history "PubBioinformatics2009": ZHANGroup

~1) Xiaorong Yang, Xiaobo Zhou, Wan-Ting Huang, Lingyun Wu, Federico A. Monzon, Chung-Che Chang, and Stephen T.C. Wong. ---**[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005054;jsessionid=83175FC69984C8734C471F8B425ADB36.ambra01 Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays.]]**--- //PLoS One//, Vol. 4, No. 4, e5054, 2009. ---SCI

~1) Xiaorong Yang, Xiaobo Zhou, Wan-Ting Huang, Lingyun Wu, Federico A. Monzon, Chung-Che Chang, and Stephen T.C. Wong. ---**[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005054;jsessionid=83175FC69984C8734C471F8B425ADB36.ambra01 Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays.]]**--- //PLoS One//, Vol. 4, No. 4, e5054, 2009. SCI

~1) Xiaorong Yang, Xiaobo Zhou, Wan-Ting Huang, Lingyun Wu, Federico A. Monzon, Chung-Che Chang, and Stephen T.C. Wong. ---**Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays.**--- //Plos One//, Vol. 4, No. 4, e5054, 2009. (PubMed: 19352488)

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=5345886&arnumber=5346814&count=898&index=727 Dynamically dysfunctional protein interactions in the development of Alzheimer's disease]]. **--- IEEE International Conference on Systems, Man and Cybernetics, pp. 4262-4267. San Antonio, TX, USA, 2009. ---EI

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=5345886&arnumber=5346814&count=898&index=727 Dynamically dysfunctional protein interactions in the development of Alzheimer's disease]]. **--- IEEE International Conference on Systems, Man and Cybernetics, pp. 4262-4267. San Antonio, TX, USA, 2009.

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 79(10), 3026-3037, 2009 --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), NSFC(60873205)
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics//, 2009, 10(Suppl 4):S6 --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070)

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 79(10), 3026-3037, 2009 --- SCI; Funding: NSFC-JSPS, NSFC(60503004), NSFC(10631070), NSFC(60873205)
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics//, 2009, 10(Suppl 4):S6 --- SCI; Funding: NSFC-JSPS, NSFC(10701080), NSFC(10631070)

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters,// 87, 38002, 2009. --- SCI; Funding: NSFC(10701080), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905), CAS(kjcx-yw-s7)
~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/ Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8. ---SCI; NSFC(60873205)
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,6;journal,4,12;linkingpublicationresults,1:120129,1 A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.]]**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009. ---SCI; NSFC(10631070), CAS(kjcx-yw-s7)

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters,// 87, 38002, 2009. --- SCI; Funding: NSFC(10701080), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/ Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8. ---SCIE; NSFC(60873205)
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,6;journal,4,12;linkingpublicationresults,1:120129,1 A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.]]**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009. ---SCI; NSFC(10631070)

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.]] **--- //PLoS Computational Biology,// 9(5), e1000521, 2009. --- SCI; Funding: NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070), 973(2006CB503905), CAS(kjcx-yw-s7)

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.]] **--- //PLoS Computational Biology,// 9(5), e1000521, 2009. --- SCI; Funding: NSFC(10801131), NSFC(10631070), 973(2006CB503905)
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070)

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009. --- SCI; Funding: NSFC(10631070), NSFC(60873205), NSFC(10801131), CAS(kjcx-yw-s7)
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics//, 2009, 10(Suppl 4):S6 --- SCI; Funding: NSFC-JSPS, NSFC(10701080), NSFC(10631070)

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009. --- SCI; Funding: NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics//, 2009, 10(Suppl 4):S6

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009. --- SCI; Funding: NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.]] **--- //PLoS Computational Biology,// 9(5), e1000521, 2009. --- SCI; Funding: NSFC(10801131), NSFC(10631070), 973(2006CB503905)
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters,// 87, 38002, 2009. --- SCI; Funding: NSFC(10701080), NSFC(10801131), NSFC(10631070), NSFC(60873205), 973(2006CB503905)
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. --- SCI; Funding: NSFC-JSPS, NSFC(10801131), NSFC(10631070)
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 79(10), 3026-3037, 2009 --- SCI; Funding: NSFC-JSPS, NSFC(60503004), NSFC(10631070), NSFC(60873205)
~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/ Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8. ---SCIE; NSFC(60873205)
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,6;journal,4,12;linkingpublicationresults,1:120129,1 A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.]]**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009. ---SCI; NSFC(10631070)
~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Zhong-Yuan Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. ---**[[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Xuemei Ning, Shihua Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Zhi-Ping Liu, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F42.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Shihua Zhang, Xuemei Ning, Chris Ding. ---**[[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Junhua Zhang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009. ---ISTP

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009.
~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009.
~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.]] **--- //PLoS Computational Biology,// 9(5), e1000521, 2009.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters,// 87, 38002, 2009.
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009.
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 79(10), 3026-3037, 2009
~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/ Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,6;journal,4,12;linkingpublicationresults,1:120129,1 A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.]]**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.
~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhong-Yuan Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. ---**[[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xuemei Ning, Shihua Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhi-Ping Liu, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F42.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
~1) Shihua Zhang, Xuemei Ning, Chris Ding. ---**[[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
~1) Junhua Zhang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.

