X. Zhang, Z. Yu, G. Hao, Q.Yao, X. Chen, L. LIU, Y. Hu, K. Wong, X. Li*, “Quantitative Characterization and Interpretation of Rare Spatial and Transcriptomic Heterogeneity from Spatial Omics using GARDEN,” Nature Communications, 2026.
G. Hao, Y. Fan, Z. Yu, Y. Su, H. Zhu, F. Wang, X. Chen, Y. Yang, G. Wang, K. Wong, X. Li*, Topological Identification and Interpretation for Single-cell Epigenetic Regulation Elucidation in Multi-tasks using scAGDE, Nature Communications, 2025.
H. Zhu, Y. Yang, Y. Wang, F. Wang, Y. Huang, Y. Chang, K. Wong*, X. Li*, Dynamic characterization and interpretation for protein–RNA interactions across diverse cellular conditions using HDRNet, Nature Communications, 2023.
Z. Yu, Y. Su, Y. Lu, F. Wang, S. Zhang, Y. Chang, K. Wong*, X. Li*, Topological Identification and Interpretation for Single-cell Gene Regulation Elucidation across Multiple Platforms using scMGCA, Nature Communications, 2023.
W. Ma, F. Wang, Y. Fan, G. Hao, Y. Su, K. Wong, X. Li*, DeepNanoHi-C: Deep Learning Enables Accurate Single-Cell Nanopore Long-read Data Analysis and 3D Genome Interpretation, Nucleic Acids Research, 2025, (IF = 16.7, Q1)
Y. Cheng, Y. Su, Y. Fan, Y. Yang, X. Chen, F. Wang, K. Wong, X. Li*, “Aligned Cross-modal Integration and Regulatory Heterogeneity Characterization of Single-Cell Multiomic Data with Deep Contrastive Learning,” Genome Medicine , 2025, (IF = 11.2, Q1)
Q. Qi, Y. Su, Y. Fan, Z. Yu, Y. Huang, K. Wong, X. Li*, “scSuperAnnotator: a platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data,” Nucleic Acids Research (2025).
Y. Su, Z. Yu, Y. Yang, X. Li*, Distribution-agnostic Deep Learning Enables Accurate Single‐Cell Data Recovery and Transcriptional Regulation Interpretation, Advanced Science, 2024. (IF= 17.521, Q1)
Y. Fan, Y. Wang, F. Wang, L. Huang, Y. Yang, K. Wong, X. Li*, Reliable Identification and Interpretation of Single-cell Molecular Heterogeneity and Transcriptional Regulation using Dynamic Ensemble Pruning, Advanced Science, 2023. (IF= 17.694, Q1)
Y. Yang, G. Li, K. Pan, W. Cao, Z. Zhang*, X. Li*, Deciphering 3’ UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning, Advanced Science, 2024. (IF= 14.3, Q1)
Z. Yu, Y. Yang, X. Chen, K. Wong, Z. Zhang, Y. Zhao*, X. Li*, Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning, Advanced Science, 2024. (IF= 17.521, Q1)
F. Wang, J. Lin, H. Alinejad-Rokny, W. MA, L. Meng, L. Huang, J. Yu, N. Chen, Y. Wang, Z. Yao, W. Xie, K. Wong*, X. Li*, Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE, Advanced Science, 2025. (IF= 14.3, Q1)
Z. Zheng, J. Chen, X. Chen, L. Huang, W. Xie, Q. Lin, X. Li*, K. Wong*, Enabling Single-cell Drug Response Annotations from Bulk RNA- seq using SCAD, Advanced Science, 2023. (IF=17.521, Q1)
F. Wang, H. Alinejad-Rokny, J. Lin, T. Gao, X. Chen, L. Meng, X. Li*, K. Wong*, A lightweight framework for chromatin loop detection on single-cell Hi-C, Advanced Science, 2023. (IF= 17.521, Q1)
Y. Shi, Y. Su, Y. Cheng, K. Wong, Y. Wang*, X. Li*, “Dynamic Synthesis of Multi-Modal Representations for CITE-seq Data Integration and Analysis,” Advanced Science (2025).
