Revision history for PubBioinformatics


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===== Publications - Bioinformatics =====
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=== Refereed Journal Articles ===
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 2009, in press
~1) Jiguang Wang, Yuqing Qiu, Rui-Sheng Wang, Xiang-Sun Zhang [[http://www.springerlink.com/content/7241802320q57g74/?p=f9a87302648f43d3b9d7c0386b86459f&pi=10 Remarks on network community
properties]], //Jrl Syst Sci & Complexity//, 21: 637-644, 2008.
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiang-Sun Zhang [[http://www.springerlink.com/content/d4h192615n72u162/?p=185e3bcdc33c4d7f89ebaab55da19ae5&pi=0 Recognition of structure similarities in proteins]], //Jrl Syst Sci & Complexity//, 21: 665-675, 2008.
~1) Ji-Hong Zhang, Ling-Yun Wu, Jian Chen, Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V8V-4S92TGC-2-DT&_cdi=5880&_user=489277&_orig=na&_coverDate=07%2F15%2F2008&_sk=999479988&view=c&wchp=dGLbVtb-zSkWz&md5=9751f4fc0d811005cf1726cb58667b45&ie=/sdarticle.pdf A fast haplotype inference method for large population genotype data]], //Computational Statistics and Data Analysis//, 52(11): 4891-4902, 2008.
~1) Guangxu Jin, Xiaobo Zhou, Honghui Wang, Hong Zhao, Kemi Cui, Xiang-Sun Zhang, Luonan Chen, Stanley L. Hazen, King Li, and Stephen T. C. Wong. [[http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2008/7/i09/abs/pr8002886.html The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events]]. //J Proteome Res. // 7(9): 4013-4021, 2008.
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen. [[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/trans/tb/&toc=comp/trans/tb/5555/01/n1toc.xml&DOI=10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]]. //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen, Protein cavity clustering based on community structure of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, Vol. 4, No. 4, pp.445–460, 2008.
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V10-4TC34VB-1&_user=1999482&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=1999482&md5=9886acbe27f2e27e4885cb5177ee3650 Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures]]. //Neurocomputing//, 72, 134–141, 2008.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.springerlink.com/content/7629t35314811l89/ Bridging protein local structures and protein functions]]. //Amino Acids//, DOI: 10.1007/s00726-008-0088-8, 2008.
~1) Zhenping Li, Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000077000003036109000001&idtype=cvips&gifs=yes Quantitative function for community detection]]. //Physical Review E//, 77, 036109, 2008.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.bentham.org/ppl/contabs/ppl15-5.htm Analysis of Protein Surface Patterns by Pocket Similarity Network]]. //Protein and Peptide Letters//, 15:448-455, 2008.
~1) Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang. Detecting community structure in complex networks based on a measure of information discrepancy. //Physica A//, 2008, 387(7), 1675-1682.
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2245906 Biomolecular network querying: a promising approach in systems biology]]. //BMC Systems Biology//, 2008, 2:5.
~1) Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen (2007) [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18030341 Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast]]. //PLoS ONE// 2(11): e1207
~1) Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen. [[http://www.molcells.org/home/journal/article_read.asp?volume=24&number=3&startpage=307 Inferring transcriptional interactions and regulator activities from experimental data]]. //Molecules and Cell//s, 24(3), 307-315, 2007
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen and Xiang-Sun Zhang. [[http://www.biomedcentral.com/1471-2105/8/475/abstract Predicting Gene Ontology functions from protein's regional surface structures]]. //BMC Bioinformatics//, 8:475, 2007.
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun Zhang, L.Chen. [[http://www3.interscience.wiley.com/cgi-bin/abstract/115804878/ABSTRACT?CRETRY=1&SRETRY=0 Discovering functions and revealing mechanisms at molecular level from biological networks]]. //Proteomics//, 7(16), 2856-2869, 2007.
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[http://link.aps.org/abstract/PRE/v76/e046103 Uncovering fuzzy community structure in complex networks]]. //Physical Review E//, 76, 046103, 2007
~1) Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen. [[http://www.biomedcentral.com/1471-2105/8/391/abstract Analysis on multi-domain cooperation for predicting protein-protein interactions]]. //BMC Bioinformatics//, 8:391, 2007
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm465v1 Inferring transcriptional regulatory networks from high-throughput data]]. //Bioinformatics//, Vol. 23, pp. 3056-3064, 2007.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, [[http://www.sciencedirect.com/science/article/B6VCT-4M7CDFJ-2/2/9fb83fa0273062e2d3caf5104d139c74 An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors]]. //European J. of Operational research//, 182, pp.413-427, 2007.
~1) Zhenping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun.Zhang, Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/short/23/13/1631?rss=1 Alignment of molecular networks by integer quadratic programming]]. //Bioinformatics//, Vol. 23, No. 13, 1631-1639, 2007.
~1)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, [[http://www.pressekatalog.de/ARTID/10.1007/s10255-006-0315-6.html A dynamic programming algorithm for the k-haplotyping problem]], //Acta Mathematicae Applicatae Sinica//, Vol.22, No.3, pp.405-412, 2006.
~1) Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. [[http://www.springerlink.com/content/k4t1580815513725/ Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.]] //Eur. Phys. J. B//, 57, 67-74, 2007.
~1) Yong Wang, Ling-Yun Wu, Luonan Chen and Xiang-Sun Zhang. [[http://www.inderscience.com/search/index.php?action=record&rec_id=13598&prevQuery=&ps=10&m=or Supervised classification of protein structures based on convex hull representation]]. //International Journal of Bioinformatics Research and Applications//, Vol. 3, No. 2, 123-144, 2007.
~1) Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B73G2-4MBCB7W-1&_user=1002903&_coverDate=12%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050165&_version=1&_urlVersion=0&_userid=1002903&md5=7b057b3033feab5a08f5cc7f6592ee98 Identification of functional modules in a PPI network by clique percolation clustering]]. //Computational biology and chemistry//, 30(6), 445-451, 2006.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, and Wei Zhang. [[http://la-press.com/cr_data/files/f_EBO-2-Wang-et-al-Ruisheng_193.pdf Minimum conflict individual haplotyping from SNP fragments and related genotype]]. //Evolutionary Bioinformatics//, 2006, 2, 271-280.
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal/GIW06/GIW06F019.pdf A Markov Chain Model for Haplotype Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.
~1) Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. //Physica A//, 2007, 374, 483–490.
~1) Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. [[http://www.biomedcentral.com/1472-6807/6/18 Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison]]. //BMC Structural Biology//, 2006, 6:18, doi:10.1186/1472-6807-6-18.
~1) Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2413 Inferring gene regulatory networks from multiple microarray datasets]]. //Bioinformatics//, 22(19):2413-2420; doi:10.1093/bioinformatics/btl396, 2006.
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16395667 Inferring Protein Interactions from Experimental Data by Association Probabilistic Method]]. //Proteins: Structure, Function, and Bioinformatics//, Vol. 62, pp. 833-837, 2006.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.ripublication.com/ijcir/ijcirv2n1.htm Exploring the classification of protein structures on geometric patterns by neural networks]]. //International Journal of Computational Intelligence Research//, Vol. 2, No. 1, pp. 105-109, 2006.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. [[http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000001/art00011 Models and algorithms for the haplotyping problem]]. //Current Bioinformatics//, Vol. 1, No. 1, pp. 105-114, 2006.
~1) Shi-Hua Zhang and Xiang-Sun Zhang. Visualization of conformational space based on CA-CA distance. //Chinese journal of Bioinformatics//. Vol. 4, No.4, pp. 153-156, 2006.
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, Vol. 4, No. 2, pp. 105-116, 2005.
~1) Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shuihua Zhang and Xiang-Sun Zhang. [[http://www.jsbi.org/journal.html Comparison of Protein Structures by Multi-Objective Optimization]]. //Genome Informatics//, Vol. 16, No. 2, pp. 114-124, 2005.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. A reconstruction algorithm to DNA sequencing by hybridization with target DNA length error. //Acta Mathematicae Applicatae Sinica//, Vol. 28, No. 3, pp. 385-395, 2005. (in Chinese)
~1) Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/short/21/17/3475 A parsimonious tree-grow method for haplotype inference]]. //Bioinformatics//, Vol. 21, No. 17, pp. 3475-3481, 2005.
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%2311514%232005%23999709995%23603158%23FLA%23&_auth=y&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=dd477912d5c6d6f4a0ccf43dd82605df Haplotype assembly from aligned weighted SNP fragments]]. //Computational Biology and Chemistry//, Vol. 29, No. 4, pp. 281-287, 2005.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. An improved self-organizing map algorithm for protein folding and its realization. //Journal of Systems Science and Mathematical Sciences//, Vol. 25, No. 5, pp. 562-573, 2005.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. [[http://www.worldscinet.com/jbcb/03/0304/S0219720005001351.html Aligning multiple protein structures by deterministic annealing]]. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 4, pp. 837-860, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/21/10/2456 Haplotype reconstruction from SNP fragments by minimum error correction.]] //Bioinformatics//, Vol. 21, No. 10, pp. 2456-2462, 2005.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. [[http://www.worldscinet.com/jbcb/03/0302/S0219720005001107.html Exploring protein's optimal HP configurations by self-organizing]]. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, pp. 385-400, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang. Algorithms for the SNP haplotype assembly problem. //Applied Mathematics, A Journal of Chinese Universities (Series A)//, Vol. 19, Supplement, pp. 515-528, 2004.
