A convergence theorem of Rosen's gradient projection method. - Ding-Zhu Du; Xiang-Sun Zhang (Math. Program., 1986)

Global convergence of Rosen's gradient projection method. - Ding-Zhu Du; Xiang-Sun Zhang (Math. Program., 1989)

A Note on the Continuity of Solutions of Parametric Linear Programs. - Xiang-Sun Zhang; De-Gang Liu (Math. Program., 1990)

A Neural Network Model for Quadratic Programming with Simple Upper and Lower Bounds and its Application to Linear Programming. - Xiang-Sun Zhang; Hui-Can Zhu (ISAAC, 1994)

Test Problem Generator by Neural Network for Algorithms that Try Solving Nonlinear Programming Problems Globally. - De-Gang Liu; Xiang-Sun Zhang (J. Glob. Optim., 2000)

A Modified SQP Method with Nonmonotone Linesearch Technique. - Ju-Liang Zhang; Xiang-Sun Zhang (J. Glob. Optim., 2001)

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

A parsimonious tree-grow method for haplotype inference. - Zhen-Ping Li; Wenfeng Zhou; Xiang-Sun Zhang; Luonan Chen (Bioinform., 2005)

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)

Aligning Multiple Protein Structures by Deterministic Annealing. - Tianshou Zhou; Luonan Chen; Yun Tang; Xiang-Sun Zhang (J. Bioinform. Comput. Biol., 2005)

Alignment of Protein Interaction Networks by Integer Quadratic Programming. - Zhen-Ping Li; Yong Wang 001; Shihua Zhang; Xiang-Sun Zhang; Luonan Chen (EMBC, 2006)

A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks. - Shi-Hua Zhang; Hong-Wei Liu; Xue-Mei Ning; Xiang-Sun Zhang (ICDM Workshops, 2006)

Supervised Inference of Gene Regulatory Networks by Linear Programming. - Yong Wang 001; Trupti Joshi; Dong Xu 002; Xiang-Sun Zhang; Luonan Chen (ICIC (3), 2006)

Prediction of Protein Complexes Based on Protein Interaction Data and Functional Annotation Data Using Kernel Methods. - Shi-Hua Zhang; Xue-Mei Ning; Hong-Wei Liu; Xiang-Sun Zhang (ICIC (3), 2006)

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)

A smoothing Levenberg-Marquardt method for NCP. - Ju-Liang Zhang; Xiang-Sun Zhang (Appl. Math. Comput., 2006)

Inferring gene regulatory networks from multiple microarray datasets. - Yong Wang 001; Trupti Joshi; Xiang-Sun Zhang; Dong Xu 002; Luonan Chen (Bioinform., 2006)

Identification of functional modules in a PPI network by clique percolation clustering. - Shi-Hua Zhang; Xue-Mei Ning; Xiang-Sun Zhang (Comput. Biol. Chem., 2006)

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

Binary Matrix Factorization with Applications. - Zhongyuan Zhang; Tao Li 001; Chris H. Q. Ding; Xiang-Sun Zhang (ICDM, 2007)

Identifying Modules in Complex Networks by a Graph-Theoretical Method and Its Application in Protein Interaction Networks. - Rui-Sheng Wang; Shi-Hua Zhang; Xiang-Sun Zhang; Luonan Chen (ICIC (2), 2007)

Detecting Community Structure in Complex Networks by Optimal Rearrangement Clustering. - Rui-Sheng Wang; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (PAKDD Workshops, 2007)

Alignment of molecular networks by integer quadratic programming. - Zhen-Ping Li; Shi-Hua Zhang; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Bioinform., 2007)

Inferring transcriptional regulatory networks from high-throughput data. - Rui-Sheng Wang; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Bioinform., 2007)

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)

Convergence analysis of adaptive trust region methods. - Zhen-Jun Shi; Xiang-Sun Zhang; Jie Shen 009 (RAIRO Oper. Res., 2007)

Reconstruction of Regulator Activity in E. coli Post-Transcription Processes. - Rui-Sheng Wang; Guangxu Jin; Xiang-Sun Zhang; Luonan Chen (BIBM, 2008)

Biomolecular network querying: a promising approach in systems biology. - Shihua Zhang; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2008)

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)

Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. - Rui-Sheng Wang; Shi-Hua Zhang; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (Neurocomputing, 2008)

Remarks on Network Community Properties. - Jiguang Wang; Yu-Qing Qiu; Rui-Sheng Wang; Xiang-Sun Zhang (J. Syst. Sci. Complex., 2008)

Recognition of Structure Similarities in Proteins. - Lin Wang; Yu-Qing Qiu; Jiguang Wang; Xiang-Sun Zhang (J. Syst. Sci. Complex., 2008)

Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. - Zhi-Ping Liu; Yong Wang 001; Tieqiao Wen; Xiang-Sun Zhang; Weiming Xia; Luonan Chen (SMC, 2009)

Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli. - Rui-Sheng Wang; Guangxu Jin; Xiang-Sun Zhang; Luonan Chen (BMC Bioinform., 2009)

A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks. - Shi-Hua Zhang; Hong-Wei Liu; Xue-Mei Ning; Xiang-Sun Zhang (Int. J. Data Min. 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)

Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases. - Jiguang Wang; Shi-Hua Zhang; Yong Wang 001; Luonan Chen; Xiang-Sun Zhang (PLoS Comput. Biol., 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)

