ArticleBMC bioinformatics2022
iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Genomic language model for predicting enhancers and their allele-specific activity in the human genome.Bioinformatics (Oxford, England) · 2026Article
- Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models.Bioinformatics (Oxford, England) · 2026Article
- ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia.Genome biology · 2025Article
- DeepPlantAllergy: deep learning for explainable prediction of allergenicity in plant proteins.Briefings in bioinformatics · 2025Article
- AttnW2V-Enhancer: Leveraging attention and Word2Vec for enhanced enhancer prediction.Computational and structural biotechnology journal · 2025Article
- DNA sequence analysis landscape: a comprehensive review of DNA sequence analysis task types, databases, datasets, word embedding methods, and language models.Frontiers in medicine · 2025Review
- DeepEnhancerPPO: An Interpretable Deep Learning Approach for Enhancer Classification.International journal of molecular sciences · 2024Article
- Application progress of deep generative models in de novo drug design.Molecular diversity · 2024Review
- AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors.Molecules (Basel, Switzerland) · 2024Review
- A deep learning model for DNA enhancer prediction based on nucleotide position aware feature encoding.iScience · 2024Article
- ADH-Enhancer: an attention-based deep hybrid framework for enhancer identification and strength prediction.Briefings in bioinformatics · 2024Article
- Meta-2OM: A multi-classifier meta-model for the accurate prediction of RNA 2'-O-methylation sites in human RNA.PloS one · 2024Article
- A deep learning-based model (DeepMPM) to help predict survival in patients with malignant pleural mesothelioma.Translational cancer research · 2023Article
- PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks.Animals : an open access journal from MDPI · 2023Article
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Authors and funding
4 authors.
Funding
Abstract
Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be acted on, because the entanglement structure of chromatin allows the positions far apart in the sequence to have the opportunity to contact each other. Therefore, identifying enhancers and their strength is a complex and challenging task. In this article, a new prediction method based on deep learning is proposed to identify enhancers and enhancer strength, called iEnhancer-DCLA. Firstly, we use word2vec to convert k-mers into number vectors to construct an input matrix. Secondly, we use convolutional neural network and bidirectional long short-term memory network to extract sequence features, and finally use the attention mechanism to extract relatively important features. In the task of predicting enhancers and their strengths, this method has improved to a certain extent in most evaluation indexes. In summary, we believe that this method provides new ideas in the analysis of enhancers.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.