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How to improve polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features?
Wanwen Zeng, Hanmin Guo, Qiao Liu, Wing Hung Wong. PNAS, 2025.
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Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data
In recent years, computational methods for quantifying cell-type proportions from transcription data have gained significant attention, …
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Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation
Erpai Luo, Lei Wei, Minsheng Hao, Xuegong Zhang†, Qiao Liu†. bioRxiv 2025 (Nat. Commun. in revision)
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Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation
CREATE: cell-type-specific cis-regulatory elements identification via discrete embedding
Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Shengquan Chen, Qiao Liu, Wanwen Zeng, Rui Jiang. bioRxiv, 2024.
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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-basedlanguage model for context-specific humanepigenomics
Zijing Gao*, Qiao Liu*,†, Wanwen Zeng, Rui Jiang†, Wing Hung Wong†. Genome Biology, 2024.
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EpiGePT: a pretrained transformer-basedlanguage model for context-specific humanepigenomics
DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies
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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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