RNAlien – Unsupervised RNA family model construction

Ambivalent covariance models

(2015) Stefan Janssen et al.   BMC BIOINFORMATICS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: an international database of ncRNA sequences

(2014)   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

CMCompare webserver: comparing RNA families via covariance models

(2013) Florian Eggenhofer et al.   NUCLEIC ACIDS RESEARCH

RNA Binding Protein/RNA Element Interactions and the Control of Translation

(2012) Xavier Pichon et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of noncoding RNAs

(2012) Stefan Washietl et al.   Wiley Interdisciplinary Reviews-RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

(2011) J. Zhang et al.   Molecular Systems Biology

RNAcentral: A vision for an international database of RNA sequences

(2011) A. Bateman et al.   RNA

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Discriminatory power of RNA family models

(2010) C. H. z. Siederdissen et al.   BIOINFORMATICS

Nematode sbRNAs: Homologs of Vertebrate Y RNAs

(2010) Ilenia Boria et al.   JOURNAL OF MOLECULAR EVOLUTION

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Evolution of Vault RNAs

(2009) P. F. Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tedious task of finding homologous noncoding RNA genes

(2009) P. Menzel et al.   RNA

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Invertebrate 7SK snRNAs

(2008) Andreas R. Gruber et al.   JOURNAL OF MOLECULAR EVOLUTION

Arthropod 7SK RNA

(2008) A. R. Gruber et al.   MOLECULAR BIOLOGY AND EVOLUTION