Fuzzy System Methods in Modeling Gene Expression and Analyzing Protein Networks. - Shi-Hua Zhang; Rui-Sheng Wang; Xiang-Sun Zhang; Luonan Chen (Fuzzy Systems in Bioinformatics and Computational Biology, 2009)

Inferring gene regulatory networks from expression data with prior knowledge by linear programming. - Zhi-Ping Liu; Xiang-Sun Zhang; Luonan Chen (ICMLC, 2010)

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)

Detecting disease associated modules and prioritizing active genes based on high throughput data. - Yu-Qing Qiu; Shi-Hua Zhang; Xiang-Sun Zhang; Luonan Chen (BMC Bioinform., 2010)

Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. - Zhi-Ping Liu; Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 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)

Optimization meets systems biology. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2010)

Determining modular organization of protein interaction networks by maximizing modularity density. - Shi-Hua Zhang; Xue-Mei Ning; Chris H. Q. Ding; Xiang-Sun Zhang (BMC Syst. Biol., 2010)

Binary matrix factorization for analyzing gene expression data. - Zhongyuan Zhang; Tao Li 001; Chris H. Q. Ding; Xian-Wen Ren; Xiang-Sun Zhang (Data Min. Knowl. Discov., 2010)

Editorial. - Luonan Chen; Xiang-Sun Zhang (J. Syst. Sci. Complex., 2010)

Self-organizing map of complex networks for community detection. - Zhen-Ping Li; Rui-Sheng Wang; Xiang-Sun Zhang; Luonan Chen (J. Syst. Sci. Complex., 2010)

A linear programming model based on network flow for pathway inference. - Xian-Wen Ren; Xiang-Sun Zhang (J. Syst. Sci. Complex., 2010)

Detecting community structure: From parsimony to weighted parsimony. - Junhua Zhang 002; Yu-Qing Qiu; Xiang-Sun Zhang (J. Syst. Sci. Complex., 2010)

Inferring Protein-Protein Interactions Based on Sequences and Interologs in Mycobacterium Tuberculosis. - Zhi-Ping Liu; Jiguang Wang; Yu-Qing Qiu; Ross K. K. Leung; Xiang-Sun Zhang; Stephen Kwok-Wing Tsui; Luonan Chen (ICIC (3), 2011)

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

Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. - Xian-Wen Ren; Yong-Cui Wang; Yong Wang 001; Xiang-Sun Zhang; Nai-Yang Deng (BMC Bioinform., 2011)

Two-stage flux balance analysis of metabolic networks for drug target identification. - Zhen-Ping Li; Rui-Sheng Wang; Xiang-Sun Zhang (BMC Syst. Biol., 2011)

Computational systems biology: integration of sequence, structure, network, and dynamics. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2011)

Co-community Structure in Multiple Evolving Networks - Shi-Hua Zhang; Junfei Zhao; Xiang-Sun Zhang (CoRR, 2011)

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

Identifying mutated core modules in glioblastoma by integrative network analysis. - Junhua Zhang 002; Shi-Hua Zhang; Yong Wang 001; Junfei Zhao; 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)

Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. - Zhi-Ping Liu; Jiguang Wang; Yu-Qing Qiu; Ross K. K. Leung; Xiang-Sun Zhang; Stephen Kwok-Wing Tsui; Luonan Chen (BMC Bioinform., 2012)

A unified computational model for revealing and predicting subtle subtypes of cancers. - Xian-Wen Ren; Yong Wang 001; Jiguang Wang; Xiang-Sun Zhang (BMC Bioinform., 2012)

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. - Chen Chen; Junfei Zhao; Qiang Huang; Rui-Sheng Wang; Xiang-Sun Zhang (BMC Syst. Biol., 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)

Modelling biological systems from molecules to dynamical networks. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2012)

A combinatorial model and algorithm for globally searching community structure in complex networks. - Xiang-Sun Zhang; Zhen-Ping Li; Rui-Sheng Wang; Yong Wang 001 (J. Comb. Optim., 2012)

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

Computational systems biology in the big data era. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2013)

Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. - Junhua Zhang 002; Shi-Hua Zhang; Yong Wang 001; Xiang-Sun Zhang (BMC Syst. Biol., 2013)

Multiple birth support vector machine for multi-class classification. - Zhi-Xia Yang; Yuan-Hai Shao 001; Xiang-Sun Zhang (Neural Comput. Appl., 2013)

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

NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data. - Meng Zou; Zhaoqi Liu; Xiang-Sun Zhang; Yong Wang 001 (Bioinform., 2015)

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)

Analysis of stability of community structure across multiple hierarchical levels. - Hui-Jia Li; Xiang-Sun Zhang (CoRR, 2015)

Identifying overlapping communities in social networks using multi-scale local information expansion. - Hui-Jia Li; Junhua Zhang 002; Zhi-Ping Liu; Luonan Chen; Xiang-Sun Zhang (CoRR, 2015)

Quantitative function and algorithm for community detection in bipartite networks. - Zhen-Ping Li; Rui-Sheng Wang; Shihua Zhang; Xiang-Sun Zhang (Inf. Sci., 2016)

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)

Understanding biological systems through the lens of data. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2017)

Integrating data- and model-driven strategies in systems biology. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC Syst. Biol., 2018)

Systems biology intertwines with single cell and AI. - Yong Wang 001; Xiang-Sun Zhang; Luonan Chen (BMC 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)