N. Chen, J. Yu, Z. Liu, L. Meng, X. Li*, K. Wong*, Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation, Nucleic Acids Research, 2024, (IF = 14.9, Q1)
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Y. Zhang, Z. Yu, K. Wong, X. Li*, Unraveling Spatial Domain Characterization in Spatially Resolved Transcriptomics with Robust Graph Contrastive Clustering, Bioinformatics, 2024. (IF=6.931,Q1)
Y. Wang, H. Zhu, Y. Wang, Y. Yang, Y. Huang*, J. Zhang*, K. Wong, X. Li*, EnrichRBP: an automated and interpretable computational platform for predicting and analyzing RNA-binding protein events, Bioinformatics, 2024. (IF=6.931,Q1)
Y. Wang, Y. Zhu, S. Li, C. Bian, Y. Liang, K. Wong, X. Li*, scBGEDA: Deep Single-cell Clustering Analysis via a Dual Denoising Autoencoder with Bipartite Graph Ensemble Clustering, Bioinformatics, 2023. (IF=6.931,Q1)
Q. Qi, Y. Wang, Y. Huang, Y. Fan*, X. Li*, PredGCN: A Pruning-enabled Gene-Cell Net for Automatic Cell Annotation of Single Cell Transcriptome Data , Bioinformatics, 2024. (IF=4.4,Q1)
P. Sun, S. Fan, S. Li, Y. Zhao, C. Lu*, K. Wong, X. Li*, Automated Exploitation of Deep Learning for Cancer Patient Stratification across Multiple Types, Bioinformatics, 2023. (IF=6.931,Q1)
Y. Su, F. Wang, S. Zhang, Y. Liang, K. Wong, X. Li*, scWMC: Weighted Matrix Completion-based Imputation of scRNA-seq Data via Prior Subspace Information, Bioinformatics, 2022. (IF=6.931,Q1)
F. Lu, Z. Yu, Y. Wang, Z. Ma, K. Wong, X. Li*, GMHCC: High-throughput Analysis of Biomolecular Data using Graph-based Multiple Hierarchical Consensus Clustering, Bioinformatics, 2022. (IF=6.931,Q1)
Y. Wang, Y. Yang, Z. Ma, K. Wong, X. Li*, EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network, Bioinformatics, 2021. (IF=6.931, Q1)
X. Li, S. Zhang, K. Wong. Single-cell RNA-seq Interpretations using Evolutionary Multiobjective Ensemble Pruning, Bioinformatics, 2019. (IF=6.937, Q1)
Y. Wang, C. Bian, K. Wong, X. Li*, S. Yang*. Multiobjective Deep Clustering and Its Applications in Single-cell RNA-seq Data, IEEE Transactions on Systems, Man, and Cybernetics: Systems, 2021. (IF=13.451, Q1)
Su, H. Zhu, K. Wong, Y. Chang, X. Li*, Hyperspectral Image Denoising via Weighted Multidirectional Low-rank Tensor Recovery, IEEE Transactions on Cybernetics, 2022. (IF=19.118,Q1)
Y. Wang, X. Li*, K. Wong, Y. Chang, S. Yang. Evolutionary Multiobjective Clustering Algorithms with Ensemble for Patient Stratification, IEEE Transactions on Cybernetics, 2021. (IF=19.118,Q1)
X. Li, S. Zhang, K. Wong. Multiobjective Genome-Wide RNA-Binding Event Identification from CLIP-seq Data, IEEE Transactions on Cybernetics, 2019. (IF=19.118,Q1)
X. Li, K. Wong. Evolutionary Multi-objective Clustering and Its Applications to Patient Stratification, IEEE Transactions on Cybernetics, 2018. (IF=19.118,Q1)
Y. Wang, Z. Hou, Y. Yang, K. Wong, X. Li*, Genome-wide Identification and Characterization of DNA Enhancers with a Stacked Multivariate Fusion Framework, PLOS Computational Biology, 2022. (Q1)
X. Li, S. Li, L. Huang, S. Zhang, K. Wong. High-throughput Single-cell RNA-seq Data Imputation and Characterization with Surrogate-assisted Automated Deep Learning, Briefings in Bioinformatics, 2021. (IF=13.994, Q1)
Y. Cheng, Y. Su, Z. Yu, Y. Liang, K. Wong, X. Li*, Unsupervised Deep Embedded Fusion Representation of Single-cell Transcriptomics, Thirty-Seventh AAAI Conference on Artificial Intelligence (AAAI 2023), 2022. (Q1, Oral)
Z. Yu, Y. Lu, Y. Wang, F. Tang, K. Wong, X. Li*, ZINB-based Graph Embedding Autoencoder for Single-cell RNA-seq Interpretations, Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI 2022), 2021. (Q1, Oral)
Z. Hou, Y. Yang. Z. Ma, K. Wong, X. Li*, Learning the Protein Language of Proteome-wide Protein-protein Binding Sites via Explainable Ensemble Deep Learning, Communications Biology, 2022.
L. Huang, J. Lin, R. Liu, Z. Zhang, L. Meng, X. Chen, X. Li*, K. Wong*, CoaDTI: Multi-modal Co-attention based framework for drug-target interaction annotation, Briefings in Bioinformatics, 2022. (IF=13.994, Q1)
Y. Yang, Z. Hou, Y. Wang, H. Ma, P. Sun, Z. Ma, K. Wong, X. Li*, HCRNet: High-throughput circRNA-Binding Event Identification from CLIP-seq Data using Deep Temporal Convolutional Network, Briefings in Bioinformatics, 2022. (IF=11.622, Q1)
X. Li, S. Li, L. Huang, S. Zhang, K. Wong. High-throughput Single-cell RNA-seq Data Imputation and Characterization with Surrogate-assisted Automated Deep Learning, Briefings in Bioinformatics, 2021. (IF=11.622, Q1)
Z. Hou, Y. Yang, H. Li, K. Wong, X. Li*. iDeepSubMito: Identification of protein sub-mitochondrial localization with deep learning, Briefings in Bioinformatics, 2021. (IF=11.622, Q1)
Z. Yu, C. Bian, G. Liu, S. Zhang, K. Wong, X. Li*. Elucidating Transcriptomic Profiles from Single-cell RNA sequencing Data using Nature-Inspired Compressed Sensing, Briefings in Bioinformatics, 2021. (IF=11.622, Q1)
X. Li, S. Zhang, K. Wong. Deep Embedded Clustering with Multiple Objectives on scRNA-seq Data, Briefings in Bioinformatics, 2021. (IF=11.622, Q1)
Y. Yang, S. Li, Y. Wang, K. Wong, X. Li*. Identification of Haploinsufficient Genes from Epigenomic Data using Deep Forest, Briefings in Bioinformatics, 2020. (IF=11.622, Q1)
