Publications

Wei Zheng, Qiqige Wuyun, and Yang Zhang. (2024). One step forward towards deep-learning protein complex structure prediction by precise multiple sequence alignment construction. Clinical and Translational Medicine, 14(6).

Qiqige Wuyun, Yihan Chen, Yifeng Shen, Yang Cao, Gang Hu, Wei Cui, Jianzhao Gao, and Wei Zheng. (2024). Recent Progress of Protein Tertiary Structure Prediction. Molecules, 29(4), 832.

Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, P. Lydia Freddolino, and Yang Zhang. (2024). Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods, 1-11.

Wei Zheng, Qiqige Wuyun, Peter L. Freddolino, and Yang Zhang. (2023). Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins: Structure, Function, and Bioinformatics, 91(12): 1684-1703.

Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter L. Freddolino, and Yang Zhang. (2022). LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Research, 50 (W1), W454-W464. 

Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, and Yang Zhang. (2020). FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, 36(12), 3749-3757. 

Wei Wang, Qiqige Wuyun, and Kevin Liu. (2019). An application of random walk resampling to phylogenetic hidden Markov model inference and learning. IEEE Transactions on NanoBioscience, 19(3), 506-517. 

Sean P. Mullen, Nicholas W. VanKuren, Wei Zhang, Sumitha Nalluz, Evan B. Kristiansen, Qiqige Wuyun, Kevin Liu, Ryan I. Hill, Adriana D. Briscoe, and Marcus R. Kronforst. (2020). Disentangling population history and character evolution among hybridizing lineages. Molecular Biology and Evolution, 37(5), 1295-1305. 

Wei Zheng†, Qiqige Wuyun†, Micah Cheng, Gang Hu, and Yanping Zhang. (2020). Two-Level Protein Methylation Prediction using structure model-based features. Scientific Reports, 10(1), 6008. 

Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, and Yang Zhang. (2019). Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLoS computational biology, 15(10), e1007411. 

Wei Wang, Qiqige Wuyun, and Kevin Liu. (2019). An application of random walk resampling to phylogenetic hidden Markov model inference and learning. In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 44-51).   

Qiqige Wuyun, Nicholas W. VanKuren, Marcus Kronforst, Sean P. Mullen, and Kevin J. Liu. (2019). Scalable statistical introgression mapping using approximate coalescent-based inference. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics(pp. 504-513). 

Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, and Yang Zhang. (2019). LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic acids research, 47(W1), W429-W436. 

Honglin Bao, Qiqige Wuyun, and Wolfgang Banzhaf. (2018). Evolution of cooperation through genetic collective learning and imitation in multiagent societies. In Artificial Life Conference Proceedings (pp. 436-443).

Qiqige Wuyun†, Wei Zheng†, Zhenling Peng, and Jianyi Yang. (2018). A large-scale comparative assessment of methods for residue–residue contact prediction. Briefings in bioinformatics, 19(2), 219-230. 

Yang Li, Wei Zheng, Qiqige Wuyun, Shujuan Cao, Jishou Ruan, and Yanping Zhang. (2018). A novel method for drug screen to regulate G protein-coupled receptors in the metabolic network of Alzheimer’s disease. BioMed research international, 2018. 

Tong Wang, Wei Zheng, Qiqige Wuyun, Zhenfeng Wu, Jishou Ruan, Gang Hu, and Jianzhao Gao. (2017). PrAS: Prediction of amidation sites using a multiple feature extraction. Computational biology and chemistry, 66, 57-62. 

Yanping Zhang, Wuyunqiqige (Qiqige Wuyun), Wei Zheng, Shuyi Liu, and Chunguang Zhao. (2016). gDNA-Prot: predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of Protein. Journal of Theoretical Biology, 406: 8-16. 

Qiqige Wuyun, Wei Zheng, Yanping Zhang, Jishou Ruan, and Gang Hu. (2016). Improved species-specific lysine acetylation site prediction based on a large variety of features set. PloS one, 11(5), e0155370.