Base-resolution prediction of transcription factor binding signals by a deep learning framework
Zhang, Qinhu, He, Ying, Wang, Siguo, Chen, Zhanheng, Guo, Zhenhao, Cui, Zhen, Liu, Qi, Huang, De-Shuang
Published in PLoS computational biology (01.03.2022)
Published in PLoS computational biology (01.03.2022)
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Journal Article
Prediction of Back-splicing sites for CircRNA formation based on convolutional neural networks
Shen, Zhen, Shao, Yan Ling, Liu, Wei, Zhang, Qinhu, Yuan, Lin
Published in BMC genomics (12.08.2022)
Published in BMC genomics (12.08.2022)
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Journal Article
DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes
Wang, Siguo, Zhang, Qinhu, He, Ying, Cui, Zhen, Guo, Zhenghao, Han, Kyungsook, Huang, De-Shuang
Published in PLoS computational biology (01.10.2022)
Published in PLoS computational biology (01.10.2022)
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Journal Article
iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites
Yuan, Lin, Zhao, Ling, Lai, Jinling, Jiang, Yufeng, Zhang, Qinhu, Shen, Zhen, Zheng, Chun-Hou, Huang, De-Shuang
Published in PLoS computational biology (22.08.2024)
Published in PLoS computational biology (22.08.2024)
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Journal Article
Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture
Wang, Siguo, Zhang, Qinhu, Shen, Zhen, He, Ying, Chen, Zhen-Heng, Li, Jianqiang, Huang, De-Shuang
Published in Molecular therapy. Nucleic acids (04.06.2021)
Published in Molecular therapy. Nucleic acids (04.06.2021)
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Journal Article
iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction
Yuan, Lin, Zhao, Jiawang, Shen, Zhen, Zhang, Qinhu, Geng, Yushui, Zheng, Chun-Hou, Huang, De-Shuang
Published in PLoS computational biology (01.08.2023)
Published in PLoS computational biology (01.08.2023)
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Journal Article
scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data
Guo, Zhen-Hao, Wu, Yan, Wang, Siguo, Zhang, Qinhu, Shi, Jin-Ming, Wang, Yan-Bin, Chen, Zhan-Heng
Published in BMC bioinformatics (16.12.2023)
Published in BMC bioinformatics (16.12.2023)
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Journal Article
Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network
Shen, Zhen, Liu, Wei, Zhao, ShuJun, Zhang, QinHu, Wang, SiGuo, Yuan, Lin
Published in Frontiers in genetics (06.10.2023)
Published in Frontiers in genetics (06.10.2023)
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Journal Article
Locating transcription factor binding sites by fully convolutional neural network
Zhang, Qinhu, Wang, Siguo, Chen, Zhanheng, He, Ying, Liu, Qi, Huang, De-Shuang
Published in Briefings in bioinformatics (02.09.2021)
Published in Briefings in bioinformatics (02.09.2021)
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Journal Article
A survey on deep learning in DNA/RNA motif mining
He, Ying, Shen, Zhen, Zhang, Qinhu, Wang, Siguo, Huang, De-Shuang
Published in Briefings in bioinformatics (01.07.2021)
Published in Briefings in bioinformatics (01.07.2021)
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Journal Article
iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction
Lin Yuan, Jiawang Zhao, Zhen Shen, Qinhu Zhang, Yushui Geng, Chun-Hou Zheng, De-Shuang Huang
Published in PLoS computational biology (01.08.2023)
Published in PLoS computational biology (01.08.2023)
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Journal Article