~1) Xiaorong Yang, Xiaobo Zhou, Wan-Ting Huang, Lingyun Wu, Federico A. Monzon, Chung-Che Chang, and Stephen T.C. Wong. ---**Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays.**--- //Plos One//, Vol. 4, No. 4, e5054, 2009. (PubMed: 19352488)

~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F42.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.

~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F41.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.

=== Working Papers ===
=== Accepted Papers ===

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=5345886&arnumber=5346814&count=898&index=727 Dynamically dysfunctional protein interactions in the development of Alzheimer's disease]]. **--- IEEE International Conference on Systems, Man and Cybernetics, pp. 4262-4267. San Antonio, TX, USA, 2009.

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=5345886&arnumber=5346814&count=898&index=727 Dynamically dysfunctional protein interactions in the development of Alzheimer's disease]]. **--- IEEE International Conference on Systems, Man, and Cybernetics, pp. 4262-4267. San Antonio, TX, USA, 2009.

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. **--- 2009 IEEE International Conference on Systems, Man, and Cybernetics.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/ Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000475000001&idtype=cvips&gifs=Yes Identifying differentially expressed pathways via a mixed integer linear programming model.]] **--- //IET Systems Biology//, 3(6), 475-486, 2009
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000523000001&idtype=cvips&gifs=Yes Detecting drug targets with minimum side effects in metabolic networks.]] **--- //IET Systems Biology//, 3(6), 523-533, 2009

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000475000001&idtype=cvips&gifs=YesIdentifying Differentially expressed pathways via a mixed integer linear programming model.]] **--- //IET Systems Biology//, 3(6), 475-486, 2009
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000523000001&idtype=cvips&gifs=YesDetecting Drug targets with minimum side effects in metabolic networks.]] **--- //IET Systems Biology//, 3(6), 523-533, 2009

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000475000001&idtype=cvips&gifs=YesIdentifying differentially expressed pathways via a mixed integer linear programming model.]] **--- //IET Systems Biology//, 3(6), 475-486, 2009
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000523000001&idtype=cvips&gifs=YesDetecting drug targets with minimum side effects in metabolic networks.]] **--- //IET Systems Biology//, 3(6), 523-533, 2009

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[http://www.springerlink.com/content/m71504561v141721/Exploring the constrained maximum edge-weight connected graph problem.]]**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,5,6;journal,4,12;linkingpublicationresults,1:120129,1 A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.]]**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**Exploring the Constrained Maximum Edge-Weight Connected Graph Problem.**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Guangxu Jin, Xiaobo Zhou, Kemin Cui, Xiang-Sun Zhang, Luonan Chen, and Steve T.C. Wong. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000475000001&idtype=cvips&gifs=Yes Cross-platform method for identifying candidate network biomarkers for prostate cancer.]] **--- //IET Systems Biology//, 3(6), 505-512, 2009
~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000475000001&idtype=cvips&gifs=YesIdentifying differentially expressed pathways via a mixed integer linear programming model.]] **--- //IET Systems Biology//, 3(6), 475-486, 2009

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**Identifying differentially expressed pathways via a mixed integer linear programming model. **--- //IET Systems Biology//, 3(6), 475-486, 2009

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**Identifying differentially expressed pathways via a mixed integer linear programming model. **--- //IET Systems Biology//, 3(6), 475-486, 2009
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000003000006000523000001&idtype=cvips&gifs=YesDetecting drug targets with minimum side effects in metabolic networks.]] **--- //IET Systems Biology//, 3(6), 523-533, 2009

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**Identifying differentially expressed pathways via a mixed integer linear programming model. **--- //IET Systems Biology.// In press.
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**Detecting drug targets with minimum side effects in metabolic networks. **--- //IET Systems Biology.// In press.

~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhong-Yuan Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. ---**[[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xuemei Ning, Shihua Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhi-Ping Liu, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F41.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
~1) Shihua Zhang, Xuemei Ning, Chris Ding. ---**[[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
~1) Junhua Zhang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], **--- Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.

~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhong-Yuan Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. ---**[[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xuemei Ning, Shihua Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhi-Ping Liu, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F41.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
~1) Shihua Zhang, Xuemei Ning, Chris Ding. ---**[[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
~1) Junhua Zhang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009.

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics.// in press.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**Exploring the Constrained Maximum Edge-Weight Connected Graph Problem.**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks.**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[ Exploring the Constrained Maximum Edge-Weight Connected Graph Problem]].**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[ A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks]].**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang.---**[[ A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks]].**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Shihua Zhang, Hong-Wei Liu Xue-Mei Ning, Xiang-Sun Zhang.---**[[ A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks]].**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Zhenping Li*, Shihua Zhang*, Xiang-Sun Zhang, Luonan Chen.---**[[ Exploring the Constrained Maximum Edge-Weight Connected Graph Problem]].**---//Acta Mathematicae Applicatae Sinica (E)//, 25(4), 697–708, 2009. DOI: 10.1007/s10255-008-8829-8.
~1) Shihua Zhang, Hong-Wei Liu Xue-Mei Ning, Xiang-Sun Zhang.---**[[ A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks]].**---//International Journal of Data Mining in Bioinformatics//, 3(1), 68-84, 2009.

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009.

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research.// in press.

