An Approximate Search Engine for Structural Databases. - Jason Tsong-Li Wang; Xiong Wang; Dennis E. Shasha; Bruce A. Shapiro; Kaizhong Zhang; Xinhuan Zheng; Qicheng Ma; Zasha Weinberg (SIGMOD Conference, 2000)

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. - Zasha Weinberg; Walter L. Ruzzo (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Faster genome annotation of non-coding RNA families without loss of accuracy. - Zasha Weinberg; Walter L. Ruzzo (RECOMB, 2004)

Accurate annotation of non-coding RNAs in practical time. - Zasha Weinberg (2005)

Sequence-based heuristics for faster annotation of non-coding RNA families. - Zasha Weinberg; Walter L. Ruzzo (Bioinform., 2006)

CMfinder - a covariance model based RNA motif finding algorithm. - Zizhen Yao; Zasha Weinberg; Walter L. Ruzzo (Bioinform., 2006)

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 (APBC, 2008)

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)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families. - Ioanna Kalvari; Eric P. Nawrocki; Nancy Ontiveros-Palacios; Joanna Argasinska; Kevin Lamkiewicz; Manja Marz; Sam Griffiths-Jones; Claire Toffano-Nioche; Daniel Gautheret; Zasha Weinberg; Elena Rivas; Sean R. Eddy; et al. (Nucleic Acids Res., 2021)

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. - Blake A. Sweeney; Anton I. Petrov; Carlos Eduardo Ribas; Robert D. Finn; Alex Bateman; Maciej Szymanski; Wojciech M. Karlowski; Stefan E. Seemann; Jan Gorodkin; Jamie J. Cannone; Robin Ray Gutell; Simon Kay; et al. (Nucleic Acids Res., 2021)