Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

De novo glycan structural identification from mass spectra using tree merging strategy. - Fusong Ju; Jingwei Zhang; Dongbo Bu; Yan Li; Jinyu Zhou; Hui Wang; Yaojun Wang; Chuncui Huang; Shiwei Sun (Comput. Biol. Chem., 2019)

Seq-SetNet: Exploring Sequence Sets for Inferring Structures. - Fusong Ju; Jianwei Zhu; Guozheng Wei; Qi Zhang; Shiwei Sun; Dongbo Bu (CoRR, 2019)

ISSEC: inferring contacts among protein secondary structure elements using deep object detection. - Qi Zhang; Jianwei Zhu; Fusong Ju; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2020)

Co-evolution Transformer for Protein Contact Prediction. - He Zhang; Fusong Ju; Jianwei Zhu; Liang He 010; Bin Shao; Nanning Zheng 001; Tie-Yan Liu (NeurIPS, 2021)

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. - Bin Huang; Guozheng Wei; Bing Wang; Fusong Ju; Yi Zhong; Zhuozheng Shi; Shiwei Sun; Dongbo Bu (BMC Bioinform., 2021)

FALCON2: a web server for high-quality prediction of protein tertiary structures. - Lupeng Kong; Fusong Ju; Haicang Zhang; Shiwei Sun; Dongbo Bu (BMC Bioinform., 2021)

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model. - Liang He 010; Shizhuo Zhang; Lijun Wu 003; Huanhuan Xia; Fusong Ju; He Zhang; Siyuan Liu 005; Yingce Xia; Jianwei Zhu; Pan Deng; Bin Shao; Tao Qin 001; et al. (CoRR, 2021)

Exploring evolution-aware & -free protein language models as protein function predictors. - Mingyang Hu; Fajie Yuan; Kevin Yang; Fusong Ju; Jin Su; Hui Wang; Fei Yang; Qiuyang Ding (NeurIPS, 2022)

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. - Fusong Ju; Jianwei Zhu; Qi Zhang; Guozheng Wei; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2022)

Exploring evolution-based & -free protein language models as protein function predictors. - Mingyang Hu; Fajie Yuan; Kevin K. Yang; Fusong Ju; Jin Su; Hui Wang; Fei Yang; Qiuyang Ding (CoRR, 2022)

ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. - Lupeng Kong; Fusong Ju; Wei-Mou Zheng; Jianwei Zhu; Shiwei Sun; Jinbo Xu; Dongbo Bu (J. Comput. Biol., 2022)

Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (CoRR, 2023)

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. - Bin Huang; Lupeng Kong; Chao Wang; Fusong Ju; Qi Zhang; Jianwei Zhu; Tiansu Gong; Haicang Zhang; Chungong Yu; Wei-Mou Zheng; Dongbo Bu (Genom. Proteom. Bioinform., 2023)

SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances. - Tiansu Gong; Fusong Ju; Shiwei Sun; Dongbo Bu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Matryoshka: Optimization of Dynamic Diverse Quantum Chemistry Systems via Elastic Parallelism Transformation. - Tuowei Wang; Kun Li 016; Donglin Bai; Fusong Ju; Leo Xia; Ting Cao; Ju Ren 001; Yaoxue Zhang; Mao Yang 004 (CoRR, 2024)

Predicting equilibrium distributions for molecular systems with deep learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (Nat. Mac. Intell., 2024)

Author Correction: Predicting equilibrium distributions for molecular systems with deep learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (Nat. Mac. Intell., 2024)