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RNA-Binding Proteins

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CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization.

BMC bioinformatics 37254080
BACKGROUND: Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-reaching implications for the p...
Binding Sites Computational Biology Neural Networks, Computer RNA-Binding Proteins RNA, Circular
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CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion.

Interdisciplinary sciences, computational life sciences 37233959
Circular RNAs (circRNAs) participate in the regulation of biological processes by binding to specific proteins and thus influence transcriptional processes. In recent years, circRNAs have become an emerging hotspot in RNA research. Due to powerful le...
Binding Sites Neural Networks, Computer RNA RNA-Binding Proteins RNA, Circular
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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning.

Genome biology 37542318
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and m...
Alleles Base Sequence Bias Binding Sites Computer Simulation Consensus Sequence Datasets as Topic Deep Learning Humans Internet Mutation Nucleotide Motifs Nucleotides RNA RNA Splice Sites RNA-Binding Proteins RNA, Messenger RNA, Viral
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WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics 37028092
RNA-binding proteins are important for the process of cell life activities. High-throughput technique experimental method to discover RNA-protein binding sites is time-consuming and expensive. Deep learning is an effective theory for predicting RNA-p...
Binding Sites Deep Learning Protein Binding RNA RNA-Binding Proteins
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DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues.

Computers in biology and medicine 38295475
DNA-binding and RNA-binding proteins are essential to an organism's normal life cycle. These proteins have diverse functions in various biological processes. DNA-binding proteins are crucial for DNA replication, transcription, repair, packaging, and ...
Algorithms Amino Acids Computational Biology Databases, Protein DNA DNA-Binding Proteins Machine Learning RNA RNA-Binding Proteins
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Predicting circRNA-RBP Binding Sites Using a Hybrid Deep Neural Network.

Interdisciplinary sciences, computational life sciences 38381315
Circular RNAs (circRNAs) are non-coding RNAs generated by reverse splicing. They are involved in biological process and human diseases by interacting with specific RNA-binding proteins (RBPs). Due to traditional biological experiments being costly, c...
Binding Sites Computational Biology Deep Learning Humans Neural Networks, Computer RNA-Binding Proteins RNA, Circular
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DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Bioinformatics (Oxford, England) 38317052
MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through intera...
Animals Computational Biology Deep Learning Humans Mice Nucleotide Motifs RNA RNA-Binding Proteins RNA, Messenger
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EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins.

The protein journal 38491248
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
Algorithms Binding Sites Computational Biology Databases, Protein DNA DNA-Binding Proteins Humans Machine Learning Protein Binding RNA RNA-Binding Proteins
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MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling.

IEEE/ACM transactions on computational biology and bioinformatics 38363672
RNA-binding proteins (RBPs) can regulate biological functions by interacting with specific RNAs, and play an important role in many life activities. Therefore, the rapid identification of RNA-protein binding sites is crucial for functional annotation...
Algorithms Binding Sites Computational Biology Neural Networks, Computer RNA RNA-Binding Proteins
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Study of prognostic splicing factors in cancer using machine learning approaches.

Human molecular genetics 38538560
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing ...
Alternative Splicing Biomarkers, Tumor Carcinoma, Hepatocellular Computational Biology Gene Expression Regulation, Neoplastic Humans Liver Neoplasms Machine Learning Neoplasms Prognosis RNA Splicing RNA Splicing Factors RNA-Binding Proteins RNA, Messenger
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