| 0 | -- | 0 | Wang Ruohan, Zhang Yuwei, Wang Mengbo, Feng Xikang, Wang Jianping, Li Shuai Cheng. Resolving single-cell copy number profiling for large datasets |
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| 0 | -- | 0 | Xinyi Xu, Xiaokang Yu, Gang Hu, Kui Wang, Jingxiao Zhang, Xiangjie Li. Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis |
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| 0 | -- | 0 | Mathew Karikomi, Peijie Zhou, Qing Nie. DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data |
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| 0 | -- | 0 | Guiying Dong, Zi-Chao Zhang 0001, Jianfeng Feng, Xing-Ming Zhao. MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network |
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| 0 | -- | 0 | Hongzhun Wang, Feng Huang, Zhankun Xiong, Wen Zhang. A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions |
| 0 | -- | 0 | Tri Minh Nguyen 0005, Thin Nguyen, Truyen Tran 0001. Mitigating cold-start problems in drug-target affinity prediction with interaction knowledge transferring |
| 0 | -- | 0 | Hui Yu, Shiyu Zhao, Jianyu Shi. STNN-DDI: a Substructure-aware Tensor Neural Network to predict Drug-Drug Interactions |
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| 0 | -- | 0 | Mengyun Jiang, Weidong Ning, Shishi Wu, Xingwei Wang 0012, Kun Zhu 0019, Aomei Li, Yongyao Li, Shifeng Cheng, Bo Song. Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames |
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| 0 | -- | 0 | Feiyue Sun, Jianqiang Sun, Qi Zhao. A deep learning method for predicting metabolite-disease associations via graph neural network |
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