~1) Zhen-Ping Li, Yong Wang, Yu-Ying Zhao and Xiang-Sun Zhang. Haplotype inference and mating graphs. //Applied Mathematics, A Journal of Chinese Universities (Series A)//, Vol. 19, Supplement, pp. 567-576, 2004.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/19/1/14 Reconstruction of DNA sequencing by hybridization.]] //Bioinformatics//, Vol. 19, No. 1, pp. 14-21, 2003.
~1) Xiang-Sun Zhang, Ji-Hong Zhang, and Ling-Yun Wu. A reconstruction algorithm to solve positional sequencing by hybridization. //Journal of Systems Science and Mathematical Sciences//, Vol. 22, No. 3, pp. 258-269, 2002. (In Chinese).
=== Proceedings Articles ===
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. [[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4684855&arnumber=4684915&count=89&index=59 Reconstruction of regulator activity in E. coli post-transcription processes]]. IEEE International Conference on Bioinformatics and Biomedicine, 2008 (IEEE BIBM'08), 339-342.
~1) Xiang-Sun Zhang and Rui-Sheng Wang. [[http://www.aporc.org/LNOR/9/OSB2008F02.pdf Optimization analysis of modularity measures for network community detection]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 13-20, World Publishing Corporation, Lijiang, 2008.
~1) Yu-Qing Qiu, Shihua Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F10.pdf Uncovering Differentially Expressed Pathways with Protein Interaction and Gene Expression Data]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 74-82, World Publishing Corporation, Lijiang, 2008.
~1) Lin Wang, Wen-Juan Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F11.pdf A New Algorithm for Sequential and Non-sequential Protein Multiple Structure Alignment]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 83-90, World Publishing Corporation, Lijiang, 2008.
~1) Guangxu Jin, Xiaobo Zhou, Kemi Cui, Stephen T.C. Wong. [[http://www.aporc.org/LNOR/9/OSB2008F19.pdf The Network Biomarker Discovery in Prostate Cancer from Both Genomics and Proteomics Levels]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 144-151, World Publishing Corporation, Lijiang, 2008.
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F24.pdf Mass Flow Model and Essentiality of Enzymes in Metabolic Networks]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 182-190, World Publishing Corporation, Lijiang, 2008.
~1) Ling-Yun Wu, Ji-Hong Zhang, Raymond Chan. [[http://www.aporc.org/LNOR/9/OSB2008F28.pdf Improved Approach for Haplotype Inference Based on Markov Chain]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 212-223, World Publishing Corporation, Lijiang, 2008.
~1) Ling-Yun Wu, Xiaobo Zhou, Chung-Che Chang, Stephen T.C. Wong. [[http://www.aporc.org/LNOR/9/OSB2008F29.pdf Model Based Probe Fitting and Selection for SNP Array]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 224-231, World Publishing Corporation, Lijiang, 2008.
~1) Zhi-Ping Liu, Weiming Xia, Luonan Chen. [[http://www.aporc.org/LNOR/9/OSB2008F30.pdf Analysis of Domain Interactions Among Gamma-secretase Substrates]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 232-241, World Publishing Corporation, Lijiang, 2008.
~1) Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/9/OSB2008F38.pdf Comparative Study on A Class of Evaluation Indices for Community Detection
]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 294-303, World Publishing Corporation, Lijiang, 2008.
~1) Junhua Zhang, Weihua Yue, and Xiang-Sun Zhang, [[www.aporc.org/LNOR/8/ISORA2008F52.pdf Multilocus analysis of case-control data to schizophrenia based on measures of information discrepancy]], Operations Research and Its Applications，Lecture Notes in Operations Research, vol. 8，pp. 442-449，World Publishing Corporation，2008
~1) Yong Wang, Yu Xia. [[http://www.aporc.org/LNOR/9/OSB2008F42.pdf Condition Specific Subnetwork Identification Using an Optimization Model]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 333-340, World Publishing Corporation, Lijiang, 2008.
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding and Xiang-Sun Zhang, [[http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/icdm/2007/3018/00/3018toc.xml&DOI=10.1109/ICDM.2007.99 Binary matrix factorization with applications]], Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007, page: 391-400. (Acceptance Ratio: 7%)
~1) Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen, [[http://www.springerlink.com/content/gp6861366h541474/?p=3a45130dcc084bd6bf6b62deab7d0cf7&pi=3 Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks]], ICIC2007, Lecture Notes in Artificial Intelligence, 4682, 1090-1101, 2007
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen，Detecting community structure in complex networks by optimal rearrangement clustering, PAKDD 2007 workshop on Data Mining in Biomedical Applications, Lecture Notes in Artificial Intelligence, 4819,119-130, 2007
~1) Zhong-Yuan Zhang and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F28.pdf Two Improvments of NMF Used for Tumor Clustering]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 242-249, World Publishing Corporation, Beijing, 2007.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F24.pdf An Approach for Clustering Protein Pockets into Similar Groups]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 204-212, World Publishing Corporation, Beijing, 2007.
~1) Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F13.pdf New Insights into Network Motif Clusters from the Views of Cellular Localizations and Signal Pathways]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 100-109, World Publishing Corporation, Beijing, 2007.
~1) Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. [[http://www.aporc.org/LNOR/7/OSB2007F11.pdf Establishing Protein Functional Linkage in a Systematic Way]]. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 75-88, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F06.pdf An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 35-41, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/6/ISORA2006F33.pdf An Optimization Model for Achieving Sparsity of Gene Regulatory Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 6, pp. 368-379, World Publishing Corporation, Beijing, 2006.
~1) Yong Wang, Zhen-Ping Li, Xiang-Sun Zhang and Luonan chen. 3D Structural Motif Finding in Protein Structures by Network Alignment, D. -S. Huang (Eds.): WICB2006, 2006.
~1) Shi-Hua Zhang, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. [[http://www.springer.com/west/home/engineering?SGWID=4-175-22-173671714-0 ICIC06]], [[http://dx.doi.org/10.1007/11816102_55 LNCS]], [[http://www.springer.com/west/home/life+sci/bioinformatics?SGWID=4-10031-69-173623629-0 Lecture Notes in Bioinformatics]], Vol. 4115, 514-524, 2006.
~1) Shihua Zhang, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang. A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks. ICDMW, 130-135, Sixth IEEE International Conference on Data Mining-Workshops (ICDMW'06), 2006. (Acceptance Ratio: 28.0%)
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. [[http://www.springerlink.com/content/b14g4687627nh348/?p=67471aa890aa493193250f9da6e9dac6&pi=0 Automatic classification of protein structures based on convex hull representation by integrated neural network]]. Theory and Applications of Models of Computation, J.-Y. Cai, S. B. Cooper, and A. Li, Eds., Vol. 3959, pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen. [[http://www.springerlink.com/content/?k=Inference+of+Gene+Regulatory+Networks+by+Linear+Programming Supervised Inference of Gene Regulatory Networks by Linear Programming]]. D. -S. Huang, K. Li and G. W. Irwin (Eds.): ICIC2006, LNBI, Vol. 4115, pp. 551-561, Springer-Verlag, 2006.
~1) Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Alignment of protein interaction networks by integer quadratic programming. 28th IEEE EMBS Annual International Conference.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. [[http://www.springerlink.com/content/nw7h142k2371p534/?p=67471aa890aa493193250f9da6e9dac6&pi=1 Protein structure comparison by both structure and sequence data]]. IFMBE Proceedings, Vol. 14, 2006, 174-177, Springer Berlin Heidelberg.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Shihua Zhang and Luonan Chen. [[http://www.springerlink.com/content/m788747500332828/?p=ee9b67db14ab4845804cf0d2b05b3e59&pi=1 Inferring Protein-Protein Interactions by Combinatorial Models]]. IFMBE Proceedings, Vol.14, 2006, 183--186, Springer Berlin Heidelberg.
~1) Xiang-Sun Zhang, Zhong-Wei Zhan, Yong Wang and Ling-Yun Wu. An attempt to explore the similarity of two proteins by their surface shapes. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 276-284, World Publishing Corporation, Beijing, 2005.
~1) Shihua Zhang, De-Gang Liu and Xiang-Sun Zhang. A framwork for structural similarity search in protein. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 285-295, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Xiang-Sun Zhang and Li Sheng. Haplotype inference by pure parsimony via genetic algorithm. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 296-306, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, and Xiang-Sun Zhang. A Genetic algorithm for the individual haplotyping problem. //Proceedings of ORSC 2004//, 814-823, Global-Link Publishing Company, Hong Kong, 2004.
~1) Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, and Xiang-Sun Zhang. Haplotyping an individual from weighted SNPs fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, Hong Kong, 2004.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yong Wang, Zheng-Ping Li, and Xiang-Sun Zhang. A statistical method based on markov chain for optimal reconstruction of haplotype from genotype data with SNP. //Proceedings of ORSC 2004//, 1268-1278, Global-Link Publishing Company, Hong Kong, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang. Structure alignment of protein by mean field annealing. ICSB2003.
~1) Ling-Yun Wu, Ji-Hong Zhang and Xiang-Sun Zhang. Neural networks approach to DNA sequencing by hybridization. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 4, pp. 312-320, World Publishing Corporation, Beijing, 2002.
=== Technical Reports ===
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Ji-Hong Zhang. A fast approach measure the protein structure similarity from the global shape view. Report of Research, IAM-R003, Institute of Applied Mathematics, AMSS, CAS, 2005.
----
CategoryPublication

