ArticleNucleic acids research2023
A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Sequence-Based Models for RNA-Protein Interactions Imputation Might Be Insufficient for Novel Signal Prediction in eCLIP Data.International journal of molecular sciences · 2026Article
- EDEN: multiscale expected density of nucleotide encoding for enhanced DNA sequence classification with hybrid deep learning.BMC bioinformatics · 2026Article
- BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.Communications biology · 2025Article
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Aquimarina rhodophyticola sp. nov. and Aquimarina besae sp. nov., Isolated from Marine Red Algae.Current microbiology · 2025Article
- BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network.Briefings in bioinformatics · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Machine learning-augmented m6A-Seq analysis without a reference genome.Briefings in bioinformatics · 2025Article
- FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.
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Registered trials
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