AIMC Topic: Enhancer Elements, Genetic
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A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information.
Briefings in bioinformatics
Sep 2, 2021
Recently, language representation models have drawn a lot of attention in the natural language processing field due to their remarkable results. Among them, bidirectional encoder representations from transformers (BERT) has proven to be a simple, yet...
Identification of haploinsufficient genes from epigenomic data using deep forest.
Briefings in bioinformatics
Sep 2, 2021
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...
Predicting enhancer-promoter interactions by deep learning and matching heuristic.
Briefings in bioinformatics
Jul 20, 2021
Enhancer-promoter interactions (EPIs) play an important role in transcriptional regulation. Recently, machine learning-based methods have been widely used in the genome-scale identification of EPIs due to their promising predictive performance. In th...
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.
Bioinformatics (Oxford, England)
Jul 12, 2021
MOTIVATION: Mapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods wit...
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network.
Bioinformatics (Oxford, England)
Jan 15, 2020
MOTIVATION: Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expres...
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