AIMC Topic: RNA-Binding Proteins

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Predicting circRNA-RBP Binding Sites Using a Hybrid Deep Neural Network.

Interdisciplinary sciences, computational life sciences Feb 21, 2024
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...
Humans Neural Networks, Computer RNA-Binding Proteins Binding Sites RNA, Circular Deep Learning Computational Biology
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DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues.

Computers in biology and medicine Jan 29, 2024
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 ...
RNA Amino Acids Algorithms DNA-Binding Proteins Machine Learning Databases, Protein RNA-Binding Proteins Computational Biology DNA
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WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
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...
Deep Learning RNA Binding Sites Protein Binding RNA-Binding Proteins
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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning.

Genome biology Aug 4, 2023
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...
RNA Datasets as Topic Base Sequence Alleles Nucleotides RNA Splice Sites Consensus Sequence Binding Sites Nucleotide Motifs RNA-Binding Proteins Bias Internet RNA, Viral Mutation Computer Simulation Deep Learning RNA, Messenger Humans
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CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization.

BMC bioinformatics May 30, 2023
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...
RNA, Circular Computational Biology RNA-Binding Proteins Neural Networks, Computer Binding Sites
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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 May 26, 2023
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...
RNA, Circular Neural Networks, Computer RNA Binding Sites RNA-Binding Proteins
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CRMSNet: A deep learning model that uses convolution and residual multi-head self-attention block to predict RBPs for RNA sequence.

Proteins Mar 28, 2023
RNA-binding proteins (RBPs) play significant roles in many biological life activities, many algorithms and tools are proposed to predict RBPs for researching biological mechanisms of RNA-protein binding sites. Deep learning algorithms based on tradit...
Neural Networks, Computer RNA-Binding Proteins RNA Deep Learning Base Sequence
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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 Feb 3, 2023
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...
RNA RNA-Binding Proteins DNA DNA-Binding Proteins Machine Learning Deep Learning Algorithms Computational Biology
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Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers.

Genes Aug 29, 2022
DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to t...
TATA-Binding Protein Associated Factors Deep Learning Genetic Markers RNA-Binding Proteins Mitochondrial Proteins DNA Methylation Carrier Proteins Female Humans Nuclear Proteins Breast Neoplasms Machine Learning
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De novo prediction of RNA-protein interactions with graph neural networks.

RNA (New York, N.Y.) Aug 25, 2022
RNA-binding proteins (RBPs) are key co- and post-transcriptional regulators of gene expression, playing a crucial role in many biological processes. Experimental methods like CLIP-seq have enabled the identification of transcriptome-wide RNA-protein ...
Neural Networks, Computer RNA Machine Learning RNA-Binding Proteins Sequence Analysis, RNA
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