Long-Chen Shen

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.
PLoS Comput. Biol.
Yan Liu, Yu Xia, He Yan, Long-Chen Shen, Yiheng Zhu, Ji-Peng Qiang, Guo Wei
2025 J jnl
MUSIC-GCN: A Novel Multi-Tasking Pipeline for Analyzing Single-Cell Transcriptomic Data Using Residual Graph Convolution Network.
IEEE Trans. Comput. Biol. Bioinform.
Yan Liu, Guo Wei, Jia-Shun Wu, Chen Li, He Yan, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2025 J jnl
Supervised contrastive learning enhances MHC-II peptide binding affinity prediction.
Expert Syst. Appl.
Long-Chen Shen, Yan Liu, Zi Liu, Yumeng Zhang, Zhikang Wang, Yuming Guo, Jamie Rossjohn, Jiangning Song, Dong-Jun Yu
2025 J jnl
scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data.
Comput. Biol. Medicine
Yan Liu, Chen Li, Long-Chen Shen, He Yan, Guo Wei, Robin B. Gasser, Xiaohua Hu, Jiangning Song, Dong-Jun Yu
2024 J jnl
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference.
Briefings Bioinform.
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
2023 J jnl
Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction.
Comput. Biol. Medicine
Zi Liu, Yi-Heng Zhu, Long-Chen Shen, Xuan Xiao, Wangren Qiu, Dong-Jun Yu
2023 J jnl
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation.
J. Chem. Inf. Model.
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
2023 J jnl
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.
Briefings Bioinform.
Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2022 J jnl
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.
Briefings Bioinform.
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
2021 J jnl
Improving protein fold recognition using triplet network and ensemble deep learning.
Briefings Bioinform.
Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu
2021 J jnl
SAResNet: self-attention residual network for predicting DNA-protein binding.
Briefings Bioinform.
Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu