Genomics

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.

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

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.

Qiao Liu, Wanwen Zeng, Hongtu Zhu, Lexin Li, Wing Hung Wong

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.

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

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).

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

EpiGePT: a Pretrained Transformer model for epigenomics

Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring

Li et al., PNAS, 2023.

Shuo Li, Xiaohui Ni, Qiao Liu, Wenyuan Li, Mary L. Stackpole, .., Wing Hung Wong, Steven M. Dubinett SDubinett, Xianghong Jasmine Zhou

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

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.

Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang

HiChIPdb: a comprehensive database of HiChIP regulatory interactions

Wanwen Zeng*, Qiao Liu*, Qijin Yin*, Rui Jiang, Wing Hung Wong. Nucleic Acids Research, 2022.

Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong

HiChIPdb: a comprehensive database of HiChIP regulatory interactions

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong. Genome Biology, 2022.

Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong

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.

Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang