Coronavirus cis-acting RNA elements

R Madhugiri, M Fricke, M Marz, J Ziebuhr - Advances in virus research, 2016 - Elsevier
Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases.
Genome replication and transcription is mediated by a multisubunit protein complex …

[HTML][HTML] Recent advances in RNA folding

J Fallmann, S Will, J Engelhardt, B Grüning… - Journal of …, 2017 - Elsevier
In the realm of nucleic acid structures, secondary structure forms a conceptually important
intermediate level of description and explains the dominating part of the free energy of …

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

M Mann, PR Wright, R Backofen - Nucleic acids research, 2017 - academic.oup.com
The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by
incorporating seed constraints and interaction site accessibility. Here, we introduce …

[HTML][HTML] NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs

S Hussain, AA Sajini, S Blanco, S Dietmann… - Cell reports, 2013 - cell.com
Autosomal-recessive loss of the NSUN2 gene has been identified as a causative link to
intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying …

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

PR Wright, J Georg, M Mann, DA Sorescu… - Nucleic acids …, 2014 - academic.oup.com
CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset
to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the …

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

OA Soutourina, M Monot, P Boudry, L Saujet… - PLoS …, 2013 - journals.plos.org
Clostridium difficile is an emergent pathogen, and the most common cause of nosocomial
diarrhea. In an effort to understand the role of small noncoding RNAs (sRNAs) in C. difficile …

Comparative genomics boosts target prediction for bacterial small RNAs

PR Wright, AS Richter, K Papenfort… - Proceedings of the …, 2013 - National Acad Sciences
Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene
expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target …

ModeRNA: a tool for comparative modeling of RNA 3D structure

M Rother, K Rother, T Puton… - Nucleic acids research, 2011 - academic.oup.com
RNA is a large group of functionally important biomacromolecules. In striking analogy to
proteins, the function of RNA depends on its structure and dynamics, which in turn is …

TGF-β mediates renal fibrosis via the Smad3-Erbb4-IR long noncoding RNA axis

M Feng, PMK Tang, XR Huang, SF Sun, YK You… - Molecular Therapy, 2018 - cell.com
Transforming growth factor β (TGF-β)/Smad3 signaling plays a role in tissue fibrosis. We
report here that Erbb4-IR is a novel long non-coding RNA (lncRNA) responsible for TGF …

The ViennaRNA web services

AR Gruber, SH Bernhart, R Lorenz - RNA bioinformatics, 2015 - Springer
The ViennaRNA package is a widely used collection of programs for thermodynamic RNA
secondary structure prediction. Over the years, many additional tools have been developed …