DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape

P Ding, Y Wang, X Zhang, X Gao, G Liu… - Briefings in …, 2023 - academic.oup.com
Precise targeting of transcription factor binding sites (TFBSs) is essential to comprehending
transcriptional regulatory processes and investigating cellular function. Although several …

TBCA: Prediction of transcription factor binding sites using a deep neural network with lightweight attention mechanism

X Wang, L Qiao, P Qu, Q Yang - IEEE Journal of Biomedical …, 2024 - ieeexplore.ieee.org
The identification of transcription factor binding sites (TFBSs) is crucial for understanding the
regulatory mechanisms of gene expression, which contributes to unraveling cellular …

A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape

Y Zhang, Z Wang, Y Zeng, Y Liu, S Xiong… - Briefings in …, 2022 - academic.oup.com
The discovery of putative transcription factor binding sites (TFBSs) is important for
understanding the underlying binding mechanism and cellular functions. Recently, many …

An integrative framework for combining sequence and epigenomic data to predict transcription factor binding sites using deep learning

F Jing, SW Zhang, Z Cao… - IEEE/ACM transactions on …, 2019 - ieeexplore.ieee.org
Knowing the transcription factor binding sites (TFBSs) is essential for modeling the
underlying binding mechanisms and follow-up cellular functions. Convolutional neural …

Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture

S Wang, Q Zhang, Z Shen, Y He, ZH Chen, J Li… - … Therapy-Nucleic Acids, 2021 - cell.com
The study of transcriptional regulation is still difficult yet fundamental in molecular biology
research. Recent research has shown that the double helix structure of nucleotides plays an …

Base-resolution prediction of transcription factor binding signals by a deep learning framework

Q Zhang, Y He, S Wang, Z Chen, Z Guo… - PLoS computational …, 2022 - journals.plos.org
Transcription factors (TFs) play an important role in regulating gene expression, thus the
identification of the sites bound by them has become a fundamental step for molecular and …

Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction

Y Yu, P Ding, H Gao, G Liu, F Zhang… - Briefings in …, 2023 - academic.oup.com
Interactions between DNA and transcription factors (TFs) play an essential role in
understanding transcriptional regulation mechanisms and gene expression. Due to the large …

High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method

Y Zhang, Z Wang, Y Zeng, J Zhou… - Briefings in …, 2021 - academic.oup.com
Transcription factors (TFs) are essential proteins in regulating the spatiotemporal expression
of genes. It is crucial to infer the potential transcription factor binding sites (TFBSs) with high …

Locating transcription factor binding sites by fully convolutional neural network

Q Zhang, S Wang, Z Chen, Y He, Q Liu… - Briefings in …, 2021 - academic.oup.com
Transcription factors (TFs) play an important role in regulating gene expression, thus
identification of the regions bound by them has become a fundamental step for molecular …

Prediction of transcription factor binding sites using a combined deep learning approach

L Cao, P Liu, J Chen, L Deng - Frontiers in Oncology, 2022 - frontiersin.org
In the process of regulating gene expression and evolution, such as DNA replication and
mRNA transcription, the binding of transcription factors (TFs) to TF binding sites (TFBS) …