AI

A Bayesian Generative Modeling Approach for Arbitrary Conditional Inference

Qiao Liu^* and Wing Hung Wong. arXiv, 2026.

Qiao Liu, Wing Hung Wong

A Bayesian Generative Modeling Approach for Arbitrary Conditional Inference

Leveraging genomic foundation models to identify genotype-brain-clinical pathways in Alzheimer's disease

Qiao Liu^†,*, Zhaoyang Zhang^†, Haochen Wang, Heping Zhang, Hongtu Zhu, Lexin Li^*, Wing Hung Wong^*. medRxiv, 2026.

Qiao Liu, Zhaoyang Zhang, Haochen Wang, Heping Zhang, Hongtu Zhu, Lexin Li, Wing Hung Wong

Leveraging genomic foundation models to identify genotype-brain-clinical pathways in Alzheimer's disease

Improving polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features

Wanwen Zeng, Hanmin Guo, Qiao Liu, Wing Hung Wong^*. PNAS, 2025.

Wanwen Zeng, Hanmin Guo, Qiao Liu, Wing Hung Wong

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding

Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Hairong Lv, Shengquan Chen, Qiao Liu, Wanwen Zeng^*, Rui Jiang^*. Nature Communications, 2025.

Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Hairong Lv, Shengquan Chen, Qiao Liu, Wanwen Zeng, Rui Jiang

Application of LLMs/Transformer-Based Models for Metabolite Annotation in Metabolomics

Yijiang Liu, Feifan Zhang, Yifei Ge, Qiao Liu, Siyu He, and Xiaotao Shen^*. Health and Metabolism, 2025.

Yijiang Liu, Feifan Zhang, Yifei Ge, Qiao Liu, Siyu He, Xiaotao Shen

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

Zijing Gao^†, Qiao Liu^†,*, Wanwen Zeng, Rui Jiang^*, Wing Hung Wong^*. Genome Biology, 2024.

Zijing Gao, Qiao Liu, Wanwen Zeng, Rui Jiang, Wing Hung Wong

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation

Wei Shao, Yuti Liu, Shuang Zhang, Shuang Chen, Qiao Liu, Jianyu Zhou, and Wanwen Zeng. BIBM, 2024.

Wei Shao, Yuti Liu, Shuang Zhang, Shuang Chen, Qiao Liu, Jianyu Zhou, Wanwen Zeng

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.

Qiao Liu, Zhongren Chen, Wing Hung Wong

An encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies

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.

Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang, Wanwen Zeng

Applications of transformer-based language models in bioinformatics: a survey

Shuang Zhang, Yuti Liu, Shuang Chen, Qiao Liu, Wanwen Zeng^*. Bioinformatics Advances, 2023.

Shuang Zhang, Rui Fan, Yuti Liu, Shuang Chen, Qiao Liu, Wanwen Zeng