~1) Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.--- **[[http://peds.oxfordjournals.org/cgi/content/short/22/11/707 Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs]].**--- //Protein Engineering, Design, and Selection//, Vol. 22, No. 11, pp. 707-712, 2009.

~1) Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.--- **Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.**--- //Protein Engineering, Design, and Selection//, Vol. 22, No. 11, pp. 707-712, 2009.

~1) Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.--- **Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.**--- //Protein Engineering, Design, and Selection.// in press.

=== Books & Chapters ===

~~=== Books ===~~

~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhong-Yuan Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. ---**[[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xuemei Ning, Shihua Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhi-Ping Liu, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. ---**[[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F41.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
~1) Shihua Zhang, Xuemei Ning, Chris Ding. ---**[[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
~1) Junhua Zhang, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], **--- Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.

~1) Naiyang Deng, Ling-Yun Wu, Xiaobo Wang. [[http://www.aporc.org/LNOR/11/OSB2009F01.pdf The Prediction of Protein Post-translational Modification Sites]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 3-4, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhong-Yuan Zhang. [[http://www.aporc.org/LNOR/11/OSB2009F08.pdf NMF-based Models for Tumor Clustering: A Systematic Comparison]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 41-47, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhenping Li, Rui-Sheng Wang, Luonan Chen. [[http://www.aporc.org/LNOR/11/OSB2009F09.pdf Extracting Community Structure of Complex networks by Self-Organizing Maps]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 48-56, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zheng Xia, Xiaobo Zhou, Youxian Sun, Ling-Yun Wu. [[http://www.aporc.org/LNOR/11/OSB2009F18.pdf Semi-supervised Drug-Protein Interaction Prediction from Heterogeneous Spaces]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 123-131, World Publishing Corporation, Zhangjiajie, 2009.
~1) Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/11/OSB2009F20.pdf A Constrained Optimization Method for Community Detection]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 142-150, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xuemei Ning, Shihua Zhang. [[http://www.aporc.org/LNOR/11/OSB2009F36.pdf A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 267-275, World Publishing Corporation, Zhangjiajie, 2009.
~1) Zhi-Ping Liu, Luonan Chen. [[http://www.aporc.org/LNOR/11/OSB2009F38.pdf Crosstalk of Dysfunctional Pathways in Alzheimer's Disease Brains]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 288-295, World Publishing Corporation, Zhangjiajie, 2009.
~1) Lin Wang, Ji-Guang Wang, Luonan Chen. [[http://www.aporc.org/LNOR/11/OSB2009F39.pdf Align Protein Surface Structures to Identify Evolutionally and Structurally Conserved Residues]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 296-303, World Publishing Corporation, Zhangjiajie, 2009.
~1) Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, Yong Wang. [[http://www.aporc.org/LNOR/11/OSB2009F41.pdf Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 319-328, World Publishing Corporation, Zhangjiajie, 2009.
~1) Shihua Zhang, Xuemei Ning, Chris Ding. [[http://www.aporc.org/LNOR/11/OSB2009F47.pdf Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 361-370, World Publishing Corporation, Zhangjiajie, 2009.
~1) Junhua Zhang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/11/OSB2009F53.pdf A Weighted Parsimony Model for Community Detection in Complex Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 419-429, World Publishing Corporation, Zhangjiajie, 2009.
~1) Xianwen Ren, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/11/OSB2009F58.pdf A Novel Approach for Pathway Inference Based on Network Flow]], Operations Research and Its Applications, Lecture Notes in Operations Research, 11, pp. 467-474, World Publishing Corporation, Zhangjiajie, 2009.

~1) Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen --- **[[http://www.springerlink.com/content/536j562174843445/ Fuzzy system methods in modeling gene expression and analyzing protein networks]]** --- Chapter 9 in [[http://www.springer.com/engineering/book/978-3-540-89967-9 Fuzzy Systems in Bioinformatics and Computational Biology]], edited by Y. Jin, L. Wang, pp:165-189, Springer Berlin/Heidelberg, 2009

~1) Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen --- **[[http://www.springerlink.com/content/536j562174843445/ Fuzzy system methods in modeling gene expression and analyzing protein networks]]**. Chapter 9 in [[http://www.springer.com/engineering/book/978-3-540-89967-9 Fuzzy Systems in Bioinformatics and Computational Biology]], edited by Y. Jin, L. Wang, pp:165-189, Springer Berlin/Heidelberg, 2009

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.]] **--- //PLoS Computational Biology,// 9(5), e1000521, 2009.

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. **--- //PLoS Computational Biology.// In press.

~1) Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.--- **Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.**--- //Protein Engineering, Design, and Selection.// in press.

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. **--- //PLoS Computational Biology.// In press.

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. **--- // PLoS Computational Biology.// In press.

~1) Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. ---**Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. **--- //PLoS Computational Biology.// In press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters,// 87, 38002, 2009.
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters.// 87, 38002, 2009.
~1) ~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology.// Vol. 13, No. 4, 2009.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters.// in press.
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology.// Vol. 13, No. 4, 2009.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002 Modularity optimization in community detection of complex networks]]. **--- // Europhysics Letters.// in press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** [[http://www.iop.org/EJ/abstract/0295-5075/87/3/38002]]Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.

