A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome
LT Phan, C Oh, T He, B Manavalan - Proteomics, 2023 - Wiley Online Library
Enhancers are non‐coding DNA elements that play a crucial role in enhancing the
transcription rate of a specific gene in the genome. Experiments for identifying enhancers …
transcription rate of a specific gene in the genome. Experiments for identifying enhancers …
Genomic benchmarks: a collection of datasets for genomic sequence classification
Background Recently, deep neural networks have been successfully applied in many
biological fields. In 2020, a deep learning model AlphaFold won the protein folding …
biological fields. In 2020, a deep learning model AlphaFold won the protein folding …
DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome
T Zhang, L Li, H Sun, G Wang - Bioinformatics, 2023 - academic.oup.com
Motivation Enhancers are vital cis-regulatory elements that regulate gene expression.
Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer …
Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer …
A Novel Predictor for the Analysis and Prediction of Enhancers and Their Strength via Multi-View Features and Deep Forest
Enhancers are short DNA segments (50–1500 bp) that effectively activate gene transcription
when transcription factors (TFs) are present. There is a correlation between the genetic …
when transcription factors (TFs) are present. There is a correlation between the genetic …
iEnhancer-DCSA: identifying enhancers via dual-scale convolution and spatial attention
W Wang, Q Wu, C Li - BMC genomics, 2023 - Springer
Background Due to the dynamic nature of enhancers, identifying enhancers and their
strength are major bioinformatics challenges. With the development of deep learning …
strength are major bioinformatics challenges. With the development of deep learning …
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information
Enhancers, a class of distal cis-regulatory elements located in the non-coding region of
DNA, play a key role in gene regulation. It is difficult to identify enhancers from DNA …
DNA, play a key role in gene regulation. It is difficult to identify enhancers from DNA …
Enhancer-LSTMAtt: a Bi-LSTM and attention-based deep learning method for enhancer recognition
G Huang, W Luo, G Zhang, P Zheng, Y Yao, J Lyu… - Biomolecules, 2022 - mdpi.com
Enhancers are short DNA segments that play a key role in biological processes, such as
accelerating transcription of target genes. Since the enhancer resides anywhere in a …
accelerating transcription of target genes. Since the enhancer resides anywhere in a …
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network
Enhancers are a class of noncoding DNA, serving as crucial regulatory elements in
governing gene expression by binding to transcription factors. The identification of …
governing gene expression by binding to transcription factors. The identification of …
W2V-repeated index: Prediction of enhancers and their strength based on repeated fragments
Enhancers are crucial in gene expression regulation, dictating the specificity and timing of
transcriptional activity, which highlights the importance of their identification for unravelling …
transcriptional activity, which highlights the importance of their identification for unravelling …
EnhancerBD identifing sequence feature
Y Wang - bioRxiv, 2024 - biorxiv.org
Deciphering the non-coding language of DNA is one of the fundamental questions in
genomic research. Previous bioinformatics methods often struggled to capture this …
genomic research. Previous bioinformatics methods often struggled to capture this …