Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. - Elena Rivas; Sean R. Eddy (Bioinform., 2000)

The language of RNA: a formal grammar that includes pseudoknots. - Elena Rivas; Sean R. Eddy (Bioinform., 2000)

Noncoding RNA gene detection using comparative sequence analysis. - Elena Rivas; Sean R. Eddy (BMC Bioinform., 2001)

Evolutionary models for insertions and deletions in a probabilistic modeling framework. - Elena Rivas (BMC Bioinform., 2005)

Probabilistic Phylogenetic Inference with Insertions and Deletions. - Elena Rivas; Sean R. Eddy (PLoS Comput. Biol., 2008)

Parameterizing sequence alignment with an explicit evolutionary model. - Elena Rivas; Sean R. Eddy (BMC Bioinform., 2015)

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. - Ioanna Kalvari; Joanna Argasinska; Natalia Quinones-Olvera; Eric P. Nawrocki; Elena Rivas; Sean R. Eddy; Alex Bateman; Robert D. Finn; Anton I. Petrov (Nucleic Acids Res., 2018)

Estimating the power of sequence covariation for detecting conserved RNA structure. - Elena Rivas; Jody Clements; Sean R. Eddy (Bioinform., 2020)

RNA structure prediction using positive and negative evolutionary information. - Elena Rivas (PLoS Comput. Biol., 2020)

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)

RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure. - Elena Rivas (PLoS Comput. Biol., 2023)