Published in International Conference on Learning Representations (ICLR) 2025 AI4NA Workshop (Accepted), 2025
Recommended citation: Zhiqi Ma, Xubin Zheng*. siRNA-mRNA dual diffusion model for RNAi drug design. International Conference on Learning Representations (ICLR) AI4NA Workshop, 2025.
Published in The 39th Annual AAAI Conference on Artificial Intelligence (AAAI), 2025
Recommended citation: Qingqiang Sun, Chaoqi Chen, Ziyue Qiao*, Xubin Zheng, Kai Wang*. Single-View Graph Contrastive Learning with Soft Neighborhood Awareness. AAAI, 2025. https://arxiv.org/abs/2412.09261
Published in The 39th Annual AAAI Conference on Artificial Intelligence (AAAI), 2025
Recommended citation: Xinlei Huang, Zhiqi Ma, Dian Meng, Yanran Liu, Shiwei Ruan, Qingqiang Sun, Xubin Zheng*, Ziyue Qiao. PRAGA: Prototype-aware Graph Adaptive Aggregation for Spatial Multi-modal Omics Analysis. AAAI, 2025. https://arxiv.org/abs/2409.12728
Published in Briefings in Bioinformatics, 2025
Recommended citation: Dian Meng, Yu Feng, Kaishen Yuan, Zitong Yu, Qin Cao, Lixin Cheng*, Xubin Zheng*. scMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics. Briefings in Bioinformatics, 2025. https://doi.org/10.1093/bib/bbaf010
Published in Plos Computational Biology, 2024
Recommended citation: Xubin Zheng, Dian Meng, Duo Chen, Wan-Ki Wong, Ka-Ho To, Lei Zhu, Jiafei Wu, Yining Liang, Kwong-Sak Leung, Man-Hon Wong, Lixin Cheng. scCaT: an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing. Plos Computational Biology, 2024. https://doi.org/10.1101/2024.04.17.590014
Published in iScience, 2024
Combined iPAGE and Transformer for infection diagnosis.
Recommended citation: Jize Xie#, Xubin Zheng#, Jianlong Yan#, Qizhi Li, Nana Jin, Shuojia Wang, Pengfei Zhao, Shuai Li, Wanfu Ding, Lixin Cheng, Qingshan Geng. Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression. iScience, 2024. https://doi.org/10.1016/j.isci.2024.109908
Published in Visual Intelligence, 2024
Multimodal fusion based on mamba
Recommended citation: Xinyu Xie, Yawen Cui, Chio-In Ieong, Tao Tan, Xiaozhi Zhang, Xubin Zheng, Zitong Yu. Fusionmamba: Dynamic feature enhancement for multimodal image fusion with mamba. Visual Intelligence, 2024. https://doi.org/10.1007/s44267-024-00072-9
Published in Computers in Biology and Medicine, 2024
Recommended citation: Pengfei Zhao#, Dian Meng#, Zunkai Hu, Yining Liang, Yating Feng, Tongjie Sun, Lixin Cheng, Xubin Zheng, Haili Li, Intra-sample reversed pairs based on differentially ranked genes reveal biosignature for ovarian cancer. Computers in Biology and Medicine, 2024. https://doi.org/10.1016/j.compbiomed.2024.108208
Published in Briefings in Bioinformatics, 2024
Recommended citation: Ying Li#, Jing Gao#, Xubin Zheng#, Guole Nie, Jican Qin, Haiping Wang, Tao He, Åsa Wheelock, Chuan-Xing Li, Lixin Cheng, Xun Li, Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model, Briefings in Bioinformatics, 2024. https://doi.org/10.1093/bib/bbad478
Published in Bioinformatics, 2023
Recommended citation: Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong Sak Leung, and Lixin Cheng. Deciphering associations between gut microbiota and clinical factors using microbial modules. Bioinformatics, 2023. https://doi.org/10.1093/bioinformatics/btad213
Published in Bioinformatics, 2023
Recommended citation: Qizhi Li#, Xubin Zheng#, Jize Xie#, Ran Wang, Mengyao Li, Man-Hon Wong, Kwong-Sak Leung, Shuai Li, Qingshan Geng*, and Lixin Cheng. bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks. Bioinformatics, 2023. https://doi.org/10.1093/bioinformatics/btad109
Published in Bioinformatics, 2023
Recommended citation: Lixin Cheng#, Haonan Wu#, Xubin Zheng, Ning Zhang, Pengfei Zhao, Ran Wang, Qiong Wu, Tao Liu, Xiaojun Yang, and Qingshan Geng. GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion. Bioinformatics, 2023. https://doi.org/10.1093/bioinformatics/btac850
Published in Computers in Biology and Medicine, 2022
In this paper, we proposed denoised individualized pairwise analysis of gene expression (deiPAGE).
Recommended citation: Haili Li#, Xubin Zheng#, Jing Gao, Kwong-Sak Leung, Man-Hon Wong, Shu Yang, Yakun Liu, Ming Dong, Huimin Bai, Xiufeng Ye, and Lixin Cheng. Whole transcriptome analysis reveals non-coding RNA’s competing endogenous gene pairs as novel form of motifs in serous ovarian cancer. Computers in Biology and Medicine, 2022. https://doi.org/10.1016/j.compbiomed.2022.105881
Published in Bioinformatics, 2022
Recommended citation: Qiong Wu#, Xubin Zheng#, Kwong-Sak Leung, Man-Hon Wong, Stephen Kwok-Wing Tsui, and Lixin Cheng. meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data. Bioinformatics, 2022. https://doi.org/10.1093/bioinformatics/btac379
Published in Briefings in Bioinformatics, 2022
Recommended citation: Ran Wang, Xubin Zheng, Jun Wang, Shibiao Wan, Fangda Song, Man-Hon Wong, Kwong-Sak Leung, and Lixin Cheng. Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia. Briefings in Bioinformatics, 2022. https://doi.org/10.1093/bib/bbac002
Published in IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2021
Recommended citation: Yueran Yang#, Yu Zhang#, Shuai Li, Xubin Zheng, Man-Hon Wong, Kwong-Sak Leung, and Lixin Cheng. A robust and generalizable immune-related signature for sepsis diagnostics. IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2021. https://ieeexplore.ieee.org/document/9523768
Published in Frontiers in Cell and Developmental Biology, 2021
Recommended citation: Xubin Zheng#, Qiong Wu#, Haonan Wu#, Man-Hon Wong, Kwong Sak Leung, Xueyan Liu, and Lixin Cheng. Evaluating the consistency of gene methylation in liver cancer using bisulfite sequencing data. Frontiers in Cell and Developmental Biology, 2021. https://doi.org/10.3389/fcell.2021.671302
Published in BMC Genomics, 2021
In this paper, we proposed individualized pairwise analysis of gene expression (iPAGE).
Recommended citation: Xubin Zheng, Kwong-Sak Leung, Man-Hon Wong, and Lixin Cheng. Long non-coding RNA Pairs to Assist in Diagnosing Sepsis. BMC Genomics, 2021. https://doi.org/10.1186/s12864-021-07576-4
Published in Clinical and Translational Medicine, 2020
Recommended citation: Xueyan Liu#, Xubin Zheng#, Jun Wang#, Ning Zhang, Kwong-Sak Leung, Xiufeng Ye, and Lixin Cheng. A long non-coding RNA signature for diagnostic prediction of sepsis upon ICU admission. Clinical and Translational Medicine, 2020. https://doi.org/10.1002/ctm2.123