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{{include page="PubBioinformaticsTOC"}}

Revision [3880]

Edited on 2009-03-12 18:00:54 by LingyunWu
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~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]**.--- //Mathematics and Computers in Simulation//, 2009, in press
Deletions:
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen. [[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]. //Mathematics and Computers in Simulation//, 2009, in press

Revision [3873]

Edited on 2009-02-17 04:50:09 by RuishengWang
Additions:
~1) Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen. [[http://dx.doi.org/10.1016/j.matcom.2009.01.021 Self-organizing map approaches for the haplotype assembly problem]]. //Mathematics and Computers in Simulation//, 2009, in press

Revision [3822]

Edited on 2008-12-29 18:52:35 by YongWang
Additions:
~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

Revision [3786]

Edited on 2008-12-02 07:04:31 by RuishengWang
Additions:
~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) Xiang-Sun Zhang, Ruisheng 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.

Revision [3785]

Edited on 2008-12-02 06:42:03 by RuishengWang
Additions:
~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.
Deletions:
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. Reconstruction of regulator activity in E. coli post-transcription processes.

Revision [3784]

Edited on 2008-12-02 06:32:55 by RuishengWang
Additions:
~1) Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. Reconstruction of regulator activity in E. coli post-transcription processes.

Revision [3783]

Edited on 2008-12-02 06:19:55 by RuishengWang
Additions:
~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
~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.
Deletions:
~1) Jiguang Wang, Yuqing Qiu, Ruisheng Wang, Xiangsun Zhang [[http://www.springerlink.com/content/7241802320q57g74/?p=f9a87302648f43d3b9d7c0386b86459f&pi=10 Remarks on network community
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiangsun 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.

Revision [3782]

Edited on 2008-12-01 16:03:45 by JiguangWang
Additions:
properties]], //Jrl Syst Sci & Complexity//, 21: 637-644, 2008.
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiangsun 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.
Deletions:
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiangsun 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.
properties]], //Jrl Syst Sci & Complexity, 21: 637-644, 2008.

Revision [3781]

Edited on 2008-12-01 16:00:07 by JiguangWang
Additions:
~1) Lin Wang, Jiguang Wang, Yuqing Qiu, Xiangsun 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) Jiguang Wang, Yuqing Qiu, Ruisheng Wang, Xiangsun Zhang [[http://www.springerlink.com/content/7241802320q57g74/?p=f9a87302648f43d3b9d7c0386b86459f&pi=10 Remarks on network community
properties]], //Jrl Syst Sci & Complexity, 21: 637-644, 2008.

Revision [3780]

Edited on 2008-12-01 02:40:32 by RuishengWang
Additions:
~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.
Deletions:
~1) Yong Wang, Yu Xia, Luonan Chen. [[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.

Revision [3772]

Edited on 2008-11-22 02:59:55 by RuishengWang
Additions:
~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.
Deletions:
~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//, DOI: 10.1016/j.neucom.2007.12.043, In press.

Revision [3766]

Edited on 2008-11-05 17:14:45 by YongWang
Additions:
~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) Yong Wang, Yu Xia, Luonan Chen. [[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 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.
Deletions:
~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.

Revision [3745]

Edited on 2008-10-22 16:08:31 by YongWang
Additions:
~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.
Deletions:
~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.

Revision [3744]

Edited on 2008-10-22 16:07:44 by YongWang
Additions:
~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.
Deletions:
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, Vol. 4, No. 4, pp.445–460, 2008.

Revision [3743]

Edited on 2008-10-22 16:06:51 by YongWang
Additions:
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, Vol. 4, No. 4, pp.445–460, 2008.
Deletions:
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, in press.

Revision [3741]

Edited on 2008-10-07 10:32:00 by YongWang
Additions:
~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.
Deletions:
~1) Ji-Hong Zhanga, 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.

Revision [3701]

Edited on 2008-09-15 13:06:34 by YongWang
Additions:
~1) Ji-Hong Zhanga, 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.

Revision [3696]

Edited on 2008-09-12 12:32:47 by JiguangWang [Del jssc paper]
Deletions:
~1) Ji-Guang Wang, Yu-Qing Qiu, Rui-Sheng Wang, and Xiang-Sun Zhang, Remarks on Network Community Properties, //Jrl Syst Sci & Complexity//, 19: 9-16, 2008.

Revision [3682]

Edited on 2008-09-08 11:33:55 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~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.

