PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Fast prediction of RNA-RNA interaction

(2010) Raheleh Salari et al.   Algorithms for Molecular Biology

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

(2010) Stefan E Seemann et al.   Algorithms for Molecular Biology

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen et al.   RNA Biology

Partition function and base pairing probabilities for RNA–RNA interaction prediction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

A partition function algorithm for interacting nucleic acid strands

(2009) Hamidreza Chitsaz et al.   BIOINFORMATICS

Local RNA structure alignment with incomplete sequence

(2009) Diana L. Kolbe et al.   BIOINFORMATICS

Target prediction and a statistical sampling algorithm for RNA–RNA interaction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

(2009) Yanga Byun et al.   BIOINFORMATICS

Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

(2009) Andreas S. Richter et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Non-coding RNA annotation of the genome of Trichoplax adhaerens

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

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence

(2009) Richard S. P. Horler et al.   NUCLEIC ACIDS RESEARCH

The tedious task of finding homologous noncoding RNA genes

(2009) P. Menzel et al.   RNA

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

(2007) E. Torarinsson et al.   GENOME RESEARCH