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. (IF= 17.694, Q1)
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. (IF= 17.694, Q1)
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)
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)
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, 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)
M. Toseef, O. O. Petinrin, F. Wang, S. Rahaman, Z. Liu, X. Li*, K. Wong*, Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results, Briefings in Bioinformatics, 2023. (IF=9.5, Q1)
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.
F. Wang, T. Gao, J. Lin, Z. Zheng, L. Huang, M. Toseef, X. Li*, K. Wong*, GILoop: robust chromatin loop calling across multiple sequencing depths on Hi-C data, iScience, 2022. (IF=6.107, Cell Press)
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)
M. Toseef, X. Li*, K. Wong*, Reducing healthcare disparities using multiple multiethnic data distributions with fine-tuning of transfer learning, Briefings in Bioinformatics, 2022. (IF=11.622, 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)
L. Huang, J. Lin, X. Li*, L. Song, Z. Zheng, and K. Wong*, EGFI: Drug-Drug Interaction Extraction and Generation with Fusion of Enriched Entity and Sentence Information, Briefings in Bioinformatics, 2021. (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)
X. Li, S. Li, Y. Wang, S. Zhang, K. Wong. Identification of Pan-cancer Ras Pathway Activation with Deep Learning, Briefings in Bioinformatics, 2020. (IF=11.622, Q1)
Y. Yang, Z. Hou, Z. Ma, X. Li*, K. Wong*, iCircRBP-DHN: identification of circRNA-RBP interaction sites using deep hierarchical network, Briefings in Bioinformatics, 2020. (IF=11.622, Q1)