Revision [3681]

Edited on 2008-09-08 11:32:52 by YongWang [Del jssc paper]
Additions:
~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) 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
Deletions:
~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) 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

Revision [3680]

Edited on 2008-09-08 11:30:23 by YongWang [Del jssc paper]
Additions:
~1) Ji-Guang Wang, Yu-Qing Qiu, Rui-Sheng Wang, and Xiang-Sun Zhang, Remarks on Network Community Properties, //Jrl Syst Sci & Complexity//, 19: 9-16, 2008.
~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) 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%)
Deletions:
~1)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, A dynamic programming algorithm for the k-haplotyping problem, //Acta Mathematicae Applicatae Sinica//, Vol.22, No.3, pp.405-412, 2006.
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding and Xiang-Sun Zhang, Binary matrix factorization with applications, Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007, page: 391-400. (Acceptance Ratio: 7%)

Revision [3679]

Edited on 2008-09-08 11:07:08 by YongWang [Del jssc paper]
Additions:
~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, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, in press.
~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//, DOI: 10.1016/j.neucom.2007.12.043, In press.
~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.
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, 2007.
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, 2007, in press.
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. //Neurocomputing//, In press
~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

Revision [3522]

Edited on 2008-06-07 13:03:56 by ZhipingLiu [Del jssc paper]
Deletions:
~1) Zhiping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Analysis of protein surface patterns by pocket similarity network. //Protein & Peptide Letters//, in press, 2007.

Revision [3521]

Edited on 2008-06-07 13:02:36 by ZhipingLiu [Del jssc paper]
Additions:
~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) 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.

Revision [3212]

Edited on 2008-04-15 17:08:07 by RuishengWang [Del jssc paper]
Additions:
~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) 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
Deletions:
~1) Zhenping Li, Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. Quantitative function for community detection. Physical Review E, 77, 036109, 2008.
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. 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) Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast. PLoS ONE 2(11): e1207

Revision [3211]

Edited on 2008-04-15 17:00:31 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Shi-Hua 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.

Revision [3210]

Edited on 2008-04-15 16:58:47 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. //Physica A//, 2007, 374, 483–490.

Revision [3209]

Edited on 2008-04-15 16:56:42 by RuishengWang [Del jssc paper]
Additions:
~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

Revision [3208]

Edited on 2008-04-15 16:53:59 by RuishengWang [Del jssc paper]
Additions:
~1) Zhenping Li, Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. Quantitative function for community detection. Physical Review E, 77, 036109, 2008.

Revision [3207]

Edited on 2008-04-15 16:52:48 by RuishengWang [Del jssc paper]
Additions:
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology, 2008, 2:5
Deletions:
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Biomolecular network querying: a promising approach in systems biology.
BMC Systems Biology, 2008, 2:5

Revision [3206]

Edited on 2008-04-15 16:52:31 by RuishengWang [Del jssc paper]
Additions:
~1) Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Biomolecular network querying: a promising approach in systems biology.
BMC Systems Biology, 2008, 2:5

Revision [3205]

Edited on 2008-04-15 16:51:03 by RuishengWang [Del jssc paper]
Additions:
~1) Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen (2007) Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast. PLoS ONE 2(11): e1207

Revision [3122]

Edited on 2008-02-02 04:18:39 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~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., 2007

Revision [3084]

Edited on 2007-12-30 00:57:16 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. //Neurocomputing//, In press
~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)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, 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) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. //Physica A//, 2007, 374, 483–490.
Deletions:
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. Neurocomputing, In press
~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 Cells, 24(3), 307-315, 2007
~1)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, 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) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description Physica A: Statistical Mechanics and its Applications]], 2007, 374, 483–490.

Revision [3083]

Edited on 2007-12-30 00:53:57 by RuishengWang [Del jssc paper]
Additions:
~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 Cells, 24(3), 307-315, 2007
Deletions:
~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 Cells, 24(3), 307-315, 2007

Revision [3082]

Edited on 2007-12-30 00:53:37 by RuishengWang [Del jssc paper]
Additions:
~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 Cells, 24(3), 307-315, 2007

Revision [2991]

Edited on 2007-12-20 11:48:15 by ZhongyuanZhang [Del jssc paper]
Additions:
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding and Xiang-Sun Zhang, Binary matrix factorization with applications, Proc. IEEE Int'l Conf. on Data Mining (ICDM) 2007, page: 391-400. (Acceptance Ratio: 7%)

Revision [2977]

Edited on 2007-12-14 00:05:46 by ZhipingLiu [Del jssc paper]
Additions:
~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.
Deletions:
~1) Zhiping 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.

Revision [2976]

Edited on 2007-12-14 00:05:23 by ZhipingLiu [Del jssc paper]
Additions:
~1) Zhiping 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.

Revision [2960]

Edited on 2007-12-01 18:18:02 by RuishengWang [Del jssc paper]
Additions:
~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
Deletions:
~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, in press

Revision [2953]

Edited on 2007-11-20 04:17:56 by YongWang [Del jssc paper]
Additions:
~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., 2007
Deletions:
~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, doi:10.1093/bioinformatics/btm465, 2007

Revision [2950]

Edited on 2007-11-17 22:46:36 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Luonan Chen, Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang. Alignment of protein interaction networks by integer quadratic programming. 28th IEEE EMBS Annual International Conference.

Revision [2917]

Edited on 2007-10-24 16:58:25 by RuishengWang [Del jssc paper]
Additions:
~1)Zhen-Ping Li, Ling-Yun Wu, Yu-Ying Zhao and Xiang-Sun Zhang, A dynamic programming algorithm for the k-haplotyping problem, Acta Mathematicae Applicatae Sinica, Vol.22, No.3, pp.405-412, 2006.

Revision [2902]

Edited on 2007-10-24 16:28:38 by RuishengWang [Del jssc paper]

No Differences

Revision [2901]

Edited on 2007-10-24 16:28:16 by RuishengWang [Del jssc paper]

No Differences

Revision [2900]

Edited on 2007-10-24 16:26:57 by RuishengWang [Del jssc paper]
Additions:
~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

Revision [2899]

Edited on 2007-10-24 16:25:03 by RuishengWang [Del jssc paper]
Additions:
~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, Xiang-Sun Zhang, Luonan Chen. [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm465v1 Inferring transcriptional regulatory networks from high-throughput data]]. Bioinformatics, doi:10.1093/bioinformatics/btm465, 2007
Deletions:
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[Uncovering fuzzy community structure in complex networks Uncovering fuzzy community structure in complex networks]]. Physical Review E, In press.
~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, In press

Revision [2893]

Edited on 2007-10-23 04:17:32 by YongWang [Del jssc paper]
Additions:
~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) 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, In press
~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.
Deletions:
~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) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics, In press
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors, //European J. of Operational research//, 182, pp.413-427, 2007.

Revision [2892]

Edited on 2007-10-23 04:10:25 by YongWang [Del jssc paper]
Additions:
~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, 2007.
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. [[Uncovering fuzzy community structure in complex networks Uncovering fuzzy community structure in complex networks]]. Physical Review E, In press.
Deletions:
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang and Luonan Chen. Evaluating protein similarity from coarse structures. //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press, 2007.
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. Uncovering fuzzy community structure in complex networks. Physical Review E, In press.

Revision [2891]

Edited on 2007-10-23 04:01:51 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, 7(16), 2856-2869, 2007.

Revision [2756]

Edited on 2007-09-09 15:42:32 by RuishengWang [Del jssc paper]
Additions:
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, 7(16), 2856-2869, 2007.
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. Neurocomputing, In press
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics, In press
Deletions:
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, in press, 2007.

Revision [2708]

Edited on 2007-08-28 14:41:35 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang and Luonan Chen. Evaluating protein similarity from coarse structures. //IEEE/ACM Transactions on Computational Biology and Bioinformatics.//, in press, 2007.
Deletions:
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang and Luonan Chen. Evaluating protein similarity from coarse structures. //IEEE Journal of Bioinformatics and Computational Biology//, in press, 2007.

