2019

R. M. Atilho, G Arachchilage, M., Greenlee, E. B., Knecht, K. M., and Breaker, R. R., “A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer”, eLife, 2019. [Link]
M. G Arachchilage, Atilho, R. M., Stav, S., Higgs, G., and Breaker, R. R., “Genome-wide Discovery of Rare Riboswitches in Bacteria”, FASEB, vol. 33, 2019. [Link]
S. Stav, Atilho, R. M., G Arachchilage, M., Nguyen, G., Higgs, G., and Breaker, R. R., “Genome-wide discovery of structured noncoding RNAs in bacteria”, BMC Microbiology, vol. 19, no. 66, 2019. [Link]

2018

R. M. Atilho, Perkins, K., and Breaker, R. R., “Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity.”, RNA, 2018. [Link]
S. Klahn, Bolay, P., Wright, P. R., Atilho, R. M., Brewer, K. I., Hagemann, M., Breaker, R. R., and Hess, W. R., “A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria”, Nucleic Acids Research, 2018. [Link]
M. E. Sherlock, Sadeeshkumar, H., and Breaker, R. R., “Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates”, Biochemistry, 2018. [Link]
K. A. Harris and Breaker, R. R., “Large noncoding RNAs in bacteria”, Microbiol Spectr, vol. 6, no. 4, 2018. [Link]
M. E. Sherlock, Sudarsan, N., and Breaker, R. R., “Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems”, PNAS, vol. 115, no. 23, p. 5, 2018. [Link]
K. A. Harris and Breaker, R. R., “A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex.”, Proc Natl Acad Sci USA, 2018. [Link]
R. R. Breaker, “Riboswitches and Translation Control.”, CSH Perspectives, 2018. [Link]
E. B. Greenlee, Stav, S., Atilho, R. M., Brewer, K. I., Harris, K. A., Malkowski, S. N., Mirihana-Arachchilage, G., Perkins, K., Sherlock, M. E., and Breaker, R. R., “Challenges of ligand identification for the second wave of orphan riboswitch candidates”, RNA Biol, vol. 15, no. 3, 2018. [Link]
M. E. Sherlock, Sudarsan, N., Stav, S., and Breaker, R. R., “Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria”, eLife, vol. 5, no. 7, 2018. [Link]
G. Mirihana-Arachchilage, Sherlock, M. E., Weinberg, Z., and Breaker, R. R., “SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches”, RNA Biol, vol. 15, no. 3, 2018. [Link]

2017

S. Li and Breaker, R. R., “Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics”, BMC Genomics, vol. 18, no. 1, 2017. [Link]
Z. Weinberg, Lünse, C. E., Corbino, K., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K., Sherlock, M. E., and Breaker, R. R., “Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions”, Nucleic Acids Research, 2017. [Link]
J. W. Nelson and Breaker, R. R., “The lost language of the RNA World”, Science Signaling, vol. 10, no. 483, 2017. [Link]
R. Nagdhi M, K, S., Wang, J. X., Wade, F., Breaker, R. R., and Perreault, J., “Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database”, Methods, 2017. [Link]
Z. Weinberg, Nelson, J. W., Lünse, C. E., Sherlock, M. E., and Breaker, R. R., “Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity”, Proc Natl Acad Sci USA, 2017. [Link]
R. R. Breaker, “Mechanistic Debris Generated by Twister Ribozymes”, ACS Chem Biol, 2017. [Link]
M. E. Sherlock and Breaker, R. R., “Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria”, Biochemistry, 2017. [Link]

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