Genomics enters the deep learning era
E Routhier, J Mozziconacci - PeerJ, 2022 - peerj.com
The tremendous amount of biological sequence data available, combined with the recent
methodological breakthrough in deep learning in domains such as computer vision or …
methodological breakthrough in deep learning in domains such as computer vision or …
[HTML][HTML] Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA
Background The accurate identification of the exon/intron boundaries is critical for the
correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) …
correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) …
An automated framework for evaluation of deep learning models for splice site predictions
A novel framework for the automated evaluation of various deep learning-based splice site
detectors is presented. The framework eliminates time-consuming development and …
detectors is presented. The framework eliminates time-consuming development and …
Prediction of N6-methyladenosine sites using convolution neural network model based on distributed feature representations
Abstract N 6-methyladenosine (m 6 A) is a well-studied and most common interior
messenger RNA (mRNA) modification that plays an important function in cell development …
messenger RNA (mRNA) modification that plays an important function in cell development …
From shallow to deep: some lessons learned from application of machine learning for recognition of functional genomic elements in human genome
B Jankovic, T Gojobori - Human Genomics, 2022 - Springer
Identification of genomic signals as indicators for functional genomic elements is one of the
areas that received early and widespread application of machine learning methods. With …
areas that received early and widespread application of machine learning methods. With …
Deep splicer: A CNN model for splice site prediction in genetic sequences
E Fernandez-Castillo, LI Barbosa-Santillán… - Genes, 2022 - mdpi.com
Many living organisms have DNA in their cells that is responsible for their biological
features. DNA is an organic molecule of two complementary strands of four different …
features. DNA is an organic molecule of two complementary strands of four different …
Neurotis: Enhancing the prediction of translation initiation sites in mrna sequences via a hybrid dependency network and deep learning framework
C Wei, J Zhang, X Yuan, Z He, G Liu, J Wu - Knowledge-Based Systems, 2021 - Elsevier
Translation initiation site prediction is crucial to understand the mechanisms of gene
expression and regulation. Many computational approaches have been proposed and …
expression and regulation. Many computational approaches have been proposed and …
[HTML][HTML] CNNSplice: Robust models for splice site prediction using convolutional neural networks
V Akpokiro, HMAM Chowdhury, S Olowofila… - Computational and …, 2023 - Elsevier
The identification of splice site, or segments of an RNA gene where noncoding and coding
sequences are connected in the 5′ and 3′ directions, is an essential post-transcriptional …
sequences are connected in the 5′ and 3′ directions, is an essential post-transcriptional …
AttentionSplice: An Interpretable Multi‐Head Self‐Attention Based Hybrid Deep Learning Model in Splice Site Prediction
W YAN, B ZHANG, M ZUO, Q ZHANG… - Chinese Journal of …, 2022 - Wiley Online Library
Pre‐mRNA splicing is an essential procedure for gene transcription. Through the cutting of
introns and exons, the DNA sequence can be decoded into different proteins related to …
introns and exons, the DNA sequence can be decoded into different proteins related to …
Deep multi-label joint learning for RNA and DNA-binding proteins prediction
X Du, J Hu - IEEE/ACM Transactions on Computational Biology …, 2022 - ieeexplore.ieee.org
The recognition of DNA-(DBPs) and RNA-binding proteins (RBPs) is not only conducive to
understanding cell function, but also a challenging task. Previous studies have shown that …
understanding cell function, but also a challenging task. Previous studies have shown that …