Genomics

Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring
Li et al., PNAS, 2023.
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Applications of transformer-based language models in bioinformatics: a survey
Shuang Zhang, Yuti Liu, Shuang Chen, Qiao Liu, Wanwen Zeng*. Bioinformatics Advances, 2023.
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Deep generative modeling and clustering of single cell Hi-C data
Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang*, Mu Zhou*, Shaoting Zhang*. Brief. Bioinform, 2022.
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Deep generative modeling and clustering of single cell Hi-C data
HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Wanwen Zeng†, Qiao Liu†, Qijin Yin†, Rui Jiang*, Wing Hung Wong*. Nucleic Acids Research, 2022.
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HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
Zhana Duren*, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong*. Genome Biology, 2022.
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DualGCN: a dual graph convolutional network model to predict cancer drug response
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang & Xuegong Zhang*. BMC Bioinformatics, 2022.
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scGraph: a graph neural network-based approach to automatically identify cell types
Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv*. Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong*, Rui Jiang*. Genomics, Proteomics & Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Multimodal single cell data integration challenge: Results and lessons learned
Christopher Lance, Malte D Luecken, Daniel B Burkhardt,…,Qiao Liu,…,Angela Oliveira Pisco*, Jonathan Bloom*, Smita Krishnaswamy*, Fabian J Theis*. Proceedings of Machine Learning Research(PMLR), 2022.
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OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang*. Nucleic Acids Research, 2021.
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