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.
PDF Cite Code DOI
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.
PDF Cite Code DOI
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.
PDF Cite Code DOI
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.
PDF Cite Code Project DOI
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).
PDF Cite Code DOI
EpiGePT: a Pretrained Transformer model for human 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.
PDF Cite Code DOI
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.
Cite DOI
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.
PDF Cite Code DOI
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.
Cite DOI
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.
Cite Code DOI