~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**Detecting drug targets with minimum side effects in metabolic networks. **--- //IET Systems Biology.// In press.

~~~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**Detecting drug targets in metabolic networks by integer linear programming. **--- //IET Systems Biology.// In press.~~

~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. ---**Detecting drug targets in metabolic networks by integer linear programming. **--- //IET Systems Biology.// In press.

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. ---**Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. **--- 2009 IEEE International Conference on Systems, Man, and Cybernetics.

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. 2009 IEEE International Conference on Systems, Man, and Cybernetics.

~1) Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. --- **[[http://www.igi-global.com/reference/details.asp?ID=34877&v=tableOfContents A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data]],**--- Chapter XIX in Computational Methodologies in Gene Regulatory Networks, Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009.

~1) Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. --- **[[http://www.igi-global.com/reference/details.asp?ID=34877&v=tableOfContents A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data]],**--- Computational Methodologies in Gene Regulatory Networks, Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009.

~1) Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. --- **[[http://www.igi-global.com/reference/details.asp?ID=34877&v=tableOfContents A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data]],**---
Computational Methodologies in Gene Regulatory Networks, Sanjoy Das,
Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009.

~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology.// Vol. 13, No. 4, 2009.

~~~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** A network biology study on circadian rhythm by integrating various omics data.**--- //OMICS: A Journal of Integrative Biology.// in press.~~

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research.// in press.

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?
ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research.// in press.

~~~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.**--- //Nucleic Acids Research.// in press.~~

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**Identifying differentially expressed pathways via a mixed integer linear programming model. **--- //IET Systems Biology.// In press.

~~~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. --**Identifying differentially expressed pathways via a mixed integer linear programming model. **-- //IET Systems Biology.// In press.~~

