. PMID 21315082 DOI: 10.1016/J.Jmb.2011.01.049  0.797
2010 Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Research. 38: 6637-51. PMID 20525796 DOI: 10.1093/Nar/Gkq454  0.838
2010 Irnov I, Winkler WC. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Molecular Microbiology. 76: 559-75. PMID 20374491 DOI: 10.1111/J.1365-2958.2010.07131.X  0.814
2010 Ramesh A, Winkler WC. Magnesium-sensing riboswitches in bacteria. Rna Biology. 7: 77-83. PMID 20023416 DOI: 10.4161/Rna.7.1.10490  0.55
2009 Wakeman CA, Ramesh A, Winkler WC. Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs. Journal of Molecular Biology. 392: 723-35. PMID 19619558 DOI: 10.1016/J.Jmb.2009.07.033  0.803
2009 Wakeman CA, Winkler WC. Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension. Methods in Molecular Biology (Clifton, N.J.). 540: 173-91. PMID 19381560 DOI: 10.1007/978-1-59745-558-9_13  0.796
2009 Brautigam CA, Wakeman CA, Winkler WC. Methods for analysis of ligand-induced RNA conformational changes. Methods in Molecular Biology (Clifton, N.J.). 540: 77-95. PMID 19381554 DOI: 10.1007/978-1-59745-558-9_7  0.781
2009 Wakeman CA, Winkler WC. Structural probing techniques on natural aptamers. Methods in Molecular Biology (Clifton, N.J.). 535: 115-33. PMID 19377977 DOI: 10.1007/978-1-59745-557-2_8  0.784
2009 Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs. Current Opinion in Microbiology. 12: 161-9. PMID 19250859 DOI: 10.1016/J.Mib.2009.01.012  0.584
2009 Fox KA, Ramesh A, Stearns JE, Bourgogne A, Reyes-Jara A, Winkler WC, Garsin DA. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proceedings of the National Academy of Sciences of the United States of America. 106: 4435-40. PMID 19246383 DOI: 10.1073/Pnas.0812194106  0.547
2008 Attia AS, Sedillo JL, Wang W, Liu W, Brautigam CA, Winkler W, Hansen EJ. Moraxella catarrhalis expresses an unusual Hfq protein Infection and Immunity. 76: 2520-2530. PMID 18362134 DOI: 10.1128/Iai.01652-07  0.424
2007 Collins JA, Irnov I, Baker S, Winkler WC. Mechanism of mRNA destabilization by the glmS ribozyme. Genes & Development. 21: 3356-68. PMID 18079181 DOI: 10.1101/Gad.1605307  0.849
2007 Dann CE, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC. Structure and mechanism of a metal-sensing regulatory RNA. Cell. 130: 878-92. PMID 17803910 DOI: 10.1016/J.Cell.2007.06.051  0.815
2007 Wakeman CA, Winkler WC, Dann CE. Structural features of metabolite-sensing riboswitches. Trends in Biochemical Sciences. 32: 415-24. PMID 17764952 DOI: 10.1016/J.Tibs.2007.08.005  0.822
2007 Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nature Structural & Molecular Biology. 14: 308-17. PMID 17384645 DOI: 10.1038/Nsmb1224  0.808
2006 Irnov, Kertsburg A, Winkler WC. Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery. Cold Spring Harbor Symposia On Quantitative Biology. 71: 239-49. PMID 17381303 DOI: 10.1101/Sqb.2006.71.021  0.632
2006 Winkler WC, Dann CE. RNA allostery glimpsed. Nature Structural & Molecular Biology. 13: 569-71. PMID 16826230 DOI: 10.1038/Nsmb0706-569  0.609
2006 Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. Molecular-recognition characteristics of SAM-binding riboswitches. Angewandte Chemie (International Ed. in English). 45: 964-8. PMID 16381055 DOI: 10.1002/Anie.200503198  0.552
2005 Winkler WC. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Current Opinion in Chemical Biology. 9: 594-602. PMID 16226486 DOI: 10.1016/J.Cbpa.2005.09.016  0.604
2005 Winkler WC, Breaker RR. Regulation of bacterial gene expression by riboswitches. Annual Review of Microbiology. 59: 487-517. PMID 16153177 DOI: 10.1146/Annurev.Micro.59.030804.121336  0.747
2005 Wickiser JK, Winkler WC, Breaker RR, Crothers DM. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell. 18: 49-60. PMID 15808508 DOI: 10.1016/J.Molcel.2005.02.032  0.767
2005 Winkler WC. Metabolic monitoring by bacterial mRNAs. Archives of Microbiology. 183: 151-9. PMID 15750802 DOI: 10.1007/S00203-005-0758-9  0.694
2004 Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proceedings of the National Academy of Sciences of the United States of America. 101: 6421-6. PMID 15096624 DOI: 10.1073/Pnas.0308014101  0.806
2004 Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 428: 281-6. PMID 15029187 DOI: 10.1038/Nature02362  0.802
2003 Winkler WC, Breaker RR. Genetic control by metabolite-binding riboswitches. Chembiochem : a European Journal of Chemical Biology. 4: 1024-32. PMID 14523920 DOI: 10.1002/Cbic.200300685  0.709
2003 Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nature Structural Biology. 10: 701-7. PMID 12910260 DOI: 10.1038/Nsb967  0.869
2003 Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell. 113: 577-86. PMID 12787499 DOI: 10.1016/S0092-8674(03)00391-X  0.773
2002 Winkler WC, Cohen-Chalamish S, Breaker RR. An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences of the United States of America. 99: 15908-13. PMID 12456892 DOI: 10.1073/Pnas.212628899  0.688
2002 Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 419: 952-6. PMID 12410317 DOI: 10.1038/Nature01145  0.844
2002 Grundy FJ, Winkler WC, Henkin TM. tRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome Proceedings of the National Academy of Sciences of the United States of America. 99: 11121-11126. PMID 12165569 DOI: 10.1073/Pnas.162366799  0.777
2001 Winkler WC, Grundy FJ, Murphy BA, Henkin TM. The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs Rna. 7: 1165-1172. PMID 11497434 DOI: 10.1017/S1355838201002370  0.734
1997 Curnow AW, Hong Kw, Yuan R, Kim Si, Martins O, Winkler W, Henkin TM, Söll D. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proceedings of the National Academy of Sciences of the United States of America. 94: 11819-26. PMID 9342321 DOI: 10.1073/Pnas.94.22.11819  0.648
1996 Winkler WC, Gonzalez G, Wittenberg JB, Hille R, Dakappagari N, Jacob A, Gonzalez LA, Gilles-Gonzalez MA. Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the rhizobial heme-based oxygen sensor FixL. Chemistry & Biology. 3: 841-50. PMID 8939703 DOI: 10.1016/S1074-5521(96)90070-8  0.314
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