| DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning P Ni, N Huang, Z Zhang, DP Wang, F Liang, Y Miao, CL Xiao, F Luo, ... Bioinformatics 35 (22), 4586–4595, 2019 | 208 | 2019 |
| DNRLMF-MDA: predicting microRNA-disease associations based on similarities of microRNAs and diseases C Yan, J Wang, P Ni, W Lan, FX Wu, Y Pan IEEE/ACM transactions on computational biology and bioinformatics 16 (1 …, 2017 | 77 | 2017 |
| Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning P Ni, N Huang, F Nie, J Zhang, Z Zhang, B Wu, L Bai, W Liu, CL Xiao, ... Nature communications 12 (1), 5976, 2021 | 71 | 2021 |
| Computational drug repositioning with random walk on a heterogeneous network H Luo, J Wang, M Li, J Luo, P Ni, K Zhao, FX Wu, Y Pan IEEE/ACM transactions on computational biology and bioinformatics 16 (6 …, 2018 | 67 | 2018 |
| Construction of refined protein interaction network for predicting essential proteins M Li, P Ni, X Chen, J Wang, FX Wu, Y Pan IEEE/ACM transactions on computational biology and bioinformatics 16 (4 …, 2017 | 59 | 2017 |
| DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing P Ni, F Nie, Z Zhong, J Xu, N Huang, J Zhang, H Zhao, Y Zou, Y Huang, ... Nature communications 14 (1), 4054, 2023 | 38 | 2023 |
| Constructing disease similarity networks based on disease module theory P Ni, J Wang, P Zhong, Y Li, FX Wu, Y Pan IEEE/ACM transactions on computational biology and bioinformatics 17 (3 …, 2018 | 37 | 2018 |
| SACall: a neural network basecaller for Oxford Nanopore sequencing data based on self-attention mechanism N Huang, F Nie, P Ni, F Luo, J Wang IEEE/ACM transactions on computational biology and bioinformatics 19 (1 …, 2020 | 32 | 2020 |
| NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks N Huang, F Nie, P Ni, F Luo, X Gao, J Wang Bioinformatics 37 (19), 3120-3127, 2021 | 17 | 2021 |
| An attention-based neural network basecaller for Oxford Nanopore sequencing data N Huang, F Nie, P Ni, F Luo, J Wang 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2019 | 10 | 2019 |
| NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data N Huang, M Xu, F Nie, P Ni, CL Xiao, F Luo, J Wang Bioinformatics 39 (1), btac824, 2023 | 6 | 2023 |
| A novel approach based on deep residual learning to predict drug’s anatomical therapeutic chemical code H Zhao, P Ni, C Yan, Y Li, J Wang 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2020 | 6 | 2020 |
| De novo diploid genome assembly using long noisy reads F Nie, P Ni, N Huang, J Zhang, Z Wang, C Xiao, F Luo, J Wang Nature Communications 15 (1), 2964, 2024 | 5* | 2024 |
| Identifying the serious clinical outcomes of adverse reactions to drugs by a multi-task deep learning framework H Zhao, P Ni, Q Zhao, X Liang, D Ai, S Erhardt, J Wang, Y Li, J Wang Communications Biology 6 (1), 870, 2023 | 4 | 2023 |
| BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer N Huang, F Nie, P Ni, X Gao, F Luo, J Wang Briefings in bioinformatics 23 (1), bbab405, 2022 | 3 | 2022 |
| Rnpredatc: a deep residual learning-based model with applications to the prediction of drug-atc code association H Zhao, G Duan, P Ni, C Yan, Y Li, J Wang IEEE/ACM Transactions on Computational Biology and Bioinformatics 20 (5 …, 2021 | 3 | 2021 |
| Identifying essential proteins by purifying protein interaction networks M Li, X Chen, P Ni, J Wang, Y Pan International Symposium on Bioinformatics Research and Applications, 106-116, 2016 | 3 | 2016 |
| Relating diseases based on disease module theory P Ni, M Li, P Zhong, G Duan, J Wang, Y Li, FX Wu Bioinformatics Research and Applications: 13th International Symposium …, 2017 | 1 | 2017 |
| HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation K Hu, P Ni, M Xu, Y Zou, J Chang, X Gao, Y Li, J Ruan, B Hu, J Wang Nature Communications 15 (1), 5573, 2024 | | 2024 |
| RNA m6A detection using raw current signals and basecalling errors from nanopore direct RNA sequencing reads P Ni, J Xu, Z Zhong, F Luo, J Wang Bioinformatics, btae375, 2024 | | 2024 |