Revision [2707]

Edited on 2007-08-28 14:40:15 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang and Luonan Chen. Evaluating protein similarity from coarse structures. //IEEE Journal of Bioinformatics and Computational Biology//, in press, 2007.

Revision [2695]

Edited on 2007-08-18 21:32:12 by RuishengWang [Del jssc paper]
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.
Deletions:
~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, 2007.

Revision [2694]

Edited on 2007-08-17 09:41:14 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal.html A Markov Chain Model for Haplotype Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.

Revision [2637]

Edited on 2007-08-15 11:35:42 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen. 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.

Revision [2636]

Edited on 2007-08-15 11:33:19 by RuishengWang [Del jssc paper]
Additions:
~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) 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.
Deletions:
~1) Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen, 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) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. 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.

Revision [2635]

Edited on 2007-08-15 11:30:45 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~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.

Revision [2634]

Edited on 2007-08-15 11:30:10 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. Protein structure comparison by both structure and sequence data. IFMBE Proceedings, Vol. 14, Kim, Sun I.; Suh, Tae Suk (Eds.) 2006, 172--175, Springer-Verlag, Berlin.

Revision [2633]

Edited on 2007-08-15 11:25:02 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Ruisheng 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) Xiang-Sun Zhang, Ruisheng 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-Verlag, Berlin.

Revision [2632]

Edited on 2007-08-15 11:23:37 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Ruisheng 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-Verlag, Berlin.
Deletions:
~1) Xiang-Sun Zhang, Ruisheng 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]]. IOMP Proceedings, Vol.2, 2006, 181--184, Springer-Verlag, Berlin.

Revision [2631]

Edited on 2007-08-15 11:21:25 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Ruisheng 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]]. IOMP Proceedings, Vol.2, 2006, 181--184, Springer-Verlag, Berlin.
Deletions:
~1) Xiang-Sun Zhang, Ruisheng Wang, Ling-Yun Wu, Shihua Zhang and Luonan Chen. Inferring Protein-Protein Interactions by Combinatorial Models. IOMP Proceedings, Vol.2, 2006, 181--184, Springer-Verlag, Berlin.

Revision [2627]

Edited on 2007-08-15 10:33:08 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~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; doi:10.1093/bioinformatics/btm156, 2007.

Revision [2626]

Edited on 2007-08-15 10:31:33 by RuishengWang [Del jssc paper]
Additions:
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors, //European J. of Operational research//, 182, pp.413-427, 2007.
Deletions:
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, An optimization approach to the reconstruction of positional DNA
sequencing by hybridization with errors, //European J. of Operational research//, 182, pp.413-427, 2007.

Revision [2625]

Edited on 2007-08-15 10:29:23 by RuishengWang [Del jssc paper]
Additions:
~1) Zhiping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Analysis of protein surface patterns by pocket similarity network. //Protein & Peptide Letters//, in press, 2007.
~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.
Deletions:
~1) Zhiping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Analysis of protein surface patterns by pocket similarity network. //Protein \& Peptide Letters//, in press, 2007.
~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 Online//, 2006, 2, 271-280.

Revision [2624]

Edited on 2007-08-15 10:26:52 by RuishengWang [Del jssc paper]
Deletions:
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures, //Neurocomputing//, in press, 2007.

Revision [2623]

Edited on 2007-08-15 09:16:25 by YongWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen, 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, in press

Revision [2622]

Edited on 2007-08-15 08:40:46 by YongWang [Del jssc paper]
Additions:
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen, Clustering protein surface cavities based on community structure feature of pocket similarity network, //International Journal of Bioinformatics Research and Applications//, 2007, in press.
~1) Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures, //Neurocomputing//, in press, 2007.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yu-Ying Zhao, Xiang-Sun Zhang, An optimization approach to the reconstruction of positional DNA
sequencing by hybridization with errors, //European J. of Operational research//, 182, pp.413-427, 2007.

Revision [2621]

Edited on 2007-08-14 21:55:54 by YongWang [Del jssc paper]
Additions:
~1) Shi-Hua Zhang, Guang-Xu Jin, Xiang-Sun. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, in press, 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; doi:10.1093/bioinformatics/btm156, 2007.
Deletions:
~1) S. Zhang, G. Jin, X-S. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, in press, 2007.
~1) Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.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; doi:10.1093/bioinformatics/btm156, 2007.

Revision [2620]

Edited on 2007-08-14 21:45:27 by YongWang [Del jssc paper]
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.
Deletions:
~1) Shi-Hua Zhang and Xiang-Sun Zhang. Visualization of conformational space based on CA-CA distance. Chinese journal of Bioinformatics. In press.

Revision [2619]

Edited on 2007-08-14 21:42:20 by YongWang [Del jssc paper]
Additions:
~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%)

Revision [2618]

Edited on 2007-08-14 21:40:49 by YongWang [Del jssc paper]
Additions:
~1) Zhiping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. Analysis of protein surface patterns by pocket similarity network. //Protein \& Peptide Letters//, in press, 2007.

Revision [2617]

Edited on 2007-08-14 21:39:23 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Yong Wang, Ling-Yun Wu, Luonan Chen and Xiang-Sun Zhang. Supervised classification of protein structures based on convex hull representation. //International Journal of Bioinformatics Research and Applications//, Vol. 3, No. 2, 2006.

Revision [2616]

Edited on 2007-08-14 21:35:01 by YongWang [Del jssc paper]
Additions:
~1) Shihua Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. Uncovering fuzzy community structure in complex networks. Physical Review E, In press.
~1) Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.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; doi:10.1093/bioinformatics/btm156, 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) 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 Online//, 2006, 2, 271-280.
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal.html A Markov Chain Model for Haplotype Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F06.pdf An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 35-41, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/6/ISORA2006F33.pdf An Optimization Model for Achieving Sparsity of Gene Regulatory Networks]], Operations Research and Its Applications, Lecture Notes in Operations Research, 6, pp. 368-379, World Publishing Corporation, Beijing, 2007.
Deletions:
~1) Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. //Bioinformatics//, in press, 2007.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, and Wei Zhang. Minimum conflict individual haplotyping from SNP fragments and related genotype. Evolutionary Bioinformatics Online, 2006, 2, 271-280.
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal.html A Markov Chain Model for Haplotype
Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/7/OSB2007F06.pdf An Optimization Model for Gene Regulatory Network Reconstruction with Known Biological Information]], Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 35-41, World Publishing Corporation, Beijing, 2007.
~1) Jinshan Li and Xiang-Sun Zhang. [[http://www.aporc.org/LNOR/6/ISORA2006F33.pdf An Optimization Model for Achieving Sparsity of Gene Regulatory Networks]],
Operations Research and Its Applications, Lecture Notes in Operations Research, 6, pp. 368-379, World Publishing Corporation, Beijing, 2007.

Revision [2615]

Edited on 2007-08-14 21:19:56 by YongWang [Del jssc paper]
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, 2007.

Revision [2613]

Edited on 2007-08-14 21:10:26 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Zhong-Yuan Zhang and Xiang-Sun Zhang. 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. 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. 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. 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. 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.

Revision [2612]

Edited on 2007-08-14 21:05:49 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. 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.
Deletions:
~1) Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen. 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.

Revision [2611]

Edited on 2007-08-14 21:05:12 by YongWang [Del jssc paper]
Additions:
~1) Zhong-Yuan Zhang and Xiang-Sun Zhang. 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. 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. 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. 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. 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.

Revision [2597]

Edited on 2007-07-28 17:57:38 by RuishengWang [Del jssc paper]
Additions:
~1) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description Physica A: Statistical Mechanics and its Applications]], 2007, 374, 483–490.
Deletions:
~1) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. Accepted by [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description Physica A: Statistical Mechanics and its Applications]].

Revision [2596]

Edited on 2007-07-28 17:55:43 by RuishengWang [Del jssc paper]
Deletions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao, and Luonan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.

