| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019 | 445 | 2019 |
| AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification R You, Z Zhang, Z Wang, S Dai, H Mamitsuka, S Zhu Advances in neural information processing systems 32, 2019 | 429* | 2019 |
| Critical assessment of metagenome interpretation: the second round of challenges F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ... Nature methods 19 (4), 429-440, 2022 | 278 | 2022 |
| GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank R You, Z Zhang, Y Xiong, F Sun, H Mamitsuka, S Zhu Bioinformatics 34 (14), 2465-2473, 2018 | 185 | 2018 |
| DeepMeSH: deep semantic representation for improving large-scale MeSH indexing S Peng, R You, H Wang, C Zhai, H Mamitsuka, S Zhu Bioinformatics 32 (12), i70-i79, 2016 | 140 | 2016 |
| NetGO: improving large-scale protein function prediction with massive network information R You, S Yao, Y Xiong, X Huang, F Sun, H Mamitsuka, S Zhu Nucleic acids research 47 (W1), W379-W387, 2019 | 138 | 2019 |
| DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction R You, S Yao, H Mamitsuka, S Zhu Bioinformatics 37 (Supplement_1), i262-i271, 2021 | 105 | 2021 |
| NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information S Yao, R You, S Wang, Y Xiong, X Huang, S Zhu Nucleic acids research 49 (W1), W469-W475, 2021 | 92 | 2021 |
| DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation R You, X Huang, S Zhu Methods 145, 82-90, 2018 | 91 | 2018 |
| NetGO 3.0: protein language model improves large-scale functional annotations S Wang, R You, Y Liu, Y Xiong, S Zhu Genomics, Proteomics & Bioinformatics 21 (2), 349-358, 2023 | 56 | 2023 |
| FullMeSH: improving large-scale MeSH indexing with full text S Dai, R You, Z Lu, X Huang, H Mamitsuka, S Zhu Bioinformatics 36 (5), 1533-1541, 2020 | 48 | 2020 |
| BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text R You, Y Liu, H Mamitsuka, S Zhu Bioinformatics 37 (5), 684-692, 2021 | 46 | 2021 |
| Cache-oblivious wavefront: improving parallelism of recursive dynamic programming algorithms without losing cache-efficiency Y Tang, R You, H Kan, JJ Tithi, P Ganapathi, RA Chowdhury Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of …, 2015 | 43 | 2015 |
| DeepDock: enhancing ligand-protein interaction prediction by a combination of ligand and structure information Z Liao, R You, X Huang, X Yao, T Huang, S Zhu 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2019 | 41 | 2019 |
| MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities Z Wang, P Huang, R You, F Sun, S Zhu Genome Biology 24 (1), 1, 2023 | 36 | 2023 |
| The fudan participation in the 2015 bioasq challenge: Large-scale biomedical semantic indexing and question answering Y Zhang, S Peng, R You, Z Xie, B Wang, S Zhu CEUR Workshop Proceedings 1391, 2015 | 36 | 2015 |
| PLMSearch: Protein language model powers accurate and fast sequence search for remote homology W Liu, Z Wang, R You, C Xie, H Wei, Y Xiong, J Yang, S Zhu Nature communications 15 (1), 2775, 2024 | 28 | 2024 |
| DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction R You, W Qu, H Mamitsuka, S Zhu Bioinformatics 38 (Supplement_1), i220-i228, 2022 | 22 | 2022 |
| ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network Z Wang, S Li, R You, S Zhu, XJ Zhou, F Sun NAR Genomics and Bioinformatics 3 (3), lqab066, 2021 | 20 | 2021 |
| Effective binning of metagenomic contigs using contrastive multi-view representation learning Z Wang, R You, H Han, W Liu, F Sun, S Zhu Nature Communications 15 (1), 585, 2024 | 19 | 2024 |
