AIMC Topic: RNA-Binding Proteins

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Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure.

BMC genomics Dec 17, 2020
BACKGROUND: RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification of RBP binding sites is a cru...
Protein Binding Neural Networks, Computer RNA-Binding Proteins Binding Sites RNA
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RBPsuite: RNA-protein binding sites prediction suite based on deep learning.

BMC genomics Dec 9, 2020
BACKGROUND: RNA-binding proteins (RBPs) play crucial roles in various biological processes. Deep learning-based methods have been demonstrated powerful on predicting RBP sites on RNAs. However, the training of deep learning models is very time-intens...
RNA Binding Sites Protein Binding Deep Learning RNA-Binding Proteins
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DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site.

Journal of biomolecular structure & dynamics Dec 4, 2020
It's important to infer the binding site of RNA-binding proteins (RBP) for understanding the interaction between RBP and its RNA targets and decipher the mechanisms of transcriptional regulation. However, experimental detection of RBP binding sites i...
RNA-Binding Proteins RNA Binding Sites Neural Networks, Computer Protein Binding
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Recent advances on the machine learning methods in predicting ncRNA-protein interactions.

Molecular genetics and genomics : MGG Oct 2, 2020
Recent transcriptomics and bioinformatics studies have shown that ncRNAs can affect chromosome structure and gene transcription, participate in the epigenetic regulation, and take part in diseases such as tumorigenesis. Biologists have found that mos...
Humans Machine Learning Gene Regulatory Networks RNA, Long Noncoding Computational Biology RNA-Binding Proteins
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iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.

Journal of molecular biology Sep 11, 2020
DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP reco...
RNA-Binding Proteins DNA-Binding Proteins Protein Binding Computational Biology RNA Binding Sites Humans Neural Networks, Computer Machine Learning
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Matrix factorization with neural network for predicting circRNA-RBP interactions.

BMC bioinformatics Jun 5, 2020
BACKGROUND: Circular RNA (circRNA) has been extensively identified in cells and tissues, and plays crucial roles in human diseases and biological processes. circRNA could act as dynamic scaffolding molecules that modulate protein-protein interactions...
RNA, Circular RNA-Binding Proteins Area Under Curve Cell Line, Tumor ROC Curve Humans Databases, Factual Neural Networks, Computer Neoplasms
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LPI-CNNCP: Prediction of lncRNA-protein interactions by using convolutional neural network with the copy-padding trick.

Analytical biochemistry May 23, 2020
Long noncoding RNAs (lncRNAs) play critical roles in many pathological and biological processes, such as post-transcription, cell differentiation and gene regulation. Increasingly more studies have shown that lncRNAs function through mainly interacti...
RNA, Long Noncoding Amino Acid Sequence Neural Networks, Computer RNA-Binding Proteins Humans
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Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction.

Genomics May 11, 2020
Long non-coding RNAs (lncRNAs) play key roles in regulating cellular biological processes through diverse molecular mechanisms including binding to RNA binding proteins. The majority of plant lncRNAs are functionally uncharacterized, thus, accurate p...
RNA, Plant Deep Learning Plant Proteins RNA, Long Noncoding Arabidopsis Zea mays RNA-Binding Proteins
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Deep neural networks for interpreting RNA-binding protein target preferences.

Genome research Jan 28, 2020
Deep learning has become a powerful paradigm to analyze the binding sites of regulatory factors including RNA-binding proteins (RBPs), owing to its strength to learn complex features from possibly multiple sources of raw data. However, the interpreta...
Nucleotide Motifs Humans Protein Binding Algorithms RNA-Binding Proteins Neural Networks, Computer Binding Sites Deep Learning
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Identifying Cancer-Specific circRNA-RBP Binding Sites Based on Deep Learning.

Molecules (Basel, Switzerland) Nov 7, 2019
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs...
RNA, Neoplasm Databases, Protein Deep Learning Binding Sites RNA, Circular Humans Neoplasm Proteins RNA-Binding Proteins Sequence Analysis, Protein Neoplasms
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