Revision [2591]

Edited on 2007-07-16 19:28:40 by RuishengWang [Del jssc paper]
Deletions:
~1) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. [[http://jbr.sagepub.com/cgi/content/abstract/20/3/257 Synchronization of gene regulatory networks by signaling molecule]]. //Journal of Biology Rhythm//, Vol. 20, 257-269, 2005.

Revision [2462]

Edited on 2007-04-24 11:31:22 by YongWang [Del jssc paper]
Additions:
~1) S. Zhang, G. Jin, X-S. Zhang, L.Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. //Proteomics//, in press, 2007.
~1) Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen. Alignment of molecular networks by integer quadratic programming. //Bioinformatics//, in press, 2007.

Revision [2434]

Edited on 2007-03-27 13:26:04 by YongWang [Del jssc paper]
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.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. 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. 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.
Deletions:
~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]], 4115, 514-524, 2006.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. 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. TAMC2006. pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen. Supervised Inference of Gene Regulatory Networks by Linear Programming. D. -S. Huang, K. Li and G. W. Irwin (Eds.): ICIC2006, LNBI 4115, pp. 551-561, Springer-Verlag, 2006.

Revision [2294]

Edited on 2006-11-21 22:10:03 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:

Revision [2244]

Edited on 2006-11-10 13:41:35 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, and Wei Zhang. Minimum conflict individual haplotyping from SNP fragments and related genotype. Evolutionary Bioinformatics Online, 2006, 2, 271-280.
Deletions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao and Wei Zhang. Minimum conflict haplotyping from genotype data and SNP fragments. Submitted to //Bioinformatics//.

Revision [2198]

Edited on 2006-10-30 09:05:19 by YongWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. [[http://www.jsbi.org/journal.html A Markov Chain Model for Haplotype
Assembly from SNP Fragments]]. //Genome Informatics//, Vol. 17, No. 2. 2006.

Revision [2189]

Edited on 2006-10-26 17:46:38 by YongWang [Del jssc paper]
Additions:
~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, Luonan Chen and Xiang-Sun Zhang. Supervised classification of protein structures based on convex hull representation. //International Journal of Bioinformatics Research and Applications//, Vol. 3, No. 2, 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) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. [[http://jbr.sagepub.com/cgi/content/abstract/20/3/257 Synchronization of gene regulatory networks by signaling molecule]]. //Journal of Biology Rhythm//, Vol. 20, 257-269, 2005.
Deletions:
~1) Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Structural Biology, 2006. In press.
~1) Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen. Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics, doi:10.1093/bioinformatics/btl396, 2006.
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. 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. 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. Models and algorithms for the haplotyping problem. //Current Bioinformatics//, Vol. 1, No. 1, pp. 105-114, 2006.
~1) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. Synchronization of gene regulatory networks by signaling molecule. //Journal of Biology Rhythm//, Vol. 20, 257-269, 2005.

Revision [2141]

Edited on 2006-10-03 18:24:49 by ShihuaZhang [Del jssc paper]

No Differences

Revision [2022]

Edited on 2006-09-02 11:27:01 by ShihuaZhang [Del jssc paper]

No Differences

Revision [2021]

Edited on 2006-09-02 11:21:44 by ShihuaZhang [Del jssc paper]

No Differences

Revision [2020]

Edited on 2006-09-02 11:20:40 by ShihuaZhang [Del jssc paper]
Additions:
~1) Shi-Hua Zhang, Ruisheng Wang, and Xiang-Sun Zhang. Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering. Accepted by [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description Physica A: Statistical Mechanics and its Applications]].
~1) Shi-Hua Zhang and Xiang-Sun Zhang. Visualization of conformational space based on CA-CA distance. Chinese journal of Bioinformatics. In press.

~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]], 4115, 514-524, 2006.

Revision [2015]

Edited on 2006-09-01 10:53:42 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. 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. TAMC2006. pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. Protein structure comparison by both structure and sequence data. IFMBE Proceedings, Vol. 14, Kim, Sun I.; Suh, Tae Suk (Eds.) 2006, 172--175, Springer-Verlag, Berlin.
~1) Xiang-Sun Zhang, Ruisheng Wang, Ling-Yun Wu, Shihua Zhang and Luonan Chen. Inferring Protein-Protein Interactions by Combinatorial Models. IOMP Proceedings, Vol.2, 2006, 181--184, Springer-Verlag, Berlin.
Deletions:
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. \textbf{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. TAMC2006. pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. Protein structure comparison by both structure and sequence data. WC2006, Seoul.

Revision [1982]

Edited on 2006-08-22 16:27:39 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. \textbf{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. TAMC2006. pp. 505--514, Springer-Verlag, 2006.
~1) Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen. Supervised Inference of Gene Regulatory Networks by Linear Programming. D. -S. Huang, K. Li and G. W. Irwin (Eds.): ICIC2006, LNBI 4115, pp. 551-561, Springer-Verlag, 2006.
~1) Luonan Chen, Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang. 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. Protein structure comparison by both structure and sequence data. WC2006, Seoul.

Revision [1981]

Edited on 2006-08-22 16:17:38 by YongWang [Del jssc paper]
Additions:
~1) Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang and Xiang-Sun Zhang. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Structural Biology, 2006. In press.
~1) Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen. Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics, doi:10.1093/bioinformatics/btl396, 2006.

Revision [1740]

Edited on 2006-06-27 17:04:17 by YongWang [Del jssc paper]
Additions:
~1) Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen. 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) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. Synchronization of gene regulatory networks by signaling molecule. //Journal of Biology Rhythm//, Vol. 20, 257-269, 2005.
Deletions:
~1) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. Synchronization of gene regulatory networks by signaling molecule. //Journal of Biology Rhythm//, in press.

Revision [1739]

Edited on 2006-06-27 17:00:40 by YongWang [Del jssc paper]
Additions:
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. Inferring Protein Interactions from Experimental Data by Association Probabilistic Method. //Proteins: Structure, Function, and Bioinformatics//, Vol. 62, pp. 833-837, 2006.
Deletions:
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. Inferring Protein Interactions from Experimental Data by Association Probabilistic Method. //Proteins: Structure, Function, and Bioinformatics//, in press.

Revision [1690]

Edited on 2006-03-24 10:44:58 by LingyunWu [Del jssc paper]
Additions:
CategoryPublication

Revision [1668]

Edited on 2006-03-23 18:31:44 by LingyunWu [Del jssc paper]
Additions:
===== Publications - Bioinformatics =====
Deletions:
===== Research Papers - Bioinformatics =====

Revision [1617]

Edited on 2006-03-23 17:03:43 by LingyunWu [Del jssc paper]
Additions:
===== Research Papers - Bioinformatics =====
Deletions:
===== Research Papers - Bioinformatics =====

Revision [1606]

Edited on 2006-03-23 17:00:03 by LingyunWu [Del jssc paper]
Additions:
===== Research Papers - Bioinformatics =====
Deletions:
==== Bioinformatics ====

Revision [1603]

Edited on 2006-03-23 16:58:00 by LingyunWu [Del jssc paper]

No Differences

Revision [1601]

Edited on 2006-03-23 16:56:32 by LingyunWu [Del jssc paper]

No Differences

Revision [1593]

Edited on 2006-03-23 16:47:54 by LingyunWu [Del jssc paper]
Additions:
==== Bioinformatics ====
----

Revision [1562]

Edited on 2006-03-13 15:40:31 by LingyunWu [Del jssc paper]
Additions:
~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.
Deletions:
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, in press.

Revision [1534]

Edited on 2006-01-19 22:41:43 by LingyunWu [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. Models and algorithms for the haplotyping problem. //Current Bioinformatics//, Vol. 1, No. 1, pp. 105-114, 2006.
Deletions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. Models and algorithms for the haplotyping problem. //Current Bioinformatics//, in press.

