AIMC Topic: 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...
Nucleotides Humans RNA, Messenger Computer Simulation RNA-Binding Proteins RNA Mutation Deep Learning Datasets as Topic Internet Nucleotide Motifs Base Sequence RNA, Viral RNA Splice Sites Bias Binding Sites Alleles Consensus Sequence
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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...
Neural Networks, Computer Computational Biology RNA-Binding Proteins Binding Sites 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 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...
Neural Networks, Computer RNA-Binding Proteins RNA Binding Sites RNA, Circular
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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...
RNA Base Sequence Deep Learning RNA-Binding Proteins Neural Networks, Computer
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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...
DNA-Binding Proteins RNA Computational Biology RNA-Binding Proteins DNA Algorithms Deep Learning Machine Learning
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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...
Mitochondrial Proteins TATA-Binding Protein Associated Factors DNA Methylation Carrier Proteins Genetic Markers RNA-Binding Proteins Nuclear Proteins Female Humans Breast Neoplasms Machine Learning Deep 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 ...
Machine Learning RNA-Binding Proteins RNA Sequence Analysis, RNA Neural Networks, Computer
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iDRBP-ECHF: Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework.

Computers in biology and medicine Aug 13, 2022
Proteins interact with nucleic acids to regulate the life activities of organisms. Therefore, how to accurately and efficiently identify nucleic acid-binding proteins (NABPs) is particularly significant. Some sequence-based computational methods have...
Algorithms Computational Biology Machine Learning DNA-Binding Proteins RNA-Binding Proteins Binding Sites DNA
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Predicting RBP Binding Sites of RNA With High-Order Encoding Features and CNN-BLSTM Hybrid Model.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
RNA binding protein (RBP) is extensively involved in various cellular regulatory processes through the interaction with RNAs. Capturing the RBP binding preferences is fundamental for revealing the pathogenesis of complex diseases. Many experimental d...
Binding Sites RNA-Binding Proteins RNA Neural Networks, Computer Protein Binding
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IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two important nucleic acid-binding proteins (NABPs), which play important roles in biological processes such as replication, translation and transcription of genetic material. Some prote...
DNA-Binding Proteins Algorithms Amino Acid Sequence Position-Specific Scoring Matrices RNA-Binding Proteins Databases, Protein Computational Biology Support Vector Machine DNA
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