Publications and Citations

Selected Publications


  • Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang, Ling-Yun Wu. CEA: Combination-based gene set functional enrichment analysis. Scientific Reports, 8:13085, 2018. [PubMed, Online]


  • Duanchen Sun, Xianwen Ren, Eszter Ari, Tamas Korcsmaros, Peter Csermely, and Ling-Yun Wu. Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. Briefings in Bioinformatics, bbx090, 2017. [PubMed, Online, Additional Materials,]


  • Peter Csermely, János Hódsági, Tamás Korcsmáros, Dezső Módos, Áron R. Perez-Lopez, Kristóf Szalay, Dániel V. Veres, Katalin Lenti, Ling-Yun Wu, Xiang-Sun Zhang. Cancer stem cells display extremely large evolvability: alternating plastic and rigid networks as a potential mechanism. Seminars in Cancer Biology, 30:42–51, 2015. [PubMed]


  • Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang. Corbi: A new R package for biological network alignment and querying. BMC Systems Biology, 7(S2):S6, 2013. [PubMed, Software]


  • Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang. An efficient network querying method based on conditional random fields. Bioinformatics, 27(22):3173-3178, 2011. [PubMed, Software]


  • Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T.C. Wong. Conditional random pattern algorithm for LOH inference and segmentation. Bioinformatics, 25(1):61-67, 2009. [PubMed, Supplementary File]


  • Ji-Hong Zhang, Ling-Yun Wu, Jian Chen, and Xiang-Sun Zhang. A fast haplotype inference method for large population genotype data. Computational Statistics and Data Analysis, 52(11):4891-4902, 2008. [ScienceDirect, Supplementary File]


  • Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang. An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors. European Journal of Operational Research, 182(1):413-427, 2007. [ScienceDirect]
  • Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. Predicting gene ontology functions from protein’s regional surface structures. BMC Bioinformatics, 8:475, 2007. [PubMed, Supplementary File]


  • Ling-Yun Wu, Xiang-Sun Zhang and Ju-Liang Zhang. Capacitated facility location problem with general setup cost. Computers & Operations Research, 33(5):1226-1241, 2006. [ScienceDirect]
  • Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. Inferring protein interactions from experimental data by association probabilistic method. Proteins: Structure, Function, and Bioinformatics, 62:833-837, 2006. [PubMed]
  • Luonan Chen, Ling-Yun Wu, Yong Wang, Shi-Hua Zhang and Xiang-Sun Zhang. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Structural Biology, 6:18, 2006. [PubMed, Software]


  • Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li and Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. Bioinformatics, 21(10):2456-2462, 2005. [PubMed]


  • Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. Bioinformatics, 19(1):14-21, 2003. [PubMed]