Additions:
~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
Deletions:
~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.
Additions:
~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)
Deletions:
~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)
Additions:
~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)
Deletions:
~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)
Additions:
~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)
Deletions:
~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)
Additions:
~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)
Deletions:
~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
Additions:
~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
Deletions:
~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.
Additions:
~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)
Additions:
~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.
Deletions:
~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.
Deletions:
=== Working Papers ===
=== Accepted Papers ===
Additions:
~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.
Deletions:
~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.
Additions:
~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.
Deletions:
~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.
Additions:
~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.
Deletions:
~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.
Additions:
~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
Deletions:
~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
Additions:
~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
Deletions:
~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
Additions:
~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.
Deletions:
~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.
Additions:
~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
Deletions:
~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
Additions:
~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
Deletions:
~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.
Additions:
~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.
Deletions:
~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.
Additions:
~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.
Deletions:
~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.