AIMC Topic: RNA-Binding Proteins

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Recent methodology progress of deep learning for RNA-protein interaction prediction.

Wiley interdisciplinary reviews. RNA May 8, 2019
Interactions between RNAs and proteins play essential roles in many important biological processes. Benefitting from the advances of next generation sequencing technologies, hundreds of RNA-binding proteins (RBP) and their associated RNAs have been r...
Deep Learning RNA-Binding Proteins RNA
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RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks.

IEEE/ACM transactions on computational biology and bioinformatics Apr 11, 2019
RNA-Protein binding plays important roles in the field of gene expression. With the development of high throughput sequencing, several conventional methods and deep learning-based methods have been proposed to predict the binding preference of RNA-pr...
Protein Binding Computational Biology RNA-Binding Proteins RNA Neural Networks, Computer Binding Sites Algorithms
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SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.

PLoS computational biology Dec 11, 2018
LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. Existing computational ...
Humans Machine Learning Databases, Protein Computational Biology Amino Acid Sequence Base Sequence Databases, Nucleic Acid Algorithms RNA-Binding Proteins RNA Processing, Post-Transcriptional RNA, Long Noncoding Protein Binding
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Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning.

Scientific reports Oct 15, 2018
RNA binding protein (RBP) plays an important role in cellular processes. Identifying RBPs by computation and experiment are both essential. Recently, an RBP predictor, RBPPred, is proposed in our group to predict RBPs. However, RBPPred is too slow fo...
Databases, Protein Amino Acid Sequence RNA-Binding Proteins Sequence Analysis, Protein Machine Learning Proteome Neural Networks, Computer Deep Learning Algorithms Computational Biology Sensitivity and Specificity
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Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network.

BMC bioinformatics Oct 11, 2018
BACKGROUND: Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interaction...
Neural Networks, Computer Computer Simulation Databases, Genetic RNA, Long Noncoding RNA-Binding Proteins
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Combining High Speed ELM Learning with a Deep Convolutional Neural Network Feature Encoding for Predicting Protein-RNA Interactions.

IEEE/ACM transactions on computational biology and bioinformatics Oct 5, 2018
Emerging evidence has shown that RNA plays a crucial role in many cellular processes, and their biological functions are primarily achieved by binding with a variety of proteins. High-throughput biological experiments provide a lot of valuable inform...
Algorithms Protein Interaction Maps RNA-Binding Proteins Neural Networks, Computer Machine Learning Caenorhabditis elegans Proteins RNA Protein Interaction Mapping
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Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.

BMC genomics Jul 3, 2018
BACKGROUND: RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs are still not well characterized. Interdependencies between sequence ...
Algorithms User-Computer Interface Computational Biology RNA-Binding Proteins Neural Networks, Computer Protein Binding Binding Sites Nucleotide Motifs RNA Nucleic Acid Conformation
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

Scientific reports Jun 22, 2018
RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these meth...
Amino Acid Sequence Machine Learning RNA Protein Binding Computational Biology RNA-Binding Proteins
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HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy.

RNA biology Jun 6, 2018
LncRNA plays an important role in many biological and disease progression by binding to related proteins. However, the experimental methods for studying lncRNA-protein interactions are time-consuming and expensive. Although there are a few models des...
RNA-Binding Proteins Sequence Analysis, RNA Support Vector Machine Databases, Nucleic Acid Humans RNA, Long Noncoding Models, Biological
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DotAligner: identification and clustering of RNA structure motifs.

Genome biology Dec 28, 2017
The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable nature of RNA structure predictions further e...
RNA, Untranslated Cluster Analysis Genomics Nucleic Acid Conformation RNA Base Sequence Computational Biology Algorithms Nucleotide Motifs RNA-Binding Proteins Reproducibility of Results
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