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 …

Genomic benchmarks: a collection of datasets for genomic sequence classification

K Grešová, V Martinek, D Čechák, P Šimeček… - BMC Genomic …, 2023 - Springer
Background Recently, deep neural networks have been successfully applied in many
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 …

A Novel Predictor for the Analysis and Prediction of Enhancers and Their Strength via Multi-View Features and Deep Forest

M Gill, S Ahmed, M Kabir, M Hayat - Information, 2023 - mdpi.com
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 …

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 …

iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information

H Wu, M Liu, P Zhang, H Zhang - Briefings in Functional …, 2023 - academic.oup.com
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 …

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 …

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network

L Yao, P Xie, J Guan, CR Chung, Y Huang… - Journal of Chemical …, 2024 - ACS Publications
Enhancers are a class of noncoding DNA, serving as crucial regulatory elements in
governing gene expression by binding to transcription factors. The identification of …

W2V-repeated index: Prediction of enhancers and their strength based on repeated fragments

W Xie, Z Yao, Y Yuan, J Too, F Li, H Wang, Y Zhan… - Genomics, 2024 - Elsevier
Enhancers are crucial in gene expression regulation, dictating the specificity and timing of
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 …