Wiki source for PubBioinformatics2005
===== Publications - Bioinformatics 2002-2005 =====
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=== Refereed Journal Articles ===
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen.--- **[[http://www.ncbi.nlm.nih.gov/pubmed/16128612 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.--- **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. (In Chinese)
~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 mapping]].**--- //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).
=== Proceedings Articles ===
~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.--- **[[http://www.aporc.org/LNOR/5/ISORA2005F25.pdf 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.
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CategoryPublication
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{{include page="PubBioinformaticsTOC"}}
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=== Refereed Journal Articles ===
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen.--- **[[http://www.ncbi.nlm.nih.gov/pubmed/16128612 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.--- **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. (In Chinese)
~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 mapping]].**--- //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).
=== Proceedings Articles ===
~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.--- **[[http://www.aporc.org/LNOR/5/ISORA2005F25.pdf 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.
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CategoryPublication
