AIMC Topic: RNA-Binding Proteins

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A deep learning framework to predict binding preference of RNA constituents on protein surface.

Nature communications Oct 30, 2019
Protein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes...
Phosphates Uracil Guanine RNA, Small Interfering RNA Argonaute Proteins Cytosine Ribose Gene Knockdown Techniques Adenine Ribonuclease III Deep Learning ROC Curve Protein Binding Mice RNA-Binding Proteins Area Under Curve Humans Animals
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Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature.

IEEE/ACM transactions on computational biology and bioinformatics Sep 24, 2019
RNA-Protein binding is involved in many different biological processes. With the progress of technology, more and more data are available for research. Based on these data, many prediction methods have been proposed to predict RNA-Protein binding pre...
Algorithms Computational Biology RNA-Binding Proteins Neural Networks, Computer RNA
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econvRBP: Improved ensemble convolutional neural networks for RNA binding protein prediction directly from sequence.

Methods (San Diego, Calif.) Sep 9, 2019
RNA binding proteins (RBPs) determine RNA process from synthesis to decay, which play a key role in RNA transport, translation and degradation. Therefore, exploring RBPs' function from the amino acid sequence using computational methods has become on...
RNA-Binding Proteins Amino Acid Sequence RNA Deep Learning Computational Biology Sequence Analysis, Protein Datasets as Topic Binding Sites
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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...
RNA Deep Learning RNA-Binding Proteins
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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...
Computational Biology RNA-Binding Proteins RNA Binding Sites Neural Networks, Computer Algorithms Protein Binding
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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 ...
Databases, Nucleic Acid RNA Processing, Post-Transcriptional Computational Biology RNA-Binding Proteins RNA, Long Noncoding Databases, Protein Machine Learning Humans Amino Acid Sequence Algorithms Base Sequence 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...
Sensitivity and Specificity Deep Learning Computational Biology Neural Networks, Computer Amino Acid Sequence RNA-Binding Proteins Machine Learning Sequence Analysis, Protein Algorithms Proteome Databases, Protein
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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...
Databases, Genetic Neural Networks, Computer RNA, Long Noncoding Computer Simulation 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...
Machine Learning Algorithms Protein Interaction Maps RNA-Binding Proteins RNA Protein Interaction Mapping Neural Networks, Computer Caenorhabditis elegans Proteins
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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 ...
RNA-Binding Proteins User-Computer Interface Binding Sites Neural Networks, Computer RNA Protein Binding Nucleotide Motifs Algorithms Nucleic Acid Conformation Computational Biology
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