IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions

Ten Simple Rules for Developing Usable Software in Computational Biology

(2017) Markus List et al.   PLoS Computational Biology

A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

(2016) Sinan Uğur Umu et al.   BIOINFORMATICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA

(2015) Bastien Cayrol et al.   Integrative Biology

A comprehensive comparison of general RNA–RNA interaction prediction methods

(2015) Daniel Lai et al.   NUCLEIC ACIDS RESEARCH

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

(2015) Stephan Klähn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An assessment of bacterial small RNA target prediction programs

(2015) Adrien Pain et al.   RNA Biology

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression

(2015) Marta Robledo et al.   PLoS Genetics

The iron-sensing aconitase B binds its own mRNA to prevent sRNA-induced mRNA cleavage

(2014) Julie-Anna M. Benjamin et al.   NUCLEIC ACIDS RESEARCH

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

(2014) Patrick R. Wright et al.   NUCLEIC ACIDS RESEARCH

Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region

(2014) Aaron Overlöper et al.   RNA Biology

Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA

(2014) Qi Yang et al.   PLoS Genetics

Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification

(2013) Kyung Moon et al.   MOLECULAR MICROBIOLOGY

The sRNA RyhB Regulates the Synthesis of the Escherichia coli Methionine Sulfoxide Reductase MsrB but Not MsrA

(2013) Julia Bos et al.   PLoS One

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

Post-Transcriptional Control of the Escherichia coli PhoQ-PhoP Two-Component System by Multiple sRNAs Involves a Novel Pairing Region of GcvB

(2013) Audrey Coornaert et al.   PLoS Genetics

Multiple factors dictate target selection by Hfq-binding small RNAs

(2012) Chase L Beisel et al.   EMBO JOURNAL

A complex network of small non-coding RNAs regulate motility inEscherichia coli

(2012) Nicholas De Lay et al.   MOLECULAR MICROBIOLOGY

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

The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli

(2011) Chase L. Beisel et al.   MOLECULAR CELL

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations

(2010) D. T. Starczynowski et al.   BLOOD

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen et al.   RNA Biology

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner 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