| scTenifoldKnk: an efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation D Osorio, Y Zhong, G Li, Q Xu, Y Yang, Y Tian, RS Chapkin, JZ Huang, ... Patterns 3 (3), 2022 | 36 | 2022 |
| Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation CW Honggui Li, Juan Zheng, Qian Xu, Yongjian Yang, Jing Zhou, Xinlei Guo ... Gastroenterology, 2022 | 26* | 2022 |
| scTenifoldXct: a semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs Y Yang, G Li, Y Zhong, Q Xu, YT Lin, C Roman-Vicharra, RS Chapkin, ... Cell systems 14 (4), 302-311. e4, 2023 | 19 | 2023 |
| Crystal structure of the choline-binding protein CbpJ from Streptococcus pneumoniae Q Xu, JW Zhang, Y Chen, Q Li, YL Jiang Biochemical and biophysical research communications 514 (4), 1192-1197, 2019 | 16 | 2019 |
| Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks Y Yang, G Li, Y Zhong, Q Xu, BJ Chen, YT Lin, RS Chapkin, JJ Cai Nucleic Acids Research 51 (13), 6578-6592, 2023 | 15 | 2023 |
| Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis Q Xu, Y Yang, X Zhang, JJ Cai ImmunoInformatics 6, 100013, 2022 | 10 | 2022 |
| scInTime: a computational method leveraging single-cell trajectory and gene regulatory networks to identify master regulators of cellular differentiation Q Xu, G Li, D Osorio, Y Zhong, Y Yang, YT Lin, X Zhang, JJ Cai Genes 13 (2), 371, 2022 | 8 | 2022 |
| Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis X Yan, C Li, K Liu, T Zhang, Q Xu, X Li, J Zhu, Z Wang, A Yusuf, S Cao, ... Nature plants 10 (7), 1126-1143, 2024 | 4 | 2024 |
| Interpretable modeling of time-resolved single-cell gene–protein expression with CrossmodalNet Y Yang, YT Lin, G Li, Y Zhong, Q Xu, JJ Cai Briefings in Bioinformatics 24 (6), bbad342, 2023 | 2 | 2023 |
| Role of RSPO3 in Estrogen-mediated Sex Differences in Body Fat Distribution: A Single-cell Data-driven Study Q Xu, Y Yang, S Gupta, BJ Chen, G Li, M Chamberlain, JJ Cai bioRxiv, 2025.01. 03.631121, 2025 | | 2025 |
| HFD feeding for seven months abolishes STING disruption-driven but not female sex-based protection against hepatic steatosis and inflammation in mice X Guo, H Li, B Zhu, X Wang, Q Xu, E Aquino, M Koo, Q Li, J Cai, S Glaser, ... The Journal of nutritional biochemistry 135, 109770, 2025 | | 2025 |
| Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet Y Yang, YT Lin, G Li, Y Zhong, Q Xu, JJ Cai bioRxiv, 2023.05. 16.541011, 2023 | | 2023 |
James J. CaiProfessor, Texas A&M UniversityVerified email at tamu.edu