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. --**Identifying differentially expressed pathways via a mixed integer linear programming model. **-- //IET Systems Biology.// In press.

~~~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Identifying differentially expressed pathways via a mixed integer linear programming model, //IET Systems Biology// In press.~~

~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Identifying differentially expressed pathways via a mixed integer linear programming model, //IET Systems Biology// In press.

~1) Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. 2009 IEEE International Conference on Systems, Man, and Cybernetics.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. ---** Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Ling Wang, and Luonan Chen. ---** Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, and Luonan Chen. ---** Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.**--- //Nucleic Acids Research.// in press.

~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** Predicting eukaryotic transcriptional cooperativity by Bayesian
network integration of genome-wide data.**--- //Nucleic Acids Research.// in press.

~1) Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, and Luonan Chen. ---** Modularity optimization in community detection of complex networks. **--- // Europhysics Letters.// in press.
~1) Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** Predicting eukaryotic transcriptional cooperativity by Bayesian
network integration of genome-wide data.**--- //Nucleic Acids Research.// in press.
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics.// in press.
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** A network biology study on circadian rhythm by integrating various omics data.**--- //OMICS: A Journal of Integrative Biology.// in press.

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press.
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** A network biology study on circadian rhythm by integrating various omics data.**--- //OMICS: A Journal of Integrative Biology.//, in press.

~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** A network biology study on circadian rhythm by integrating various omics data.**--- //OMICS: A Journal of Integrative Biology.//, in press.

~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 79(10), 3026-3037, 2009

~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 2009, in press.

~1) Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.--- **[[http://www.amazon.com/Biomolecular-Networks-Methods-Applications-Bioinformatics/dp/0470243732 Biomolecular Networks: Methods and Applications in Systems Biology]]**.--- [[http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470243732.html John Wiley & Sons]], Hoboken, New Jersey. July, 2009.

~1) Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.--- **[[http://www.amazon.com/Biomolecular-Networks-Methods-Applications-Bioinformatics/dp/0470243732 Biomolecular Networks: Methods and Applications in Systems Biology]]**.--- John Wiley & Sons, Hoboken, New Jersey. July, 2009.--- Online information:
~- [[http://www.amazon.com/Biomolecular-Networks-Methods-Applications-Bioinformatics/dp/0470243732]]
~- [[http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470243732.html]]

~1) Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.--- **[[http://www.amazon.com/Biomolecular-Networks-Methods-Applications-Bioinformatics/dp/0470243732 Biomolecular Networks: Methods and Applications in Systems Biology]]**.--- John Wiley & Sons, Hoboken, New Jersey. July, 2009.--- Online information:

~1) Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.--- **Biomolecular Networks: Methods and Applications in Systems Biology**.--- John Wiley & Sons, Hoboken, New Jersey. July, 2009.--- Online information:

=== Books ===
~1) Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang.--- **Biomolecular Networks: Methods and Applications in Systems Biology**.--- John Wiley & Sons, Hoboken, New Jersey. July, 2009.--- Online information:
~- [[http://www.amazon.com/Biomolecular-Networks-Methods-Applications-Bioinformatics/dp/0470243732]]
~- [[http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470243732.html]]

~1) W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.--- **[[http://www.ncbi.nlm.nih.gov/pubmed/19084271 Multiple distinct clones may co-exist in different lineages in myelodysplastic syndromes.]]**--- //Leukemia Research//, 33(6), 847-853, 2009

~1) W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.--- **Multiple distinct clones may co-exist in different lineages in myelodysplastic syndromes.**--- //Leukemia Research//, in press.

~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics//, 2009, 10(Suppl 4):S6

~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics, 2009, 10(Suppl 4):S6

~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.biomedcentral.com/1471-2105/10/S4/S6 Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli]].**--- //BMC Bioinformatics, 2009, 10(Suppl 4):S6, doi:10.1186/1471-2105-10-S4-S6//

~1) Xiaojian Shao, Yingjie Tian, Lingyun Wu, Yong Wang, Naiyang Deng.--- **[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-4VJBTXH-1&_user=1999482&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=d800ddf673d447e33e4c848a9a32da6e Predicting DNA-and RNA-binding proteins from sequences with kernel methods]].**--- //Journal of Theoretical Biology//, 258 (2009) 289–293.

~1) Xiaojian Shao, Yingjie Tian, Lingyun Wu, Yong Wang, Naiyang Deng.--- **Predicting DNA-and RNA-binding proteins from sequences with kernel methods.**--- //Journal of Theoretical Biology//, in press.

~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 2009, in press.

~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 2009, in press

~1) Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T.C. Wong.--- **[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/1/61 Conditional random pattern algorithm for LOH inference and segmentation]].**--- //Bioinformatics//, Vol. 25, No. 1, 61-67, 2009.

~1) 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//, Vol. 25, No. 1, 61-67, 2009.

~1) W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.--- **Multiple distinct clones may co-exist in different lineages in myelodysplastic syndromes.**--- //Leukemia Research//, in press.

~1) W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.--- **Multiple
distinct clones may co-exist in different lineages in myelodysplastic syndromes.**--- //Leukemia Research//, in press.

~1) Xiaojian Shao, Yingjie Tian, Lingyun Wu, Yong Wang, Naiyang Deng.--- **Predicting DNA-and RNA-binding proteins from sequences with kernel methods.**--- //Journal of Theoretical Biology//, in press.
~1) W.T. Huang, X. Yang, X. Zhou, F.A. Monzon, J. Wen, J.M. Hagenkord, L.Y. Wu, C. Keever-Taylor, L. Novoa-Takara, S.T.C. Wong, K. Young, and C.C. Chang.--- **Multiple
distinct clones may co-exist in different lineages in myelodysplastic syndromes.**--- //Leukemia Research//, in press.
