| Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis P Savas, B Virassamy, C Ye, A Salim, CP Mintoff, F Caramia, R Salgado, ... Nature medicine 24 (7), 986-993, 2018 | 952 | 2018 |
| Data denoising with transfer learning in single-cell transcriptomics J Wang, D Agarwal, M Huang, G Hu, Z Zhou, C Ye, NR Zhang Nature methods 16 (9), 875-878, 2019 | 186 | 2019 |
| Surface protein imputation from single cell transcriptomes by deep neural networks Z Zhou, C Ye, J Wang, NR Zhang Nature communications 11 (1), 651, 2020 | 84 | 2020 |
| DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data C Ye, TP Speed, A Salim Bioinformatics 35 (24), 5155-5162, 2019 | 53 | 2019 |
| Cross-protein transfer learning substantially improves disease variant prediction M Jagota, C Ye, C Albors, R Rastogi, A Koehl, N Ioannidis, YS Song Genome Biology 24 (1), 1-19, 2023 | 37 | 2023 |
| GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction G Benegas, C Albors, AJ Aw, C Ye, YS Song bioRxiv, 2023.10. 10.561776, 2024 | 17 | 2024 |
| Genomic language models: opportunities and challenges G Benegas, C Ye, C Albors, JC Li, YS Song Trends in Genetics, 2025 | 12 | 2025 |
| Learning epistatic polygenic phenotypes with Boolean interactions M Behr, K Kumbier, A Cordova-Palomera, M Aguirre, O Ronen, C Ye, ... Plos one 19 (4), e0298906, 2024 | 9 | 2024 |
| Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. P Savas, B Virassamy, C Ye, A Salim, CP Mintoff, F Caramia, R Salgado, ... Nature medicine 24 (12), 1941-1941, 2018 | 9 | 2018 |
| A DNA language model based on multispecies alignment predicts the effects of genome-wide variants G Benegas, C Albors, AJ Aw, C Ye, YS Song Nature Biotechnology, 1-6, 2025 | 1 | 2025 |
| Characterization of high TIL breast cancers reveals a prognostic and functionally distinct tissue-resident memory subpopulation P Savas, B Virassamy, C Ye, A Salim, CP Mintoff, F Caramia, R Salgado, ... CANCER RESEARCH 79 (4), 2019 | | 2019 |
