Convolutional neural networks (CNNs): Concepts and applications in pharmacogenomics
JM Vaz, S Balaji - Molecular diversity, 2021 - Springer
Convolutional neural networks (CNNs) have been used to extract information from various
datasets of different dimensions. This approach has led to accurate interpretations in several …
datasets of different dimensions. This approach has led to accurate interpretations in several …
Recent methodology progress of deep learning for RNA–protein interaction prediction
Interactions between RNAs and proteins play essential roles in many important biological
processes. Benefitting from the advances of next generation sequencing technologies …
processes. Benefitting from the advances of next generation sequencing technologies …
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
Modelling both primary sequence and secondary structure preferences for RNA binding
proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure …
proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure …
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP
Background Crosslinking and immunoprecipitation (CLIP) is a method used to identify in
vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts …
vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts …
Sodium butyrate induces ferroptosis in endometrial cancer cells via the RBM3/SLC7A11 axis
Z Wang, W Shu, R Zhao, Y Liu, H Wang - Apoptosis, 2023 - Springer
Ferroptosis is a form of programmed cell death with important biological functions in the
progression of various diseases, and targeting ferroptosis is a new tumor treatment strategy …
progression of various diseases, and targeting ferroptosis is a new tumor treatment strategy …
RBPmap: a tool for mapping and predicting the binding sites of RNA-binding proteins considering the motif environment
I Paz, A Argoetti, N Cohen, N Even… - Post-Transcriptional …, 2022 - Springer
RNA-binding proteins (RBPs) play a key role in post-transcriptional regulation via binding to
coding and non-coding RNAs. Recent development in experimental technologies, aimed to …
coding and non-coding RNAs. Recent development in experimental technologies, aimed to …
Pseudo-RNA-binding domains mediate RNA structure specificity in upstream of N-Ras
NM Hollmann, PKA Jagtap, P Masiewicz, T Guitart… - Cell Reports, 2020 - cell.com
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs),
which provide these proteins with a modular architecture. Accumulating evidence supports …
which provide these proteins with a modular architecture. Accumulating evidence supports …
BRIO: a web server for RNA sequence and structure motif scan
The interaction between RNA and RNA-binding proteins (RBPs) has a key role in the
regulation of gene expression, in RNA stability, and in many other biological processes …
regulation of gene expression, in RNA stability, and in many other biological processes …
RNA-centric approaches to study RNA-protein interactions in vitro and in silico
Given their central role in translation, splicing, localization and stability of transcripts, RNA
binding proteins (RBPs) are key regulators of several cellular processes. While experimental …
binding proteins (RBPs) are key regulators of several cellular processes. While experimental …
Discovering sequence and structure landscapes in RNA interaction motifs
RNA molecules are able to bind proteins, DNA and other small or long RNAs using
information at primary, secondary or tertiary structure level. Recent techniques that use cross …
information at primary, secondary or tertiary structure level. Recent techniques that use cross …