| Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes Y Hu, J Rong, Y Xu, R Xie, J Peng, L Gao, K Tan Nature Methods, 1-12, 2024 | 6* | 2024 |
| Cancer subclone detection based on DNA copy number in single cell and spatial omic sequencing data CY Wu, A Sathe, J Rong, PR Hess, BT Lau, SM Grimes, HP Ji, NR Zhang bioRxiv, 2022.07. 05.498882, 2022 | 5 | 2022 |
| Bedtk: finding interval overlap with implicit interval tree H Li, J Rong Bioinformatics 37 (9), 1315-1316, 2021 | 5 | 2021 |
| Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions K Mason, A Sathe, PR Hess, J Rong, CY Wu, E Furth, K Susztak, ... Genome Biology 25 (1), 14, 2024 | 1 | 2024 |
| Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma RA Gier, RAR Hueros, J Rong, M DeMarshall, TA Karakasheva, AB Muir, ... bioRxiv, 2023 | 1 | 2023 |
| A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma JH Sussman, DA Oldridge, W Yu, CH Chen, AM Zellmer, J Rong, ... bioRxiv, 2024.03. 06.583588, 2024 | | 2024 |
| ntsm: an alignment-free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection J Chu, J Rong, X Feng, H Li bioRxiv, 2023.11. 01.565041, 2023 | | 2023 |