Revision [1533]

Edited on 2006-01-17 17:54:36 by YongWang [Del jssc paper]
Additions:
~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.

Revision [1530]

Edited on 2006-01-10 10:16:04 by YongWang [Del jssc paper]
Additions:
~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.
Deletions:
~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. 4, 2005.

Revision [880]

Edited on 2005-09-07 11:44:49 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. Aligning multiple protein structures by deterministic annealing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 4, pp. 837-860, 2005.

Revision [879]

Edited on 2005-09-07 11:40:20 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen. A parsimonious tree-grow method for haplotype inference. //Bioinformatics//, Vol. 21, No. 17, pp. 3475-3481, 2005.

Revision [878]

Edited on 2005-09-07 11:37:36 by RuishengWang [Del jssc paper]
Additions:
~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.
Deletions:
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. Haplotype assembly from aligned weighted SNP fragments. //[[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 Computational Biology and Chemistry]]//, Vol. 29, No. 4, pp. 281-287, 2005.

Revision [877]

Edited on 2005-09-07 11:36:27 by RuishengWang [Del jssc paper]
Additions:
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. Haplotype assembly from aligned weighted SNP fragments. //[[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 Computational Biology and Chemistry]]//, Vol. 29, No. 4, pp. 281-287, 2005.
Deletions:
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. The SNPs haplotype assembly problem of a single individual. //Computational Biology and Chemistry//, Vol. 29, No. 4, pp. 281-287, 2005.

Revision [862]

Edited on 2005-09-03 12:12:36 by LingyunWu [Del jssc paper]
Additions:
~1) Luonan Chen, Ling-Yun Wu, Yong Wang and Xiang-Sun Zhang. Inferring Protein Interactions from Experimental Data by Association Probabilistic Method. //Proteins: Structure, Function, and Bioinformatics//, in press.

Revision [855]

Edited on 2005-08-31 11:03:21 by LingyunWu [Del jssc paper]
Additions:
~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. A parsimonious tree-grow method for haplotype inference. //Bioinformatics//, Vol. 21, No. 17, pp. 3475-3481, 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.
Deletions:
~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)//, in press.
~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)//, in press.
~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//, in press. (in Chinese)
~1) Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen. A parsimonious tree-grow method for haplotype inference. //Bioinformatics//, doi:10.1093/bioinformatics/bti572, advance published on July 7, 2005.

Revision [831]

Edited on 2005-08-01 16:12:14 by LingyunWu [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. Models and algorithms for the haplotyping problem. //Current Bioinformatics//, in press.
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. The SNPs haplotype assembly problem of a single individual. //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. 4, 2005.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. 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) 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).
Deletions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. Models and algorithms for the haplotyping problem. Submitted to //Current Bioinformatics//.
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. The SNPs haplotype assembly problem of a single individual. //Computational Biology and Chemistry//, in press.
~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//, 25(4), 2005.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. Aligning multiple protein structures by deterministic annealing. //Journal of Bioinformatics and Computational Biology//, 3(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//, 21(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//, 3(2), pp. 385-400, 2005.
~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//, 19(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//, 22(3), pp. 258-269, 2002. (In Chinese).

Revision [814]

Edited on 2005-07-24 20:51:17 by YongWang [Del jssc paper]
Additions:
~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) Shi-Hua 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.
Deletions:
~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) Shi-Hua 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.

Revision [811]

Edited on 2005-07-24 20:38:25 by YongWang [Del jssc paper]
Additions:
~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//, 25(4), 2005.
Deletions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. An emproved self-organizing map algorithm for protein folding and its realization. //Journal of Systems Science and Mathematical Sciences//, 25(4), 2005.

Revision [804]

Edited on 2005-07-24 17:48:21 by LingyunWu [Del jssc paper]
Additions:
=== Refereed Journal Articles ===
=== Proceedings Articles ===
=== Technical Reports ===
Deletions:
== Refereed Journal Articles ==
== Proceedings Articles ==
== Technical Reports ==

Revision [792]

Edited on 2005-07-24 17:06:25 by LingyunWu [Del jssc paper]
Additions:
~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) Shi-Hua Zhang, De-Gang Liu and Xiang-Sun Zhang. A framwork for structural similarity search in protein. //Operations Research and Its Applications, Lecture Notes in Operations
Research//, 5, pp. 285-295, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Xiang-Sun Zhang and Li Sheng. Haplotype inference by pure parsimony via genetic algorithm. //Operations Research and Its Applications, Lecture Notes in Operations Research//, 5, pp. 296-306, World Publishing Corporation, Beijing, 2005.
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, and Xiang-Sun Zhang. A Genetic algorithm for the individual haplotyping problem. //Proceedings of ORSC 2004//, 814-823, Global-Link Publishing Company, Hong Kong, 2004.
~1) Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, and Xiang-Sun Zhang. Haplotyping an individual from weighted SNPs fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, Hong Kong, 2004.
~1) Ji-Hong Zhang, Ling-Yun Wu, Yong Wang, Zheng-Ping Li, and Xiang-Sun Zhang. A statistical method based on markov chain for optimal reconstruction of haplotype from genotype data with SNP. //Proceedings of ORSC 2004//, 1268-1278, Global-Link Publishing Company, Hong Kong, 2004.
~1) 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.
Deletions:
~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, 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, 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, 2004.

Revision [791]

Edited on 2005-07-24 16:58:55 by LingyunWu [Del jssc paper]
Additions:
~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)//, in press.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. Aligning multiple protein structures by deterministic annealing. //Journal of Bioinformatics and Computational Biology//, 3(4), pp. 837-860, 2005.
Deletions:
~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)//, in press.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. Aligning multiple protein structures by deterministic annealing. //Journal of Bioinformatics and Computational Biology//, 3(4),
pp. 837-860, 2005.

Revision [790]

Edited on 2005-07-24 16:57:48 by LingyunWu [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Luonan Chen. Models and algorithms for the haplotyping problem. Submitted to //Current Bioinformatics//.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao and Wei Zhang. Minimum conflict haplotyping from genotype data and SNP fragments. Submitted to //Bioinformatics//.
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, in press.
~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)//, in press.
~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)//, in press.
~1) Ruiqi Wang, Xiang-Sun Zhang and Luonan Chen. Synchronization of gene regulatory networks by signaling molecule. //Journal of Biology Rhythm//, in press.
~1) Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang and Xiang-Sun Zhang. The SNPs haplotype assembly problem of a single individual. //Computational Biology and Chemistry//, in press.
~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//, in press. (in Chinese)
~1) Zhen-Ping Li, Wen-Feng Zhou, Xiang-Sun Zhang and Luonan Chen. A parsimonious tree-grow method for haplotype inference. //Bioinformatics//, doi:10.1093/bioinformatics/bti572, advance published on July 7, 2005.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. An emproved self-organizing map algorithm for protein folding and its realization. //Journal of Systems Science and Mathematical Sciences//, 25(4), 2005.
~1) Tianshou Zhou, Luonan Chen, Yun Tang and Xiang-Sun Zhang. Aligning multiple protein structures by deterministic annealing. //Journal of Bioinformatics and Computational Biology//, 3(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//, 21(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//, 3(2), pp. 385-400, 2005.
~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//, 19(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//, 22(3), pp. 258-269, 2002. (In Chinese).
Deletions:
~1) Zhen-Ping Li, Xiang-Sun Zhang, and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Systems Science and Mathematical Sciences//, to appear. (In Chinese)
~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//, 2005, 21(10), pp: 2456-2462.
~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//, 2005, 3(2), pp:385-400.
~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//, 2003, 19(1), pp:14-21.
~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//, 2002, 22(3), pp:258-269. (In Chinese).

