Revision history for PubBioinformatics2006
Additions:
~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.
Deletions:
Additions:
~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)
Deletions:
Additions:
~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.
Deletions:
No Differences
Additions:
===== Publications - Bioinformatics 2006 =====
Deletions:
Additions:
~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) 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.
Deletions:
~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.
Additions:
~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://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) 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) 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) 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.
Deletions:
~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) 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.
Additions:
~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.
Deletions:
~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) 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, 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) 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) 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.
