Welcome to join our lab, let's keep this list rolling together!

^#: Equal Contribution, ^*: Corresponding Author

2026

• Improving mutation pathogenicity prediction of metal-binding sites in proteins with a panoramic attention mechanism.
  Yuan Zhang, Jiafeng Wu, Qiuye Zhao, Mingyuan Dong, Junsheng Deng, Xieping Gao, Kai Hu, Dapeng Xiong^*.
  Pattern Recognition, 2026, 169:1111935.

2025

• A structurally informed human protein–protein interactome reveals proteome-wide perturbations caused by disease mutations.
  Dapeng Xiong^#, Yunguang Qiu^#, Junfei Zhao^#, Yadi Zhou^#, Dongjin Lee^#, Shobhita Gupta, Mateo Torres, Weiqiang Lu, Siqi Liang, Jin Joo Kang, Charis Eng, Joseph Loscalzo, Feixiong Cheng^*, Haiyuan Yu^*.
  Nature Biotechnology, 2025, 43:1510-1524.
• PILOT: Deep Siamese network with hybrid attention improves prediction of mutation impact on protein stability.
  Yuan Zhang, Junsheng Deng, Mingyuan Dong, Jiafeng Wu, Qiuye Zhao^*, Xieping Gao^*, Dapeng Xiong^*.
  Neural Networks, 2025, 188:107476.
• PyPropel: a Python-based tool for efficiently processing and characterising protein data.
  Jianfeng Sun^*, Jinlong Ru, Adam P. Cribbs, Dapeng Xiong^*.
  BMC Bioinformatics, 2025, 26:70.

2024

• Graph masked self-distillation learning for prediction of mutation impact on protein–protein interactions.
  Yuan Zhang, Mingyuan Dong, Junsheng Deng, Jiafeng Wu, Qiuye Zhao^*, Xieping Gao^*, Dapeng Xiong^*.
  Communications Biology, 2024, 7:1400.
• PLMC: Language model of protein sequences enhances protein crystallization prediction.
  Dapeng Xiong^*, Kaicheng U, Jianfeng Sun^*, Adam P. Cribbs.
  Interdisciplinary Sciences: Computational Life Sciences, 2024, 16:802-813.

2023

• Polyp segmentation with distraction separation.
  Tongtong Liu^#, Xiongjun Ye^#, Kai Hu, Dapeng Xiong, Yuan Zhang^*, Xuanya Li, Xieping Gao^*.
  Expert Systems with Applications, 2023, 228:120434.
• Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications.
  Jianfeng Sun^#*, Miaoer Xu^#, Jinlong Ru, Anna James-Bott, Dapeng Xiong, Xia Wang^*, Adam P Cribbs^*.
  European Journal of Medicinal Chemistry, 2023, 257:115500.
• Boundary-guided and Region-aware Network with Global Scale-adaptive for Accurate Segmentation of Breast Tumors in Ultrasound Images.
  Kai Hu, Xiang Zhang, Dongjin Lee, Dapeng Xiong, Yuan Zhang^*, Xieping Gao^*.
  IEEE Journal of Biomedical and Health Informatics, 2023, 27(9):4421-4432.

2022

• AS-Net: Attention Synergy Network for skin lesion segmentation.
  Kai Hu, Jing Lu, Dongjin Lee, Dapeng Xiong, Zhineng Chen^*.
  Expert Systems with Applications, 2022, 201:117112.
• Deep learning methods for 3D structural proteome and interactome modeling.
  Dongjin Lee^#, Dapeng Xiong^#, Shayne Wierbowski^#, Le Li^#, Siqi Liang^#, Haiyuan Yu^*.
  Current Opinion in Structural Biology, 2022, 73:102329.
• Implications of disease-related mutations at protein–protein interfaces.
  Dapeng Xiong^#, Dongjin Lee^#, Le Li^#, Qiuye Zhao^#, Haiyuan Yu^*.
  Current Opinion in Structural Biology, 2022, 72:219-225.

2021

• Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry.
  Kumar Yugandhar^#, Qiuye Zhao^#, Shobhita Gupta^#, Dapeng Xiong^#, Haiyuan Yu^*.
  Proteomics, 2021, 21:2100145.

2020

• LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting.
  Yuan Zhang^#, Fei Ye^#, Dapeng Xiong, Xieping Gao^*.
  BMC Bioinformatics, 2020, 21: 377.

2017

• Predicting the helix-helix interactions from correlated residue mutations.
  Dapeng Xiong^#, Wenzhi Mao^#, Haipeng Gong^*.
  Proteins: Structure, Function and Bioinformatics, 2017, 85(12): 2162-2169.
• A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy.
  Dapeng Xiong, Jianyang Zeng^*, Haipeng Gong^*.
  Bioinformatics, 2017, 33(17): 2675-2683.

2015

• RBRIdent: an algorithm for improved identification of RNA-binding residues in proteins from primary sequences.
  Dapeng Xiong, Jianyang Zeng, Haipeng Gong^*.
  Proteins: Structure, Function and Bioinformatics, 2015, 83(6): 1068-1077.

2014

• ProMT: effective human promoter prediction using markov chain model based on DNA structural properties.
  Dapeng Xiong, Rongjie Liu, Fen Xiao, Xieping Gao^*.
  IEEE Transactions on NanoBioscience, 2014, 13(4): 374-383.

2012

• Towards a better detection of horizontally transferred genes by combining unusual properties effectively.
  Dapeng Xiong, Fen Xiao, Li Liu, Kai Hu, Yanping Tan, Shunmin He^*, Xieping Gao^*.
  PLoS ONE, 2012, 7(8): e43126.
• A novel image segmentation algorithm based on Hidden Markov Random Field model and Finite Mixture Model parameter estimation.
  Kai Hu^*, Guangyu Tang, Dapeng Xiong, Quan Qiu.
  Proceedings of the 2012 International Conference on Wavelet Analysis and Pattern Recognition, Xian, July 15-17, 2012.