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Elena Rivas
Researcher at Harvard University
Publications - 46
Citations - 4602
Elena Rivas is an academic researcher from Harvard University. The author has contributed to research in topics: Fermion & Gene. The author has an hindex of 18, co-authored 42 publications receiving 3784 citations. Previous affiliations of Elena Rivas include Washington University in St. Louis & Howard Hughes Medical Institute.
Papers
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Journal ArticleDOI
A dynamic programming algorithm for RNA structure prediction including pseudoknots
Elena Rivas,Sean R. Eddy +1 more
TL;DR: This is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model and a useful graphical representation borrowed from quantum field theory is adopted.
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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 +8 more
TL;DR: This paper introduces Rfam release 13.0, which switches to a new genome-centric approach that annotates a non-redundant set of reference genomes with RNA families, and describes new web interface features including faceted text search and R-scape secondary structure visualizations.
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Noncoding RNA gene detection using comparative sequence analysis
Elena Rivas,Sean R. Eddy +1 more
TL;DR: A comparative sequence analysis algorithm for detecting novel structural RNA genes by test the pattern of substitutions observed in a pairwise alignment of two homologous sequences to suggest that this approach detects noncoding RNA genes with a fair degree of reliability.
Journal ArticleDOI
Computational identification of noncoding RNAs in E. coli by comparative genomics.
TL;DR: A computational comparative genomic screen for ncRNA genes is described, to distinguish conserved RNA secondary structures from a background of other conserved sequences using probabilistic models of expected mutational patterns in pairwise sequence alignments.
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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,Sean R. Eddy,Robert D. Finn,Alex Bateman,Anton I. Petrov +15 more
TL;DR: The first phase of synchronising microRNA families in Rfam and miRBase is completed, creating 356 new Rfam families and updating 40, and a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs is established.