Publication / 论著

Publications and Citations / 论著与引用

Selected Publications / 代表性论著

  • Jiating Yu, Jiacheng Leng, Zhichao Hou, Duanchen Sun, and Ling-Yun Wu. Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis. Briefings in Bioinformatics, 25(2):bbae093, 2024. [Online, BioRxiv]
  • Tao Ren, Canping Chen, Alexey V. Danilov, Susan Liu, Xiangnan Guan, Shunyi Du, Xiwei Wu, Mara H. Sherman, Paul T. Spellman , Lisa M. Coussens, Andrew C. Adey, Gordon B. Mills, Ling-Yun Wu, and Zheng Xia. Supervised learning of high-confidence phenotypic subpopulations from single-cell data. Nature Machine Intelligence, 5:528–541, 2023. [Online, BioRxiv]
  • Jiating Yu, Jiacheng Leng, Duanchen Sun and Ling-Yun Wu. Network Refinement: denoising complex networks for better community detection. Physica A: Statistical Mechanics and its Applications, 617:128681, 2023. [Online]
  • Jiacheng Leng, Ling-Yun Wu. Interaction-based transcriptome analysis via differential network inference. Briefings in Bioinformatics, 23(6):bbac466, 2022. [Online]
  • Jiating Yu, Ling-Yun Wu. Multiple Order Local Information model for link prediction in complex networks. Physica A: Statistical Mechanics and its Applications, 600:127522, 2022. [Online]
  • Jiacheng Leng, Ling-Yun Wu. Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. Bioinformatics, 38(3):770–777, 2022. [Online]
  • Xu Wang, Guohua Gan, Ling-Yun Wu. Framework and algorithms for identifying honest blocks in blockchain. PLoS ONE, 15(1):e0227531, 2020. [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, 20(1):89-101, 2019. [PubMed, Online, Additional Materials, https://doi.org/10.1093/bib/bbx090]
  • 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]
  • 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, 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. [Online]
  • 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. [Online]
  • 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]