AIMC Topic: RNA-Binding Proteins

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DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleic acids research Jul 27, 2020
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling...
Computational Biology RNA-Binding Proteins Mutation Protein Binding Mice Nucleic Acid Conformation Binding Sites Nucleotide Motifs RNA Base Sequence Humans Animals Deep Learning Computer Simulation
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Recent Advances on the Semi-Supervised Learning for Long Non-Coding RNA-Protein Interactions Prediction: A Review.

Protein and peptide letters Jan 1, 2020
In recent years, more and more evidence indicates that long non-coding RNA (lncRNA) plays a significant role in the development of complex biological processes, especially in RNA progressing, chromatin modification, and cell differentiation, as well ...
Humans Protein Binding RNA-Binding Proteins RNA, Long Noncoding Software Computer Simulation Models, Molecular Supervised Machine Learning Proteins Databases, Protein Databases, Nucleic Acid
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Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.

Bioinformatics (Oxford, England) Dec 1, 2019
MOTIVATION: In recent years, multiple circular RNAs (circRNA) biogenesis mechanisms have been discovered. Although each reported mechanism has been experimentally verified in different circRNAs, no single biogenesis mechanism has been proposed that c...
RNA, Circular RNA Splicing RNA Splice Sites Machine Learning RNA-Binding Proteins Humans
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Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data.

Bioinformatics (Oxford, England) Sep 15, 2019
MOTIVATION: Network analysis and unsupervised machine learning processing of single-molecule localization microscopy of caveolin-1 (Cav1) antibody labeling of prostate cancer cells identified biosignatures and structures for caveolae and three distin...
Caveolae Caveolin 1 RNA-Binding Proteins Prostatic Neoplasms Machine Learning Male Humans
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Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions.

Protein and peptide letters Jan 1, 2019
The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to det...
Molecular Dynamics Simulation RNA Nucleic Acid Conformation Hydrophobic and Hydrophilic Interactions Computational Biology Machine Learning RNA-Binding Proteins Algorithms
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A deep neural network approach for learning intrinsic protein-RNA binding preferences.

Bioinformatics (Oxford, England) Sep 1, 2018
MOTIVATION: The complexes formed by binding of proteins to RNAs play key roles in many biological processes, such as splicing, gene expression regulation, translation and viral replication. Understanding protein-RNA binding may thus provide important...
Neural Networks, Computer Software RNA-Binding Proteins RNA Deep Learning
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A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data.

Nucleic acids research Aug 21, 2017
Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-s...
Binding, Competitive 3' Untranslated Regions Binding Sites Nucleotide Motifs Computational Biology RNA-Binding Proteins Reproducibility of Results Protein Binding High-Throughput Nucleotide Sequencing Gene Expression Regulation Base Sequence Mutation Internet Machine Learning Algorithms Humans
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RBPPred: predicting RNA-binding proteins from sequence using SVM.

Bioinformatics (Oxford, England) Mar 15, 2017
MOTIVATION: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computationa...
Computational Biology Humans Support Vector Machine RNA-Binding Proteins RNA Software
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