~1) 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//, Vol. 25, No. 1, 61-67, 2009.

===== Publications - Bioinformatics 2009 =====

~~===== Publications - Bioinformatics =====~~

=== Working Papers ===
=== Accepted Papers ===
=== Refereed Journal Papers ===
=== Proceedings Papers ===

=== Refereed Journal Articles ===
=== Proceedings Articles ===

~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press.

~1) Jiguang Wang, Yuqing Qiu, Rui-Sheng Wang, Xiang-Sun Zhang [[http://www.springerlink.com/content/7241802320q57g74/?p=f9a87302648f43d3b9d7c0386b86459f&pi=10 Remarks on network community
properties]], //Jrl Syst Sci & Complexity//, 21: 637-644, 2008.
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiang-Sun Zhang [[http://www.springerlink.com/content/d4h192615n72u162/?p=185e3bcdc33c4d7f89ebaab55da19ae5&pi=0 Recognition of structure similarities in proteins]], //Jrl Syst Sci & Complexity//, 21: 665-675, 2008.
~1) Ji-Hong Zhang, Ling-Yun Wu, Jian Chen, Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V8V-4S92TGC-2-DT&_cdi=5880&_user=489277&_orig=na&_coverDate=07%2F15%2F2008&_sk=999479988&view=c&wchp=dGLbVtb-zSkWz&md5=9751f4fc0d811005cf1726cb58667b45&ie=/sdarticle.pdf A fast haplotype inference method for large population genotype data]], //Computational Statistics and Data Analysis//, 52(11): 4891-4902, 2008.
~1) Guangxu Jin, Xiaobo Zhou, Honghui Wang, Hong Zhao, Kemi Cui, Xiang-Sun Zhang, Luonan Chen, Stanley L. Hazen, King Li, and Stephen T. C. Wong. [[http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2008/7/i09/abs/pr8002886.html The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events]]. //J Proteome Res. // 7(9): 4013-4021, 2008.
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen. [[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]]. //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen, Protein cavity clustering based on community structure of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, Vol. 4, No. 4, pp.445–460, 2008.
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V10-4TC34VB-1&_user=1999482&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=1999482&md5=9886acbe27f2e27e4885cb5177ee3650 Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures]]. //Neurocomputing//, 72, 134–141, 2008.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.springerlink.com/content/7629t35314811l89/ Bridging protein local structures and protein functions]]. //Amino Acids//, DOI: 10.1007/s00726-008-0088-8, 2008.
~1) Zhenping Li, Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000077000003036109000001&idtype=cvips&gifs=yes Quantitative function for community detection]]. //Physical Review E//, 77, 036109, 2008.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.bentham.org/ppl/contabs/ppl15-5.htm Analysis of Protein Surface Patterns by Pocket Similarity Network]]. //Protein and Peptide Letters//, 15:448-455, 2008.
~1) Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang. Detecting community structure in complex networks based on a measure of information discrepancy. //Physica A//, 2008, 387(7), 1675-1682.
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2245906 Biomolecular network querying: a promising approach in systems biology]]. //BMC Systems Biology//, 2008, 2:5.
~1) Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen (2007) [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18030341 Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast]]. //PLoS ONE// 2(11): e1207
~1) Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen. [[http://www.molcells.org/home/journal/article_read.asp?volume=24&number=3&startpage=307 Inferring transcriptional interactions and regulator activities from experimental data]]. //Molecules and Cell//s, 24(3), 307-315, 2007
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen and Xiang-Sun Zhang. [[http://www.biomedcentral.com/1471-2105/8/475/abstract Predicting Gene Ontology functions from protein's regional surface structures]]. //BMC Bioinformatics//, 8:475, 2007.
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun Zhang, L.Chen. [[http://www3.interscience.wiley.com/cgi-bin/abstract/115804878/ABSTRACT?CRETRY=1&SRETRY=0 Discovering functions and revealing mechanisms at molecular level from biological networks]]. //Proteomics//, 7(16), 2856-2869, 2007.
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[http://link.aps.org/abstract/PRE/v76/e046103 Uncovering fuzzy community structure in complex networks]]. //Physical Review E//, 76, 046103, 2007
~1) Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen. [[http://www.biomedcentral.com/1471-2105/8/391/abstract Analysis on multi-domain cooperation for predicting protein-protein interactions]]. //BMC Bioinformatics//, 8:391, 2007
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm465v1 Inferring transcriptional regulatory networks from high-throughput data]]. //Bioinformatics//, Vol. 23, pp. 3056-3064, 2007.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, [[http://www.sciencedirect.com/science/article/B6VCT-4M7CDFJ-2/2/9fb83fa0273062e2d3caf5104d139c74 An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors]]. //European J. of Operational research//, 182, pp.413-427, 2007.
~1) Zhenping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun.Zhang, Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/short/23/13/1631?rss=1 Alignment of molecular networks by integer quadratic programming]]. //Bioinformatics//, Vol. 23, No. 13, 1631-1639, 2007.
~1)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, [[http://www.pressekatalog.de/ARTID/10.1007/s10255-006-0315-6.html A dynamic programming algorithm for the k-haplotyping problem]], //Acta Mathematicae Applicatae Sinica//, Vol.22, No.3, pp.405-412, 2006.
~1) Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. [[http://www.springerlink.com/content/k4t1580815513725/ Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.]] //Eur. Phys. J. B//, 57, 67-74, 2007.
~1) Yong Wang, Ling-Yun Wu, Luonan Chen and Xiang-Sun Zhang. [[http://www.inderscience.com/search/index.php?action=record&rec_id=13598&prevQuery=&ps=10&m=or Supervised classification of protein structures based on convex hull representation]]. //International Journal of Bioinformatics Research and Applications//, Vol. 3, No. 2, 123-144, 2007.
~1) Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B73G2-4MBCB7W-1&_user=1002903&_coverDate=12%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050165&_version=1&_urlVersion=0&_userid=1002903&md5=7b057b3033feab5a08f5cc7f6592ee98 Identification of functional modules in a PPI network by clique percolation clustering]]. //Computational biology and chemistry//, 30(6), 445-451, 2006.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, and Wei Zhang. [[http://la-press.com/cr_data/files/f_EBO-2-Wang-et-al-Ruisheng_193.pdf Minimum conflict individual haplotyping from SNP fragments and related genotype]]. //Evolutionary Bioinformatics//, 2006, 2, 271-280.
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal/GIW06/GIW06F019.pdf A Markov Chain Model for Haplotype Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.
