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RNA-Binding Proteins

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miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.

PloS one 34637468
Formation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in t...
Bayes Theorem Databases, Genetic Humans Machine Learning MicroRNAs Protein Binding RNA-Binding Proteins User-Computer Interface
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PRPI-SC: an ensemble deep learning model for predicting plant lncRNA-protein interactions.

BMC bioinformatics 34429059
BACKGROUND: Plant long non-coding RNAs (lncRNAs) play vital roles in many biological processes mainly through interactions with RNA-binding protein (RBP). To understand the function of lncRNAs, a fundamental method is to identify which types of prote...
Computational Biology Deep Learning Neural Networks, Computer RNA-Binding Proteins RNA, Long Noncoding
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A novel lncRNA-protein interaction prediction method based on deep forest with cascade forest structure.

Scientific reports 34556758
Long noncoding RNAs (lncRNAs) regulate many biological processes by interacting with corresponding RNA-binding proteins. The identification of lncRNA-protein Interactions (LPIs) is significantly important to well characterize the biological functions...
Arabidopsis Computational Biology Datasets as Topic Humans Machine Learning RNA-Binding Proteins RNA, Long Noncoding Zea mays
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LGFC-CNN: Prediction of lncRNA-Protein Interactions by Using Multiple Types of Features through Deep Learning.

Genes 34828296
Long noncoding RNA (lncRNA) plays a crucial role in many critical biological processes and participates in complex human diseases through interaction with proteins. Considering that identifying lncRNA-protein interactions through experimental methods...
Animals Computational Biology Datasets as Topic Deep Learning Gene Regulatory Networks Humans Neural Networks, Computer Protein Interaction Maps RNA-Binding Proteins RNA, Long Noncoding
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Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture.

Briefings in bioinformatics 34415289
Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is ...
Algorithms Base Sequence Binding Sites Computational Biology Databases, Genetic Deep Learning Reproducibility of Results RNA-Binding Proteins RNA, Circular ROC Curve
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CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.

PLoS computational biology 35051187
Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism. Increasing evidence shows that circular RNAs can directly bind to RNA-binding proteins (RBP) and play an important role ...
Algorithms Animals Binding Sites Computational Biology Machine Learning Models, Biological Neural Networks, Computer RNA Splicing RNA-Binding Proteins RNA, Circular
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Protein-RNA interaction prediction with deep learning: structure matters.

Briefings in bioinformatics 34929730
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lac...
Algorithms Binding Sites Computational Biology Deep Learning Protein Conformation RNA RNA-Binding Proteins
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DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Briefings in bioinformatics 34905768
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
Computational Biology Deep Learning DNA DNA-Binding Proteins Humans Intrinsically Disordered Proteins Neural Networks, Computer Nucleic Acids Protein Binding Proteome RNA RNA-Binding Proteins
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EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network.

Bioinformatics (Oxford, England) 34694393
MOTIVATION: RNA-binding proteins (RBPs) are a group of proteins associated with RNA regulation and metabolism, and play an essential role in mediating the maturation, transport, localization and translation of RNA. Recently, Genome-wide RNA-binding e...
Algorithms Neural Networks, Computer RNA RNA-Binding Proteins Software
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iDRBP-EL: Identifying DNA- and RNA- Binding Proteins Based on Hierarchical Ensemble Learning.

IEEE/ACM transactions on computational biology and bioinformatics 34932484
Identification of DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) from the primary sequences is essential for further exploring protein-nucleic acid interactions. Previous studies have shown that machine-learning-based methods can efficie...
Algorithms Computational Biology Deep Learning DNA DNA-Binding Proteins Machine Learning RNA RNA-Binding Proteins
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