A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. - Zizhen Yao; Jeffrey E. Barrick; Zasha Weinberg; Shane J. Neph; Ronald R. Breaker; Martin Tompa; Walter L. Ruzzo (PLoS Comput. Biol., 2007)

Finding Non-Coding RNAs through genome-Scale Clustering. - Huei-Hun Elizabeth Tseng; Zasha Weinberg; Jeremy Gore; Ronald R. Breaker; Walter L. Ruzzo (J. Bioinform. Comput. Biol., 2009)

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. - Zasha Weinberg; Ronald R. Breaker (BMC Bioinform., 2011)

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations. - Jonathan Perreault; Zasha Weinberg; Adam Roth; Olivia Popescu; Pascal Chartrand; Gerardo Ferbeyre; Ronald R. Breaker (PLoS Comput. Biol., 2011)

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. - Kenneth I Brewer; Glenn J. Gaffield; Malavika Puri; Ronald R. Breaker (Bioinform., 2022)