Genomics

scGraph: a graph neural network-based approach to automatically identify cell types
Qijin Yin, Qiao Liu, Zhuoran Fu, Rui Jiang. Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang. Genomics, Proteomics & Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Multimodal single cell data integration challenge: Results and lessons learned
Christopher Lance, Malte D Luecken, Daniel B Burkhardt,…,Qiao Liu,…,Fabian J Theis. Proceedings of Machine Learning Research(PMLR), 2022.
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OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang. Nucleic Acids Research, 2021.
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Simultaneous deep generative modelling and clustering of single-cell genomic data
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong. Nature Machine Intelligence, 2021.
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Simultaneous deep generative modelling and clustering of single-cell genomic data
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response
Qiao Liu, Zhiqiang Hu, Rui Jiang, Mu Zhou. ECCB Proceedings/Bioinformatics, 2020
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DeepCDR: a hybrid graph convolutional network for predicting cancer drug response
Feature-enhanced graph networks for genetic mutational prediction using histopathological images in colon cancer
Kexin Ding, Qiao Liu, Edward Lee, Mu Zhou, Aidong Lu & Shaoting Zhang. MICCAI, 2020.
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Mstree: a multispecies coalescent approach for estimating ancestral population size and divergence time during speciation with gene flow
Junfeng Liu, Qiao Liu, Qingzhu Yang. Genome biology and evolution, 2020.
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Quantifying functional impact of non-coding variants with multi-task Bayesian neural network
Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang. Bioinformatics, 2020.
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EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information
Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang. Quantitative Biology, 2019.
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