Publications

Wanwen Zeng, Hanmin Guo, Qiao Liu, Wing Hung Wong (2024). How to improve polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features?. medRxiv, 2024.

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Qiao Liu, Wanwen Zeng, Hongtu Zhu, Lexin Li, Wing Hung Wong (2024). Leveraging genomic large language models to enhance causal genotype-brain-clinical pathways in Alzheimer's disease. medRxiv, 2024.

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Xuejian Cui, Qijin Yin, Zijing Gao, Zhen Li, Xiaoyang Chen, Shengquan Chen, Qiao Liu, Wanwen Zeng, Rui Jiang (2024). CREATE: cell-type-specific cis-regulatory elements identification via discrete embedding. bioRxiv, 2024.

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Qiao Liu, Zhongren Chen, Wing Hung Wong (2024). An encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies. Proceedings of the National Academy of Sciences, 121(23), e2322376121, 2024.

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Zijing Gao, Qiao Liu, Wanwen Zeng, Rui Jiang, Wing Hung Wong (2024). EpiGePT: a Pretrained Transformer model for human epigenomics. Genome Biology, 2024 (in press).

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Shuo Li, Xiaohui Ni, Qiao Liu, Wenyuan Li, Mary L. Stackpole, .., Wing Hung Wong, Steven M. Dubinett SDubinett, Xianghong Jasmine Zhou (2023). Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring. Proceedings of the National Academy of Sciences, 120(28), e2305236120, 2013..

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Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu#, Rui Jiang#, Wanwen Zeng# (2023). DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction. Quantitative Biology, 11(3), 260-274, 2023.

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Shuang Zhang, Rui Fan, Yuti Liu, Shuang Chen, Qiao Liu, Wanwen Zeng (2023). Applications of transformer-based language models in bioinformatics: a survey. Bioinformatics Advances, 3(1), vbad001, 2023.

Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang (2022). Deep generative modeling and clustering of single cell Hi-C data. Briefings in Bioinformatics, 24(1), bbac494, 2023.

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Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong (2022). HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic acids research, 51(D1), D159-D166, 2022.

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Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv (2022). AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data. Transactions on Intelligent Systems and Technology (TIST), 13(6), 1-25, 2022.

Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong (2022). Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. Genome biology, 23(1), 114, 2022.

Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang (2022). DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC bioinformatics, 23(Suppl 4), 129, 2022.

Qijin Yin, Qiao Liu, Zhuoran Fu, Rui Jiang (2022). scGraph: a graph neural network-based approach to automatically identify cell types. Bioinformatics, 38(11), 2996-3003, 2022.

Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang (2022). DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility. Genomics, Proteomics and Bioinformatics, 20(3), 496-507, 2022.

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Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach, Aidyn Ubingazhibov, Zhi-Jie Cao, Kaiwen Deng, Sumeer Khan, Qiao Liu, .., Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis (2022). Multimodal single cell data integration challenge: Results and lessons learned. NeurIPS 2021 Competitions and Demonstrations Track (pp. 162-176). Proceedings of Machine Learning Research, 2022.

Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang (2021). OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Research, 49(W1), W483-W490, 2021.

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Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong (2021). Simultaneous deep generative modelling and clustering of single-cell genomic data. Nature Machine Intelligence, 3(6), 536-544, 2021.

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Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong (2021). Density estimation using deep generative neural networks. Proceedings of the National Academy of Sciences, 118 (15), e2101344118, 2021.

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Feng Wang, Guoyizhe Wei, Qiao Liu, Jinxiang Ou, Xian Wei, Hairong Lv (2021). Boost Neural Networks by Checkpoints. Advances in Neural Information Processing Systems (NeurIPS), 34, 19719-19729, 2021.

Qiao Liu, Zhiqiang Hu, Rui Jiang, Mu Zhou (2020). DeepCDR: a hybrid graph convolutional network for predicting cancer drug response. ECCB Proceedings/Bioinformatics, 36(2), i911-i918, 2020.

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Kexin Ding, Qiao Liu, Edward Lee, Mu Zhou, Aidong Lu, Shaoting Zhang (2020). Feature-enhanced graph networks for genetic mutational prediction using histopathological images in colon cancer. Medical Image Computing and Computer Assisted Intervention (MICCAI) 2020.

Junfeng Liu, Qiao Liu, Qingzhu Yang (2020). Mstree: a multispecies coalescent approach for estimating ancestral population size and divergence time during speciation with gene flow. Genome Biology and Evolution, 12(5), 715-719, 2020.

Chencheng Xu, Qiao Liu, Minlie Huang, Tao Jiang (2020). Reinforced molecular optimization with neighborhood-controlled grammars. Advances in neural information processing systems (NeurIPS), 33, 8366-8377, 2020.

Qingzhu Yang, Qiao Liu, Hairong Lv (2020). A decentralized system for medical data management via blockchain. Journal of Internet Technology, 21(5): 1335-1345, 2020.

Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang (2019). Quantifying functional impact of non-coding variants with multi-task Bayesian neural network. Bioinformatics, 36(5), 1397-1404, 2020.

Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang (2019). EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information . Quantitative Biology, 7(3), 233-243, 2019.

Qiao Liu, Hairong Lv, Rui Jiang (2019). hicGAN infers super resolution Hi-C data with generative adversarial networks. ISMB Proceedings/Bioinformatics, 35(14), i99-i107, 2019.

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Pengyu Chen, Qiao Liu, Lan Wei, Beier Zhao, Yin Jia, Hairong Lv, Xiaolu Fe (2019). Automatically structuring on Chinese ultrasound report of cerebrovascular diseases via natural language processing. IEEE Access, 7, 89043-89050, 2019..

Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang (2019). DeepHistone: a deep learning approach to predicting histone modifications. BMC genomics, 20, 11-23, 2019.

Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang (2017). Chromatin accessibility prediction via a hybrid deep convolutional neural network . Bioinformatics, 34(5), 732-738, 2017.

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Qiao Liu, Mingxin Gan, Rui Jiang (2017). A sequence-based method to predict the impact of regulatory variants using random forest. BMC Systems Biology 11 (Suppl 2), 7, 2017..

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Bai Li, Mu Lin, Qiao Liu, Ya Li, Changjun Zhou (2015). Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm. Journal of molecular modeling, 21, 1-15, 2015.