Wiki source for PubBioinformatics2006
===== Publications - Bioinformatics 2006 =====
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=== Refereed Journal Articles ===
~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.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://www.la-press.com/minimum-conflict-individual-haplotyping-from-snp-fragments-and-related-a133 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/pdfs/journal1/GIW06/GIW06F019.html A Markov Chain Model for Haplotype Assembly from SNP Fragments]].**--- //Genome Informatics//, Vol. 17, No. 2. 2006.
~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. (In Chinese)
=== Proceedings Articles ===
~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.
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CategoryPublication
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{{include page="PubBioinformaticsTOC"}}
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=== Refereed Journal Articles ===
~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.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://www.la-press.com/minimum-conflict-individual-haplotyping-from-snp-fragments-and-related-a133 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/pdfs/journal1/GIW06/GIW06F019.html A Markov Chain Model for Haplotype Assembly from SNP Fragments]].**--- //Genome Informatics//, Vol. 17, No. 2. 2006.
~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. (In Chinese)
=== Proceedings Articles ===
~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.
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