Publications

# Co-first authors; * Co-corresponding authors

Journal Articles

2024

  1. Lei Wang#, Zilu Zeng#, Zhidong Xue*, and Yan Wang*. (2024). DeepNeuropePred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model. Computational and Structural Biotechnology Journal, 23, 309–315. https://doi.org/10.1016/j.csbj.2023.12.004
  2. Mingxia Wang#, Lei Wang#, Wei Xu, Ziqiang Chu, Hengzhi Wang, Jingxiang Lu, Zhidong Xue, and Yan Wang. (2024). NeuroPep 2.0: An Updated Database Dedicated to Neuropeptide and Its Receptor Annotations. Journal of Molecular Biology, 436(4), 168416. https://doi.org/10.1016/j.jmb.2023.168416

2023

  1. Lei Wang, Chen Huang, Mingxia Wang, Zhidong Xue*, and Yan Wang*. (2023). NeuroPred-PLM: An interpretable and robust model for neuropeptide prediction by protein language model. Briefings in Bioinformatics, 24(2), bbad077. https://doi.org/10.1093/bib/bbad077
  2. Lei Wang, Hui Zhang, Wei Xu, Zhidong Xue*, and Yan Wang*. (2023). Deciphering the protein landscape with ProtFlash, a lightweight language model. Cell Reports Physical Science, 4(10). https://doi.org/10.1016/j.xcrp.2023.101600

2022

  1. Lei Wang, Haolin Zhong, Zhidong Xue*, and Yan Wang*. (2022). Improving the topology prediction of α-helical transmembrane proteins with deep transfer learning. Computational and Structural Biotechnology Journal, 20, 1993–2000. https://doi.org/10.1016/j.csbj.2022.04.024
  2. Lei Wang, Haolin Zhong, Zhidong Xue*, and Yan Wang*. (2022). Res-Dom: Predicting protein domain boundary from sequence using deep residual network and Bi-LSTM. Bioinformatics Advances, 2(1), vbac060. https://doi.org/10.1093/bioadv/vbac060

2021

  1. Yan Wang, Hang Zhang, Haolin Zhong, and Zhidong Xue. (2021). Protein domain identification methods and online resources. Computational and Structural Biotechnology Journal, 19, 1145–1153. https://doi.org/10.1016/j.csbj.2021.01.041

2020

  1. Weiya Chen, Chenchen Yu, Chenyu Tu, Zehua Lyu, Jing Tang, Shiqi Ou*, Yan Fu*, and Zhidong Xue*. (2020). A Survey on Hand Pose Estimation with Wearable Sensors and Computer-Vision-Based Methods. Sensors, 20(4), Article 4. https://doi.org/10.3390/s20041074
  2. Weiya Chen, Chun Yao, Yingzhong Guo, Yan Wang, and Zhidong Xue. (2020). pmTM-align: Scalable pairwise and multiple structure alignment with Apache Spark and OpenMP. BMC Bioinformatics, 21(1), 426. https://doi.org/10.1186/s12859-020-03757-2

2019

  1. Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang*, and Zhidong Xue*. (2019). Deep learning for mining the protein data. Briefings in Bioinformatics, 22(1), 194–218. https://doi.org/10.1093/bib/bbz156
  2. Yan Wang#, Qiang Shi#, Pengshuo Yang#, Chengxin Zhang#, S. M. Mortuza, Zhidong Xue*, Kang Ning*,and Yang Zhang*. (2019). Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. Genome Biology, 20(1), 229. https://doi.org/10.1186/s13059-019-1823-z
  3. Qiang Shi, Weiya Chen, Siqi Huang, Fanglin Jin, Yinghao Dong, Yan Wang*, and Zhidong Xue*. (2019). DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network. Bioinformatics, 35(24), 5128–5136. https://doi.org/10.1093/bioinformatics/btz464

2018

  1. Qiang Shi#, Weiya Chen#, Ye Pan, Shan Yin, Yan Fu, Jiacai Mei*, and Zhidong Xue*.(2018). An Automatic Classification Method on Chronic Venous InSufficiency Images. Scientific Reports, 8(1), 17952. https://doi.org/10.1038/s41598-018-36284-5
  2. Jian Wang#, Tailang Yin#, Xuwen Xiao, Dan He, Zhidong Xue, Xinnong Jiang*, and Yan Wang*. (2018). StraPep: a Structure Database of Bioactive Peptides. Database, 2018, bay038. https://doi.org/10.1093/database/bay038

2017

  1. Yan Wang, Jian Wang, Ruiming Li, Qiang Shi, Zhidong Xue*, and Yang Zhang*. (2017). ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Research, 45(W1), W400–W407. https://doi.org/10.1093/nar/gkx410
  2. Yan Wang, Jouko Virtanen, Zhidong Xue*, and Yang Zhang*. (2017). I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. Nucleic Acids Research, 45(W1), W429–W434. https://doi.org/10.1093/nar/gkx349

2016

  1. Yan Wang, Jouko Virtanen, Zhidong Xue, John J. G. Tesmer, and Yang Zhang. (2016). Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallographica Section D: Structural Biology, 72(5), 616–628. https://doi.org/10.1107/S2059798316003016
  2. Jianyi Yang, Yan Wang, and Yang Zhang*. (2016). ResQ: An Approach to Unified Estimation of B-Factor and Residue-Specific Error in Protein Structure Prediction. Journal of Molecular Biology, 428(4), 693–701. https://doi.org/10.1016/j.jmb.2015.09.024

2015

  1. Zhidong Xue*, Richard Jang, Brandon Govindarajoo, Yichu Huang, and Yan Wang*. (2015). Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PLOS ONE, 10(10), e0141541. https://doi.org/10.1371/journal.pone.0141541