AI

How to improve polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features?
Wanwen Zeng, Hanmin Guo, Qiao Liu, Wing Hung Wong. medRxiv, 2024.
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Leveraging genomic large language models to enhance causal genotype-brain-clinical pathways in Alzheimer's disease
Qiao Liu*, Wanwen Zeng*, Hongtu Zhu, Lexin Li, Wing Hung Wong. medRxiv, 2024.
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Leveraging genomic large language models to enhance causal genotype-brain-clinical pathways in Alzheimer's disease
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 model for epigenomics
Zijing Gao*, Qiao Liu*,†, Wanwen Zeng, Rui Jiang†, Wing Hung Wong†. bioRxiv, 2024 (minor revision at Genome Biology).
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EpiGePT: a Pretrained Transformer model for epigenomics
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
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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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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