Evolutionary conservation of RNA sequence and structure
E Rivas - Wiley Interdisciplinary Reviews: RNA, 2021 - Wiley Online Library
An RNA structure prediction from a single‐sequence RNA folding program is not evidence
for an RNA whose structure is important for function. Random sequences have plausible …
for an RNA whose structure is important for function. Random sequences have plausible …
[HTML][HTML] Predicting RNA secondary structures from sequence and probing data
RNA secondary structures have proven essential for understanding the regulatory functions
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
Motivation The secondary structure of RNA is of importance to its function. Over the last few
years, several papers attempted to use machine learning to improve de novo RNA …
years, several papers attempted to use machine learning to improve de novo RNA …
RNA structure prediction using positive and negative evolutionary information
E Rivas - PLoS computational biology, 2020 - journals.plos.org
Knowing the structure of conserved structural RNAs is important to elucidate their function
and mechanism of action. However, predicting a conserved RNA structure remains …
and mechanism of action. However, predicting a conserved RNA structure remains …
Modeling RNA secondary structure folding ensembles using SHAPE mapping data
RNA secondary structure prediction is widely used for developing hypotheses about the
structures of RNA sequences, and structure can provide insight about RNA function. The …
structures of RNA sequences, and structure can provide insight about RNA function. The …
Computational analysis of conserved RNA secondary structure in transcriptomes and genomes
SR Eddy - Annual review of biophysics, 2014 - annualreviews.org
Transcriptomics experiments and computational predictions both enable systematic
discovery of new functional RNAs. However, many putative noncoding transcripts arise …
discovery of new functional RNAs. However, many putative noncoding transcripts arise …
RNA folding with hard and soft constraints
Background A large class of RNA secondary structure prediction programs uses an
elaborate energy model grounded in extensive thermodynamic measurements and exact …
elaborate energy model grounded in extensive thermodynamic measurements and exact …
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data
Recently, several experimental techniques have emerged for probing RNA structures based
on high-throughput sequencing. However, most secondary structure prediction tools that …
on high-throughput sequencing. However, most secondary structure prediction tools that …
A functional riboSNitch in the 3′ untranslated region of FKBP5 alters microRNA-320a binding efficiency and mediates vulnerability to chronic post-traumatic pain
SD Linnstaedt, KD Riker, CA Rueckeis… - Journal of …, 2018 - Soc Neuroscience
Previous studies have shown that common variants of the gene coding for FK506-binding
protein 51 (FKBP5), a critical regulator of glucocorticoid sensitivity, affect vulnerability to …
protein 51 (FKBP5), a critical regulator of glucocorticoid sensitivity, affect vulnerability to …
Using SHAPE-MaP to model RNA secondary structure and identify 3′ UTR variation in Chikungunya virus
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating
arthralgia in humans. RNA secondary structure in the viral genome plays an important role …
arthralgia in humans. RNA secondary structure in the viral genome plays an important role …