Reconstruction of DNA sequencing by hybridization. - Ji-Hong Zhang; Ling-Yun Wu; Xiang-Sun Zhang (Bioinform., 2003)

Haplotype reconstruction from SNP fragments by minimum error correction. - Rui-Sheng Wang; Ling-Yun Wu; Zhen-Ping Li; Xiang-Sun Zhang (Bioinform., 2005)

Haplotype assembly from aligned weighted SNP fragments. - Yu-Ying Zhao; Ling-Yun Wu; Ji-Hong Zhang; Rui-Sheng Wang; Xiang-Sun Zhang (Comput. Biol. Chem., 2005)

Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping. - Xiang-Sun Zhang; Yong Wang 001; Zhong-Wei Zhan; Ling-Yun Wu; Luonan Chen (J. Bioinform. Comput. Biol., 2005)

Automatic Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. - Yong Wang 001; Ling-Yun Wu; Xiang-Sun Zhang; Luonan Chen (TAMC, 2006)

Capacitated facility location problem with general setup cost. - Ling-Yun Wu; Xiang-Sun Zhang; Ju-Liang Zhang (Comput. Oper. Res., 2006)

Predicting gene ontology functions from protein's regional surface structures. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Luonan Chen; Xiang-Sun Zhang (BMC Bioinform., 2007)

Analysis on multi-domain cooperation for predicting protein-protein interactions. - Rui-Sheng Wang; Yong Wang 001; Ling-Yun Wu; Xiang-Sun Zhang; Luonan Chen (BMC Bioinform., 2007)

An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors. - Ji-Hong Zhang; Ling-Yun Wu; Yu-Ying Zhao; Xiang-Sun Zhang (Eur. J. Oper. Res., 2007)

Supervised classification of protein structures based on convex hull representation. - Yong Wang 001; Ling-Yun Wu; Luonan Chen; Xiang-Sun Zhang (Int. J. Bioinform. Res. Appl., 2007)

A fast haplotype inference method for large population genotype data. - Ji-Hong Zhang; Ling-Yun Wu; Jian Chen; Xiang-Sun Zhang (Comput. Stat. Data Anal., 2008)

Protein cavity clustering based on community structure of pocket similarity network. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Int. J. Bioinform. Res. Appl., 2008)

Conditional random pattern algorithm for LOH inference and segmentation. - Ling-Yun Wu; Xiaobo Zhou 001; Fuhai Li 001; Xiaorong Yang; Chung-Che Chang; Stephen T. C. Wong (Bioinform., 2009)

Self-organizing map approaches for the haplotype assembly problem. - Ling-Yun Wu; Zhen-Ping Li; Rui-Sheng Wang; Xiang-Sun Zhang; Luonan Chen (Math. Comput. Simul., 2009)

Evaluating Protein Similarity from Coarse Structures. - Yong Wang 001; Ling-Yun Wu; Ji-Hong Zhang; Zhong-Wei Zhan; Xiang-Sun Zhang; Luonan Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Prediction of protein-RNA binding sites by a random forest method with combined features. - Zhi-Ping Liu; Ling-Yun Wu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Bioinform., 2010)

An information-flow-based model with dissipation, saturation and direction for active pathway inference. - Xian-Wen Ren; Xiaobo Zhou 001; Ling-Yun Wu; Xiang-Sun Zhang (BMC Syst. Biol., 2010)

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces. - Zheng Xia; Ling-Yun Wu; Xiaobo Zhou 001; Stephen T. C. Wong (BMC Syst. Biol., 2010)

An efficient network querying method based on conditional random fields. - Qiang Huang; Ling-Yun Wu; Xiang-Sun Zhang (Bioinform., 2011)

CNetA: Network alignment by combining biological and topological features. - Qiang Huang; Ling-Yun Wu; Xiang-Sun Zhang (ISB, 2012)

Efficient methods for identifying mutated driver pathways in cancer. - Junfei Zhao; Shi-Hua Zhang; Ling-Yun Wu; Xiang-Sun Zhang (Bioinform., 2012)

Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection. - Yong Wang 001; Qiao-Feng Wu; Chen Chen; Ling-Yun Wu; Xian-Zhong Yan; ShuGuang Yu; Xiang-Sun Zhang; Fan-Rong Liang (BMC Syst. Biol., 2012)

Corbi: a new R package for biological network alignment and querying. - Qiang Huang; Ling-Yun Wu; Xiang-Sun Zhang (BMC Syst. Biol., 2013)

Structure and dynamics of core/periphery networks. - Peter Csermely; András London; Ling-Yun Wu; Brian Uzzi (J. Complex Networks, 2013)

Discovery of co-occurring driver pathways in cancer. - Junhua Zhang 002; Ling-Yun Wu; Xiang-Sun Zhang; Shihua Zhang (BMC Bioinform., 2014)

Potts model based on a Markov process computation solves the community structure problem effectively. - Hui-Jia Li; Yong Wang 001; Ling-Yun Wu; Junhua Zhang 002; Xiang-Sun Zhang (CoRR, 2015)

Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. - Zhi-Ping Liu; Shutang Liu; Ruitang Chen; Xiaopeng Huang; Ling-Yun Wu (BMC Bioinform., 2017)

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis. - Duanchen Sun; Yinliang Liu; Xiang-Sun Zhang; Ling-Yun Wu (BMC Syst. Biol., 2017)

Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. - Duanchen Sun; Xian-Wen Ren; Eszter Ari; Tamás Korcsmáros; Peter Csermely; Ling-Yun Wu (Briefings Bioinform., 2019)

An Optimization Method for Calibrating Wireline Conveyance Tension. - Can Jin; Xin Peng; Qing Liu; Xinhan Ye; Lang Chen; Qiuyue Yuan; Xiang-Sun Zhang; Ling-Yun Wu; Yong Wang (CSDM Asia / CSDM, 2021)

Network Refinement: A unified framework for enhancing signal or removing noise of networks. - Jiating Yu; Jiacheng Leng; Ling-Yun Wu (CoRR, 2021)

Understanding the network formation pattern for better link prediction. - Jiating Yu; Ling-Yun Wu (CoRR, 2021)

Interaction-based transcriptome analysis via differential network inference. - Jiacheng Leng; Ling-Yun Wu (Briefings Bioinform., 2022)

hDirect-MAP: projection-free single-cell modeling of response to checkpoint immunotherapy. - Yong Lu; Gang Xue; Ningbo Zheng; Kun Han; Wenzhong Yang; Rui-Sheng Wang; Ling-Yun Wu; Lance D. Miller; Timothy Pardee; Pierre L. Triozzi; Hui-Wen Lo; Kounosuke Watabe; et al. (Briefings Bioinform., 2022)

Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. - Jiacheng Leng; Ling-Yun Wu (Bioinform., 2022)

Supervised learning of high-confidence phenotypic subpopulations from single-cell data. - 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; et al. (Nat. Mac. Intell., 2023)

Author Correction: Supervised learning of high-confidence phenotypic subpopulations from single-cell data. - 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; et al. (Nat. Mac. Intell., 2023)

PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery. - Zhichao Hou; Jiacheng Leng; Jiating Yu; Zheng Xia; Ling-Yun Wu (BMC Bioinform., 2023)

Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis. - Jiating Yu; Jiacheng Leng; Zhichao Hou; Duanchen Sun; Ling-Yun Wu (Briefings Bioinform., 2024)

Toward energy-efficient blockchain system: A game theoretic analysis. - Xu Wang; Ling-Yun Wu (Comput. Ind. Eng., 2025)