~1) Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. //Physica A//, 2007, 374, 483–490.
~1) Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. [[http://www.biomedcentral.com/1472-6807/6/18 Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison]]. //BMC Structural Biology//, 2006, 6:18, doi:10.1186/1472-6807-6-18.
~1) Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2413 Inferring gene regulatory networks from multiple microarray datasets]]. //Bioinformatics//, 22(19):2413-2420; doi:10.1093/bioinformatics/btl396, 2006.
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16395667 Inferring Protein Interactions from Experimental Data by Association Probabilistic Method]]. //Proteins: Structure, Function, and Bioinformatics//, Vol. 62, pp. 833-837, 2006.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.ripublication.com/ijcir/ijcirv2n1.htm Exploring the classification of protein structures on geometric patterns by neural networks]]. //International Journal of Computational Intelligence Research//, Vol. 2, No. 1, pp. 105-109, 2006.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. [[http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000001/art00011 Models and algorithms for the haplotyping problem]]. //Current Bioinformatics//, Vol. 1, No. 1, pp. 105-114, 2006.
~1) Shi-Hua Zhang and Xiang-Sun Zhang. Visualization of conformational space based on CA-CA distance. //Chinese journal of Bioinformatics//. Vol. 4, No.4, pp. 153-156, 2006.
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, Vol. 4, No. 2, pp. 105-116, 2005.
~1) Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shuihua Zhang and Xiang-Sun Zhang. [[http://www.jsbi.org/journal.html Comparison of Protein Structures by Multi-Objective Optimization]]. //Genome Informatics//, Vol. 16, No. 2, pp. 114-124, 2005.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. A reconstruction algorithm to DNA sequencing by hybridization with target DNA length error. //Acta Mathematicae Applicatae Sinica//, Vol. 28, No. 3, pp. 385-395, 2005. (in Chinese)
~1) Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/short/21/17/3475 A parsimonious tree-grow method for haplotype inference]]. //Bioinformatics//, Vol. 21, No. 17, pp. 3475-3481, 2005.
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%2311514%232005%23999709995%23603158%23FLA%23&_auth=y&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=dd477912d5c6d6f4a0ccf43dd82605df Haplotype assembly from aligned weighted SNP fragments]]. //Computational Biology and Chemistry//, Vol. 29, No. 4, pp. 281-287, 2005.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. An improved self-organizing map algorithm for protein folding and its realization. //Journal of Systems Science and Mathematical Sciences//, Vol. 25, No. 5, pp. 562-573, 2005.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. [[http://www.worldscinet.com/jbcb/03/0304/S0219720005001351.html Aligning multiple protein structures by deterministic annealing]]. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 4, pp. 837-860, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/21/10/2456 Haplotype reconstruction from SNP fragments by minimum error correction.]] //Bioinformatics//, Vol. 21, No. 10, pp. 2456-2462, 2005.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. [[http://www.worldscinet.com/jbcb/03/0302/S0219720005001107.html Exploring protein's optimal HP configurations by self-organizing]]. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, pp. 385-400, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang. Algorithms for the SNP haplotype assembly problem. //Applied Mathematics, A Journal of Chinese Universities (Series A)//, Vol. 19, Supplement, pp. 515-528, 2004.
~1) Zhen-Ping Li, Yong Wang, Yu-Ying Zhao and Xiang-Sun Zhang. Haplotype inference and mating graphs. //Applied Mathematics, A Journal of Chinese Universities (Series A)//, Vol. 19, Supplement, pp. 567-576, 2004.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/19/1/14 Reconstruction of DNA sequencing by hybridization.]] //Bioinformatics//, Vol. 19, No. 1, pp. 14-21, 2003.
~1) Xiang-Sun Zhang, Ji-Hong Zhang, and Ling-Yun Wu. A reconstruction algorithm to solve positional sequencing by hybridization. //Journal of Systems Science and Mathematical Sciences//, Vol. 22, No. 3, pp. 258-269, 2002. (In Chinese).
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. [[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4684855&arnumber=4684915&count=89&index=59 Reconstruction of regulator activity in E. coli post-transcription processes]]. IEEE International Conference on Bioinformatics and Biomedicine, 2008 (IEEE BIBM'08), 339-342.
~1) Xiang-Sun Zhang and Rui-Sheng Wang. [[http://www.aporc.org/LNOR/9/OSB2008F02.pdf Optimization analysis of modularity measures for network community detection]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 13-20, World Publishing Corporation, Lijiang, 2008.
~1) Yu-Qing Qiu, Shihua Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F10.pdf Uncovering Differentially Expressed Pathways with Protein Interaction and Gene Expression Data]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 74-82, World Publishing Corporation, Lijiang, 2008.
~1) Lin Wang, Wen-Juan Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F11.pdf A New Algorithm for Sequential and Non-sequential Protein Multiple Structure Alignment]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 83-90, World Publishing Corporation, Lijiang, 2008.
~1) Guangxu Jin, Xiaobo Zhou, Kemi Cui, Stephen T.C. Wong. [[http://www.aporc.org/LNOR/9/OSB2008F19.pdf The Network Biomarker Discovery in Prostate Cancer from Both Genomics and Proteomics Levels]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 144-151, World Publishing Corporation, Lijiang, 2008.
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F24.pdf Mass Flow Model and Essentiality of Enzymes in Metabolic Networks]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 182-190, World Publishing Corporation, Lijiang, 2008.
~1) Ling-Yun Wu, Ji-Hong Zhang, Raymond Chan. [[http://www.aporc.org/LNOR/9/OSB2008F28.pdf Improved Approach for Haplotype Inference Based on Markov Chain]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 212-223, World Publishing Corporation, Lijiang, 2008.
~1) Ling-Yun Wu, Xiaobo Zhou, Chung-Che Chang, Stephen T.C. Wong. [[http://www.aporc.org/LNOR/9/OSB2008F29.pdf Model Based Probe Fitting and Selection for SNP Array]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 224-231, World Publishing Corporation, Lijiang, 2008.
~1) Zhi-Ping Liu, Weiming Xia, Luonan Chen. [[http://www.aporc.org/LNOR/9/OSB2008F30.pdf Analysis of Domain Interactions Among Gamma-secretase Substrates]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 232-241, World Publishing Corporation, Lijiang, 2008.
~1) Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F38.pdf Comparative Study on A Class of Evaluation Indices for Community Detection
]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 294-303, World Publishing Corporation, Lijiang, 2008.
