Genomics

MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts
Haochen Wang, Charming Zhang, Mengran Zhang, Xiaoming Nie, Qiao Liu*. bioRxiv, 2026.
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MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts
RegFM: an interpretable context-aware foundation model for human transcriptional regulation
Zijing Gao, Yining Sun, Haochen Wang, Rui Jiang*, Qiao Liu*. bioRxiv, 2026.
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RegFM: an interpretable context-aware foundation model for human transcriptional regulation
scMTG reconstructs single-cell temporal dynamics with Markov transition generators
Xuejian Cui, Haochen Wang, Zijing Gao, Rui Jiang*, Wing Hung Wong*, Qiao Liu*. bioRxiv, 2026.
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scMTG reconstructs single-cell temporal dynamics with Markov transition generators
A 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*. Nature Communications, 2026.
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A Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation
Toward the simultaneous detection of multiple diseases with a highly cost-effective cell-free DNA methylome test
Weihua Zeng, Chun-Chi Liu, Shuo Li, Yonggang Zhou, Mary L. Stackpole, Ying Xiao, Ran Hu, Caitlin Tang, Qiao Liu, et al. PNAS, 2026.
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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.
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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.
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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.
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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.
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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.
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