The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been...
Read More »Summer School on RNA-protein interactions RNA Structure and Biology workshop
October 2–6 2017 CEITEC MU, University Campus Bohunice Kamenice 5, Brno, Czech Republic The objective of the summer school is to provide participants with an overview on the most up-to-date topics in RNA research. The lectures from leading experts in ...
Read More »RNA Structure Framework – automatic transcriptome-scale reconstruction of RNA structures from probing data
The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of ...
Read More »Probing RNA Structure in Cells Using Targeted Structure-Seq
Models for how lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into ...
Read More »RNA-Seq workflow for comprehensive profiling of reverse transcription encounters with m1A
The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here researchers from the ...
Read More »RNA structure from deep sequencing
from Nature Biotechnology by Eric Westhof Solving the three-dimensional structure of an RNA molecule means laborious study by X-ray crystallography or nuclear magnetic resonance spectroscopy. However, faster complementary methods are on the horizon, many involving deep sequencing and sophisticated computational ...
Read More »RNAcop – optimizing RNA structures by sequence extensions
A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to ...
Read More »The RNA structurome – transcriptome-wide structure probing with next-generation sequencing
Transcriptome-wide RNA structure probing coupled with NGS yields the RNA structurome. RNA structurome data tremendously improve prediction of in vivo RNA structure. RNA structurome data uncover relationships between RNA structure and gene regulation. RNA folds into intricate structures that enable ...
Read More »Finding RNA Thermometers with Next-Gen Sequencing
Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, the authors ...
Read More »RNA-Seq and RNA Structure Prediction
by Xiaole Shirley Liu RNA-seq Experiments Analysis: read mapping, expression index, isoform inference, differential expression RNA structure prediction Covariance model Base-pair maximization Free energy method
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