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2020 – today
- 2024
[j11]Shuxin Zheng
, Jiyan He, Chang Liu, Yu Shi, Ziheng Lu, Weitao Feng, Fusong Ju, Jiaxi Wang, Jianwei Zhu, Yaosen Min, He Zhang, Shidi Tang, Hongxia Hao, Peiran Jin, Chi Chen, Frank Noé, Haiguang Liu, Tie-Yan Liu:
Predicting equilibrium distributions for molecular systems with deep learning. Nat. Mac. Intell. 6(5): 558-567 (2024)- 2023
- [j10]Bin Huang, Lupeng Kong, Chao Wang, Fusong Ju, Qi Zhang, Jianwei Zhu, Tiansu Gong, Haicang Zhang, Chungong Yu, Wei-Mou Zheng, Dongbo Bu:
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. Genom. Proteom. Bioinform. 21(5): 913-925 (2023) - [j9]Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu:
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances. IEEE ACM Trans. Comput. Biol. Bioinform. 20(6): 3482-3488 (2023) - [i5]Shuxin Zheng, Jiyan He, Chang Liu, Yu Shi, Ziheng Lu, Weitao Feng, Fusong Ju, Jiaxi Wang, Jianwei Zhu, Yaosen Min, He Zhang, Shidi Tang, Hongxia Hao, Peiran Jin, Chi Chen, Frank Noé, Haiguang Liu, Tie-Yan Liu:
Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning. CoRR abs/2306.05445 (2023) - 2022
- [j8]Fusong Ju, Jianwei Zhu, Qi Zhang, Guozheng Wei, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. Bioinform. 38(4): 990-996 (2022) - [j7]Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu:
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. J. Comput. Biol. 29(2): 92-105 (2022) - [c3]Mingyang Hu, Fajie Yuan, Kevin Yang, Fusong Ju, Jin Su, Hui Wang, Fei Yang, Qiuyang Ding:
Exploring evolution-aware & -free protein language models as protein function predictors. NeurIPS 2022 - [i4]Mingyang Hu, Fajie Yuan, Kevin K. Yang, Fusong Ju, Jin Su, Hui Wang, Fei Yang, Qiuyang Ding:
Exploring evolution-based & -free protein language models as protein function predictors. CoRR abs/2206.06583 (2022) - 2021
- [j6]Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun, Dongbo Bu:
FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC Bioinform. 22(1): 439 (2021) - [j5]Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu:
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. BMC Bioinform. 22(3): 533 (2021) - [c2]Tiansu Gong, Fusong Ju, Shiwei Sun, Dongbo Bu:
SASA-Net: A spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances. BIBM 2021: 32-37 - [c1]He Zhang, Fusong Ju, Jianwei Zhu, Liang He, Bin Shao, Nanning Zheng, Tie-Yan Liu:
Co-evolution Transformer for Protein Contact Prediction. NeurIPS 2021: 14252-14263 - [i3]Liang He, Shizhuo Zhang, Lijun Wu, Huanhuan Xia, Fusong Ju, He Zhang, Siyuan Liu, Yingce Xia, Jianwei Zhu, Pan Deng, Bin Shao, Tao Qin, Tie-Yan Liu:
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model. CoRR abs/2110.15527 (2021) - 2020
- [j4]Qi Zhang, Jianwei Zhu, Fusong Ju, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
ISSEC: inferring contacts among protein secondary structure elements using deep object detection. BMC Bioinform. 21(1): 503 (2020)
2010 – 2019
- 2019
- [j3]Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC Bioinform. 20(1): 537:1-537:11 (2019) - [j2]Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC Bioinform. 20(1): 616:1-616:5 (2019) - [j1]Fusong Ju, Jingwei Zhang, Dongbo Bu, Yan Li, Jinyu Zhou, Hui Wang, Yaojun Wang, Chuncui Huang, Shiwei Sun:
De novo glycan structural identification from mass spectra using tree merging strategy. Comput. Biol. Chem. 80: 217-224 (2019) - [i2]Fusong Ju, Jianwei Zhu, Guozheng Wei, Qi Zhang, Shiwei Sun, Dongbo Bu:
Seq-SetNet: Exploring Sequence Sets for Inferring Structures. CoRR abs/1906.11196 (2019) - 2018
- [i1]Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Shiwei Sun, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. CoRR abs/1809.00083 (2018)
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