| Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities Q Zeng, D Li, Y He, Y Li, Z Yang, X Zhao, Y Liu, Y Wang, J Sun, X Feng, ... Scientific reports 9 (1), 13424, 2019 | 271 | 2019 |
| DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data J Chen, CW Cheong, L Lan, X Zhou, J Liu, A Lyu, WK Cheung, L Zhang Briefings in bioinformatics 22 (6), bbab325, 2021 | 29 | 2021 |
| Parameterized BLOSUM matrices for protein alignment D Song, J Chen, G Chen, N Li, J Li, J Fan, D Bu, SC Li IEEE/ACM Transactions on Computational Biology and Bioinformatics 12 (3 …, 2014 | 23 | 2014 |
| The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs Y Yang, J Yan, X Fan, J Chen, Z Wang, X Liu, G Yi, Y Liu, Y Niu, L Zhang, ... PLoS Genetics 17 (11), e1009910, 2021 | 22 | 2021 |
| Understanding horizontal gene transfer network in human gut microbiota C Li, J Chen, SC Li Gut Pathogens 12 (1), 33, 2020 | 21 | 2020 |
| On triangle inequalities of correlation-based distances for gene expression profiles J Chen, YK Ng, L Lin, X Zhang, S Li BMC bioinformatics 24 (1), 40, 2023 | 12* | 2023 |
| Association between metabolic status and gut microbiome in obese populations Q Zeng, Z Yang, F Wang, D Li, Y Liu, D Wang, X Zhao, Y Li, Y Wang, ... Microbial Genomics 7 (8), 000639, 2021 | 12 | 2021 |
| dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data Y Xu, J Chen, A Lyu, WK Cheung, L Zhang Briefings in Bioinformatics 23 (6), bbac424, 2022 | 5 | 2022 |
| Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic Y Li, Y Jiang, Z Li, Y Yu, J Chen, W Jia, YK Ng, F Ye, SC Li, B Shen Computational and Structural Biotechnology Journal 20, 1389-1401, 2022 | 5 | 2022 |
| KDiamend: a package for detecting key drivers in a molecular ecological network of disease M Lyu, J Chen, Y Jiang, W Dong, Z Fang, S Li BMC Systems Biology 12, 89-99, 2018 | 5 | 2018 |
| Deep learning for HGT insertion sites recognition C Li, J Chen, SC Li BMC genomics 21, 1-18, 2020 | 3 | 2020 |
| More accurate models for detecting gene-gene interactions from public expression compendia L Zhang, JX Chen, SC Li 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2016 | 3 | 2016 |
| A multimodal framework for detecting direct and indirect gene-gene interactions from large expression compendium L Zhang, JX Chen, SC Li bioRxiv, 680116, 2019 | 1 | 2019 |
| TENET: Triple-Enhancement based Graph Neural Network for Cell-cell Interaction Network Reconstruction from Spatial Transcriptomics Y Lee, Y Xu, P Gao, J Chen Journal of Molecular Biology, 168543, 2024 | | 2024 |
