Article-Journal

An encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies
Qiao Liu, Zhongren Chen, Wing Hung Wong. PNAS, 2024.
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An encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies
EpiGePT: a Pretrained Transformer model for human epigenomics
Zijing Gao*, Qiao Liu*,†, Wanwen Zeng, Rui Jiang†, Wing Hung Wong†. Genome Biology, 2024 (in press).
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EpiGePT: a Pretrained Transformer model for human epigenomics
Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring
Li et al., PNAS, 2023.
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DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
Qijin Yin, Rui Fan, Xusheng Cao Qiao Liu#, Rui Jiang# and Wanwen Zeng#. Quantitative Biology, 2023.
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DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
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
AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data
Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv. ACM Transactions on Intelligent Systems and Technology, 2022.
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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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