LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

BlastR—fast and accurate database searches for non-coding RNAs

(2011) Giovanni Bussotti et al.   NUCLEIC ACIDS RESEARCH

Selective Constraints in Conserved Folded RNAs of Drosophilid and Hominid Genomes

(2010) R. Piskol et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rfam: Wikipedia, clans and the "decimal" release

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

Lightweight comparison of RNAs based on exact sequence–structure matches

(2009) Steffen Heyne et al.   BIOINFORMATICS

Local RNA structure alignment with incomplete sequence

(2009) Diana L. Kolbe et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

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

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

Non-coding RNA annotation of the genome of Trichoplax adhaerens

(2009) J. Hertel et al.   NUCLEIC ACIDS RESEARCH

The tedious task of finding homologous noncoding RNA genes

(2009) P. Menzel et al.   RNA

Specific alignment of structured RNA: stochastic grammars and sequence annealing

(2008) Robert K. Bradley et al.   BIOINFORMATICS

Dinucleotide controlled null models for comparative RNA gene prediction

(2008) Tanja Gesell et al.   BMC BIOINFORMATICS

Strategies for measuring evolutionary conservation of RNA secondary structures

(2008) Andreas R Gruber et al.   BMC BIOINFORMATICS