Paper Publications
- [1] Long-Chen Shen, Yumeng Zhang, Zhikang Wang, Dene R. Littler, Yan Liu, Jinhui Tang, Jamie Rossjohn, Dong-Jun Yu*, and Jiangning Song*. Self-iterative multiple-instance learning enables the prediction of CD4+ T cell immunogenic epitopes [J]. Nature Machine Intelligence, 2025, 7(8): 1250–1265.,Nature Machine Intelligence,2025,7(8):1250–1265
- [2] Long-Chen Shen, Yan Liu, Zi Liu, Yumeng Zhang, Zhikang Wang, Yuming Guo, Jamie Rossjohn, Jiangning Song*, and Dong-Jun Yu*. Supervised contrastive learning enhances MHC-II peptide binding affinity prediction,Expert Systems with Applications,2025,269:12646
- [3] Long-Chen Shen, Dong-Jun Yu*, and Jiangning Song*. Learning conformational flexibility of immune receptors: Protein dynamics prediction,Nature Machine Intelligence,2025,7:1600–1601
- [4] Yan Liu, Sheng Guan, He Yan, Long-Chen Shen, Yiheng Zhu, Ji-Peng Qiang, and Guo Wei*. Genome- and peak-informed two-stage framework for scATAC-seq cell type identification,Bioinformatics,2026,42(2):btaf682
- [5] Yan Liu, Sheng Guan, He Yan, Long-Chen Shen, Ji-Peng Qiang*, and Guo Wei*. Cell type annotation for scATAC-seq via DNA large language model and graph domain adaptation,PLOS Computational Biology,2026,22(4):e1014226
- [6] Yan Liu, Guo Wei, Jia-Shun Wu, Chen Li, He Yan, Long-Chen Shen, Robin B. Gasser, Jiangning Song*, Dijun Chen*, and Dong-Jun Yu*. MUSIC-GCN: A novel multi-tasking pipeline for analyzing single-cell transcriptomic data using residual graph convolution network,IEEE Transactions on Computational Biology and Bioinformatics,2025,22(2):781–789
- [7] Shuo Li#, Yan Liu#, Long-Chen Shen, He Yan, Jiangning Song*, and Dong-Jun Yu*. GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference,Briefings in Bioinformatics,2024,25(2):bbad529
- [8] Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song*, Dijun Chen*, and Dong-Jun Yu*. TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level,Briefings in Bioinformatics,2023,24(3):bbad132
- [9] Ke Han#, Long-Chen Shen#, Yi-Heng Zhu, Jian Xu, Jiangning Song*, and Dong-Jun Yu*. MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network,Briefings in Bioinformatics,2022,23(1):bbab445
- [10] Yu-Hang Yin#, Long-Chen Shen#, Yuanhao Jiang, Shang Gao*, Jiangning Song*, and Dong-Jun Yu*. Improving the prediction of DNA-protein binding by integrating multi-scale dense convolutional network with fault-tolerant coding,Analytical Biochemistry,2022,656:114878
MOBILE Version