2024
Author Correction: Predicting equilibrium distributions for molecular systems with deep learning.
Nat. Mac. Intell., 2024

Predicting equilibrium distributions for molecular systems with deep learning.
Nat. Mac. Intell., 2024

Matryoshka: Optimization of Dynamic Diverse Quantum Chemistry Systems via Elastic Parallelism Transformation.
CoRR, 2024

2023
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms.
Genom. Proteom. Bioinform., 2023

Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning.
CoRR, 2023

2022
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs.
J. Comput. Biol., 2022

Exploring evolution-based & -free protein language models as protein function predictors.
CoRR, 2022

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction.
Bioinform., 2022

Exploring evolution-aware & -free protein language models as protein function predictors.
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

2021
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model.
CoRR, 2021

FALCON2: a web server for high-quality prediction of protein tertiary structures.
BMC Bioinform., 2021

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.
BMC Bioinform., 2021

Co-evolution Transformer for Protein Contact Prediction.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

2020
ISSEC: inferring contacts among protein secondary structure elements using deep object detection.
BMC Bioinform., 2020

2019
Seq-SetNet: Exploring Sequence Sets for Inferring Structures.
CoRR, 2019

De novo glycan structural identification from mass spectra using tree merging strategy.
Comput. Biol. Chem., 2019

Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
BMC Bioinform., 2019

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
BMC Bioinform., 2019