Understanding the transcriptome through RNA structure
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have
largely been parsed by primary sequences and expression levels, but it is now becoming …
largely been parsed by primary sequences and expression levels, but it is now becoming …
[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 …
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
RNAs are fundamental in living cells and perform critical functions determined by their
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …
RNAalifold: improved consensus structure prediction for RNA alignments
Background The prediction of a consensus structure for a set of related RNAs is an important
first step for subsequent analyses. RNAalifold, which computes the minimum energy …
first step for subsequent analyses. RNAalifold, which computes the minimum energy …
Interpretable RNA foundation model from unannotated data for highly accurate RNA structure and function predictions
Non-coding RNA structure and function are essential to understanding various biological
processes, such as cell signaling, gene expression, and post-transcriptional regulations …
processes, such as cell signaling, gene expression, and post-transcriptional regulations …
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions
Accurate RNA structure models are crucial for designing small molecule ligands that
modulate their functions. This study assesses six standalone RNA 3D structure prediction …
modulate their functions. This study assesses six standalone RNA 3D structure prediction …
RNA snp: efficient detection of local RNA secondary structure changes induced by SNP s
R Sabarinathan, H Tafer, SE Seemann… - Human …, 2013 - Wiley Online Library
Structural characteristics are essential for the functioning of many noncoding RNA s and cis‐
regulatory elements of m RNA s. SNP s may disrupt these structures, interfere with their …
regulatory elements of m RNA s. SNP s may disrupt these structures, interfere with their …
[HTML][HTML] rMSA: a sequence search and alignment algorithm to improve RNA structure modeling
The multiple sequence alignment (MSA) is the entry point of many RNA structure modeling
tasks, such as prediction of RNA secondary structure (rSS) and contacts. However, there are …
tasks, such as prediction of RNA secondary structure (rSS) and contacts. However, there are …
Machine learning modeling of RNA structures: methods, challenges and future perspectives
The three-dimensional structure of RNA molecules plays a critical role in a wide range of
cellular processes encompassing functions from riboswitches to epigenetic regulation …
cellular processes encompassing functions from riboswitches to epigenetic regulation …
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks
Motivation Recent years have witnessed that the inter-residue contact/distance in proteins
could be accurately predicted by deep neural networks, which significantly improve the …
could be accurately predicted by deep neural networks, which significantly improve the …