~1) Junhua Zhang, Weihua Yue, and Xiang-Sun Zhang, [[www.aporc.org/LNOR/8/ISORA2008F52.pdf Multilocus analysis of case-control data to schizophrenia based on measures of information discrepancy]], Operations Research and Its Applications，Lecture Notes in Operations Research, vol. 8，pp. 442-449，World Publishing Corporation，2008
~1) Yong Wang, Yu Xia. [[http://www.aporc.org/LNOR/9/OSB2008F42.pdf Condition Specific Subnetwork Identification Using an Optimization Model]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 333-340, World Publishing Corporation, Lijiang, 2008.
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding and Xiang-Sun Zhang, [[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/icdm/2007/3018/00/3018toc.xml&DOI=10.1109/ICDM.2007.99 Binary matrix factorization with applications]], Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007, page: 391-400. (Acceptance Ratio: 7%)
~1) Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen, [[http://www.springerlink.com/content/gp6861366h541474/?p=3a45130dcc084bd6bf6b62deab7d0cf7&pi=3 Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks]], ICIC2007, Lecture Notes in Artificial Intelligence, 4682, 1090-1101, 2007
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen，Detecting community structure in complex networks by optimal rearrangement clustering, PAKDD 2007 workshop on Data Mining in Biomedical Applications, Lecture Notes in Artificial Intelligence, 4819,119-130, 2007
~1) Zhong-Yuan Zhang and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F28.pdf Two Improvments of NMF Used for Tumor Clustering]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 242-249, World Publishing Corporation, Beijing, 2007.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F24.pdf An Approach for Clustering Protein Pockets into Similar Groups]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 204-212, World Publishing Corporation, Beijing, 2007.
~1) Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F13.pdf New Insights into Network Motif Clusters from the Views of Cellular Localizations and Signal Pathways]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 100-109, World Publishing Corporation, Beijing, 2007.
~1) Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F11.pdf Establishing Protein Functional Linkage in a Systematic Way]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 75-88, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F06.pdf An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 35-41, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/6/ISORA2006F33.pdf An Optimization Model for Achieving Sparsity of Gene Regulatory Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 6, pp. 368-379, World Publishing Corporation, Beijing, 2006.
~1) Yong Wang, Zhen-Ping Li, Xiang-Sun Zhang and Luonan chen. 3D Structural Motif Finding in Protein Structures by Network Alignment, D. -S. Huang (Eds.): WICB2006, 2006.
~1) Shi-Hua Zhang, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. [[http://www.springer.com/west/home/engineering?SGWID=4-175-22-173671714-0 ICIC06]], [[http://dx.doi.org/10.1007/11816102_55 LNCS]], [[http://www.springer.com/west/home/life+sci/bioinformatics?SGWID=4-10031-69-173623629-0 Lecture Notes in Bioinformatics]], Vol. 4115, 514-524, 2006.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang. A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks. ICDMW, 130-135, Sixth IEEE International Conference on Data Mining-Workshops (ICDMW'06), 2006. (Acceptance Ratio: 28.0%)
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. [[http://www.springerlink.com/content/b14g4687627nh348/?p=67471aa890aa493193250f9da6e9dac6&pi=0 Automatic classification of protein structures based on convex hull representation by integrated neural network]]. Theory and Applications of Models of Computation, J.-Y. Cai, S. B. Cooper, and A. Li, Eds., Vol. 3959, pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen. [[http://www.springerlink.com/content/?k=Inference+of+Gene+Regulatory+Networks+by+Linear+Programming Supervised Inference of Gene Regulatory Networks by Linear Programming]]. D. -S. Huang, K. Li and G. W. Irwin (Eds.): ICIC2006, LNBI, Vol. 4115, pp. 551-561, Springer-Verlag, 2006.
~1) Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Alignment of protein interaction networks by integer quadratic programming. 28th IEEE EMBS Annual International Conference.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. [[http://www.springerlink.com/content/nw7h142k2371p534/?p=67471aa890aa493193250f9da6e9dac6&pi=1 Protein structure comparison by both structure and sequence data]]. IFMBE Proceedings, Vol. 14, 2006, 174-177, Springer Berlin Heidelberg.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Shihua Zhang and Luonan Chen. [[http://www.springerlink.com/content/m788747500332828/?p=ee9b67db14ab4845804cf0d2b05b3e59&pi=1 Inferring Protein-Protein Interactions by Combinatorial Models]]. IFMBE Proceedings, Vol.14, 2006, 183--186, Springer Berlin Heidelberg.
~1) Xiang-Sun Zhang, Zhong-Wei Zhan, Yong Wang and Ling-Yun Wu. An attempt to explore the similarity of two proteins by their surface shapes. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 276-284, World Publishing Corporation, Beijing, 2005.
~1) Shihua Zhang, De-Gang Liu and Xiang-Sun Zhang. A framwork for structural similarity search in protein. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 285-295, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Xiang-Sun Zhang and Li Sheng. Haplotype inference by pure parsimony via genetic algorithm. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 296-306, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, and Xiang-Sun Zhang. A Genetic algorithm for the individual haplotyping problem. //Proceedings of ORSC 2004//, 814-823, Global-Link Publishing Company, Hong Kong, 2004.
~1) Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, and Xiang-Sun Zhang. Haplotyping an individual from weighted SNPs fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, Hong Kong, 2004.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yong Wang, Zheng-Ping Li, and Xiang-Sun Zhang. A statistical method based on markov chain for optimal reconstruction of haplotype from genotype data with SNP. //Proceedings of ORSC 2004//, 1268-1278, Global-Link Publishing Company, Hong Kong, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang. Structure alignment of protein by mean field annealing. ICSB2003.
~1) Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang. Neural networks approach to DNA sequencing by hybridization. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 4, pp. 312-320, World Publishing Corporation, Beijing, 2002.
=== Technical Reports ===
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Ji-Hong Zhang. A fast approach measure the protein structure similarity from the global shape view. Report of Research, IAM-R003, Institute of Applied Mathematics, AMSS, CAS, 2005.

ZHANGroup : PubBioinformatics2009

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