| High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads B Wang, X Yang, Y Jia, Y Xu, P Jia, N Dang, S Wang, T Xu, X Zhao, S Gao, ... Genomics, Proteomics and Bioinformatics 20 (1), 4-13, 2022 | 124 | 2022 |
| MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability P Jia, X Yang, L Guo, B Liu, J Lin, H Liang, J Sun, C Zhang, K Ye Genomics, Proteomics and Bioinformatics 18 (1), 65-71, 2020 | 70 | 2020 |
| Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway X Yang, S Gao, L Guo, B Wang, Y Jia, J Zhou, Y Che, P Jia, J Lin, T Xu, ... Nature Communications 12 (1), 6030, 2021 | 62 | 2021 |
| SVision: a deep learning approach to resolve complex structural variants J Lin, S Wang, PA Audano, D Meng, JI Flores, W Kosters, X Yang, P Jia, ... Nature methods 19 (10), 1230-1233, 2022 | 44 | 2022 |
| Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance L Ren, X Duan, L Dong, R Zhang, J Yang, Y Gao, R Peng, W Hou, Y Liu, ... Genome Biology 24 (1), 270, 2023 | 17 | 2023 |
| Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing X Yang, X Zhao, S Qu, P Jia, B Wang, S Gao, T Xu, W Zhang, J Huang, ... Fundamental Research 2 (6), 946-953, 2022 | 14 | 2022 |
| Transportation, germs, culture: a dynamic graph model of COVID‐19 outbreak X Yang, T Xu, P Jia, H Xia, L Guo, L Zhang, K Ye Quantitative Biology 8 (3), 238-244, 2020 | 11 | 2020 |
| MEpurity: estimating tumor purity using DNA methylation data B Liu, X Yang, T Wang, J Lin, Y Kang, P Jia, K Ye Bioinformatics 35 (24), 5298-5300, 2019 | 8 | 2019 |
| Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet P Jia, L Dong, X Yang, B Wang, SJ Bush, T Wang, J Lin, S Wang, X Zhao, ... Genome Biology 24 (1), 277, 2023 | 6 | 2023 |
| Comparison and benchmark of structural variants detected from long read and long-read assembly J Lin, P Jia, S Wang, W Kosters, K Ye Briefings in Bioinformatics, bbad188, 2023 | 6* | 2023 |
| De novo and somatic structural variant discovery with SVision-pro S Wang, J Lin, P Jia, T Xu, X Li, Y Liu, D Xu, SJ Bush, D Meng, K Ye Nature Biotechnology, 1-5, 2024 | 4 | 2024 |
| MSIsensor-RNA: microsatellite instability detection for bulk and single-cell gene expression data P Jia, X Yang, X Yang, T Wang, Y Xu, K Ye Genomics, Proteomics & Bioinformatics, qzae004, 2024 | 2 | 2024 |
| Pindel-TD: a tandem duplication detector based on a pattern growth approach X Yang, G Zheng, P Jia, S Wang, K Ye bioRxiv, 2023.10. 08.561441, 2023 | 1 | 2023 |
| D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions Y Che, X Yang, P Jia, T Wang, D Xu, T Guo, K Ye Advanced Science 9 (30), 2202149, 2022 | 1 | 2022 |
| SVision-pro: comparative sequence-to-image representation and instance segmentation for de novo and somatic structural variant discovery K Ye, S Wang, J Lin, P Jia, T Xu, DY Meng | | 2023 |