A comprehensive comparison of general RNA–RNA interaction prediction methods

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

(2015) Sebastian Will et al.   BIOINFORMATICS

An assessment of bacterial small RNA target prediction programs

(2015) Adrien Pain et al.   RNA Biology

RNA-RNA interaction prediction using genetic algorithm

(2014) Soheila Montaseri et al.   Algorithms for Molecular Biology

Assessing the efficiency of multiple sequence alignment programs

(2014) Fabiano Sviatopolk-Mirsky Pais et al.   Algorithms for Molecular Biology

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

(2014) Muhammad Tariq Pervez et al.   Evolutionary Bioinformatics

Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)

(2014) Aleksandra Helwak et al.   Nature Protocols

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast

(2014) Daniel A. Medina et al.   Frontiers in Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative genomics boosts target prediction for bacterial small RNAs

(2013) P. R. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

(2012) Anne Wenzel et al.   BIOINFORMATICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

R- chie : a web server and R package for visualizing RNA secondary structures

(2012) Daniel Lai et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

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

Accessibility and conservation: General features of bacterial small RNA–mRNA interactions?

(2012) Andreas Richter et al.   RNA Biology

RNA Accessibility in cubic time

(2011) Stephan H Bernhart et al.   Algorithms for Molecular Biology

ViennaRNA Package 2.0

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

Fast accessibility-based prediction of RNA–RNA interactions

(2011) Hakim Tafer et al.   BIOINFORMATICS

Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions

(2011) A. Peer et al.   JOURNAL OF BACTERIOLOGY

RNApredator: fast accessibility-based prediction of sRNA targets

(2011) Florian Eggenhofer et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

PLEXY: efficient target prediction for box C/D snoRNAs

(2010) Stephanie Kehr et al.   BIOINFORMATICS

RNA–RNA interaction prediction based on multiple sequence alignments

(2010) Andrew X. Li et al.   BIOINFORMATICS

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

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

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

(2010) Yuki Kato et al.   BIOINFORMATICS

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen et al.   RNA Biology

sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments

(2010) Y. Cao et al.   RNA

RNAsnoop: efficient target prediction for H/ACA snoRNAs

(2009) Hakim Tafer et al.   BIOINFORMATICS

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

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

(2009) Parvez Anandam et al.   BIOINFORMATICS

Lost in translation: an assessment and perspective for computational microRNA target identification

(2009) Panagiotis Alexiou et al.   BIOINFORMATICS

Non-coding RNA annotation of the genome of Trichoplax adhaerens

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

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

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Predicting novel RNA–RNA interactions

(2008) Irmtraud M Meyer   CURRENT OPINION IN STRUCTURAL BIOLOGY

Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

(2008) J. L. Knies et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE