2021

K. I. Brewer, Gaffield, G. J., Puri, M., and Breaker, R. R., “DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria”, Bioinformatics, 2021. [Link]
K. I. Brewer, Greenlee, E. B., Higgs, G., Yu, D., G Arachchilage, M., Chen, X., King, N., White, N., and Breaker, R. R., “Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes”, RNA Biol, 2021. [Link]
Y. Yang, Harris, K. A., Widner, D., and Breaker, R. R., “Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex”, Proc Natl Acad Sci U S A, vol. 118(9), 2021. [Link]
S. S. S. Panchapakesan and Breaker, R. R., “The case of the missing allosteric ribozymes”, Nat Chem Biol, 2021. [Link]

2020

H. Salvail, Balaji, A., Yu, D., Roth, A., and Breaker, R., “Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria”, Biochemistry, 2020. [Link]
S. S. S. Panchapakesan, Corey, L., Malkowski, S. N., Higgs, G., and Breaker, R. R., “A Second Riboswitch Class for the Enzyme Cofactor NAD”, RNA, 2020. [Link]
D. Yu and Breaker, R. R., “A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation”, RNA, vol. 26, no. 8, p. 960, 2020. [Link]
R. R. Breaker, “Imaginary Ribozymes”, ACS Chem Biol, vol. 15, no. 8, p. 2020, 2020. [Link]
S. N. Malkowski, Atilho, R. M., Greenlee, E. B., weinberg, C., and Breaker, R. R., “A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine”, RNA, 2020. [Link]
M. E. Sherlock and Breaker, R. R., “Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes”, RNA, vol. 26, no. 6, p. 675, 2020. [Link]
D. Widner, Harris, K. A., Corey, L., and Breaker, R. R., “Bacillus halodurans OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE”, J Biol Chem, vol. 295, no. 28, p. 9326, 2020. [Link]

2019

K. Perkins, Atilho, R. M., Moon, M. H., and Breaker, R. R., “Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen”, ACS Chem. Biol., vol. 14, p. 9, 2019. [Link]
S. N. Malkowski, TCJ, S., and Breaker, R. R., “Evidence that the nadA Motif is a Bacterial Riboswitch for the Ubiquitous Enzyme Cofactor NAD”, RNA, 2019. [Link]
K. A. Harris, Odzer, N., and Breaker, R. R., “Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans”, Molecular Microbiology, 2019. [Link]
X. Chen, G Arachchilage, M., and Breaker, R. R., “Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria”, RNA, 2019. [Link]
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]
M. E. Sherlock, Sadeeshkumar, H., and Breaker, R. R., “Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates”, Biochemistry, 2018. [Link]

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