Revision [485]

Edited on 2005-05-14 16:49:34 by RuishengWang [Del jssc paper]
Additions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Systems Science and Mathematical Sciences//, to appear. (In Chinese)
~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//, 2002, 22(3), pp:258-269. (In Chinese).
Deletions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Systems Science and Mathematical Sciences//, to appear. (in Chinese)
~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//, 2002, 22(3), pp:258-269. (in Chinese).

Revision [479]

Edited on 2005-05-14 16:32:47 by RuishengWang [Del jssc paper]
Deletions:
~1) Xiang-Sun Zhang, Zhen-Ping Li, and Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.

Revision [478]

Edited on 2005-05-14 16:30:16 by RuishengWang [Del jssc paper]
Additions:
~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//, 2005, 3(2), pp:385-400.
Deletions:
~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 Exploring protein's optimal HP configurations by self-organizing]]. //Journal of Bioinformatics and Computational Biology//, 2005, 3(2), pp:385-400.

Revision [475]

Edited on 2005-05-14 16:26:09 by RuishengWang [Del jssc paper]
Additions:
~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 Exploring protein's optimal HP configurations by self-organizing]]. //Journal of Bioinformatics and Computational Biology//, 2005, 3(2), pp:385-400.
Deletions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, 2005, 3(2), pp:385-400.

Revision [465]

Edited on 2005-05-14 12:12:25 by RuishengWang [Del jssc paper]
Additions:
~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//, 2003, 19(1), pp:14-21.
Deletions:
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, 2003, 19(1), pp:14-21.

Revision [464]

Edited on 2005-05-14 12:09:17 by RuishengWang [Del jssc paper]
Additions:
~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//, 2005, 21(10), pp: 2456-2462.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, 2005, 3(2), pp:385-400.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, 2003, 19(1), pp:14-21.
~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//, 2002, 22(3), pp:258-269. (in Chinese).
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, 2005, 21(10), pp: 2456-2462.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, 2005, (3)2, pp:385-400.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, 2003, (19)1, pp:14-21.
~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//, 2002, (22)3, pp:258-269. (in Chinese).

Revision [457]

Edited on 2005-05-13 10:28:37 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, 2005, 21(10), pp: 2456-2462.
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [308]

Edited on 2005-05-02 09:37:18 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/bti352v1]]. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [307]

Edited on 2005-05-01 11:58:55 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[http://bioinformatics.oupjournals.org/cgi/content/abstract/bti352v1]]. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[Haplotype reconstruction from SNP fragments by minimum error correction http://bioinformatics.oupjournals.org/cgi/content/abstract/bti352v1]]. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [306]

Edited on 2005-05-01 11:57:59 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. [[Haplotype reconstruction from SNP fragments by minimum error correction http://bioinformatics.oupjournals.org/cgi/content/abstract/bti352v1]]. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.
Deletions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [305]

Edited on 2005-05-01 11:53:06 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, 2005, (3)2, pp:385-400.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, 2003, (19)1, pp:14-21.
~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//, 2002, (22)3, pp:258-269. (in Chinese).
Deletions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 2005.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. 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).

Revision [301]

Edited on 2005-04-30 15:57:35 by RuishengWang [Del jssc paper]
Additions:
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, vol.19, no.1, pp.14-21, 2003.
Deletions:
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. Reconstruction of DNA sequencing by hybridization. //Bioinformatics//, vol.19, no.1, pp.14-21, 2003.

Revision [300]

Edited on 2005-04-30 15:56:20 by RuishengWang [Del jssc paper]
Additions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Systems Science and Mathematical Sciences//, to appear. (in Chinese)
Deletions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Mathematics and System Science//, to appear. (in Chinese)

Revision [299]

Edited on 2005-04-30 15:54:54 by RuishengWang [Del jssc paper]
Additions:
~1) Zhen-Ping Li, Xiang-Sun Zhang, and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.
Deletions:
~1) Zhen-Ping Li, Xiang-Sun Zhang, and Luo-Nan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.

Revision [298]

Edited on 2005-04-30 15:54:36 by RuishengWang [Del jssc paper]
Additions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on self-organizing map algorithm for the 2-Dimensional HP model of protein folding. //Journal of Mathematics and System Science//, to appear. (in Chinese)
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring protein's optimal HP configurations by self-organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 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, 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, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang. Structure alignment of protein by mean field annealing. ICSB2003.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao, and Luonan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~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.
Deletions:
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding. //Journal of Mathematics and System Science//, to apperar. (in Chinese)
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 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, 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, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang. Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao, and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~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.

Revision [293]

Edited on 2005-04-30 11:58:13 by YuyingZhao [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Zhen-Ping Li, and Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao, and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
Deletions:
~1) Xiang-Sun Zhang, Zhen-Ping Li , and Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying, Zhao and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.

Revision [292]

Edited on 2005-04-30 11:57:35 by YuyingZhao [Del jssc paper]
Additions:
~1) Zhen-Ping Li, Xiang-Sun Zhang, and Luo-Nan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Xiang-Sun Zhang. Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding. //Journal of Mathematics and System Science//, to apperar. (in Chinese)
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 2005.
~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, 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, 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, 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, 2004.
~1) Xiang-Sun Zhang, Zhen-Ping Li , and Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, and Xiang-Sun Zhang. Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying, Zhao and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~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.
Deletions:
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luo-Nan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Xiang-Sun Zhang. Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding. //Journal of Mathematics and System Science//, to apperar. (in Chinese)
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 2005.
~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, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. A Genetic Algorithm for the Individual Haplotyping Problem. //Proceedings of ORSC 2004//, 814-823, Global-Link Publishing Company, 2004.
~1) Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, Xiang-Sun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, 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, 2004.
~1) Xiang-Sun Zhang, Zhen-Ping Li , Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, Xiang-Sun Zhang. Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, 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.

Revision [280]

Edited on 2005-04-29 22:45:21 by RuishengWang [Del jssc paper]
Additions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385-400, 2005.
Deletions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385--400, 2005.

Revision [279]

Edited on 2005-04-29 22:42:50 by RuishengWang [Del jssc paper]
Additions:
~1) Yu-Ying Zhao, Ling-Yun Wu, Rui-Sheng Wang, Zhen-Ping Li, Xiang-Sun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, 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, 2004.
~1) Xiang-Sun Zhang, Zhen-Ping Li , Wen-Feng Zhou. A neural network algorithm for the (m,d)-coloring problem of a graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yu-Ying Zhao and Luo-Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, 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.
Deletions:
~1) Yuying Zhao, Lingyun Wu, Ruisheng Wang, Zhenping Li, Xiangsun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, 2004.
~1) Zhang Jihong, Wu Lingyun, Wang Yong, Li Zhengping and Zhang Xiangsun. 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, 2004.
~1) Zhang Xiangsun, Li Zhenping, Zhou Wenfeng. A Neural Network Algorithm for the (m,d)-Coloring Problem of a Graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Xiang Sun Zhang, Rui Sheng Wang, Ling Yun Wu, Yu-Ying Zhao and Luo Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) Xiang Sun Zhang, Yong Wang, Zhong Wei Zhan, Ling-Yun Wu, 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.

Revision [278]

Edited on 2005-04-29 22:41:16 by YuyingZhao [Del jssc paper]
Additions:
~1) Zhang Jihong, Wu Lingyun, Wang Yong, Li Zhengping and Zhang Xiangsun. 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, 2004.
Deletions:
~1) Zhang Jihong, Wu Lingyun, Wang Yong, Li Zhengping and Zhang Xiangshun. 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, 2004.

Revision [277]

Edited on 2005-04-29 22:40:34 by YuyingZhao [Del jssc paper]
Additions:
~1) Zhang Jihong, Wu Lingyun, Wang Yong, Li Zhengping and Zhang Xiangshun. 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, 2004.
Deletions:
~1) Zhang Jihong, Wu Lingyun,Wang Yong,Li Zhengping and Zhang Xiangshun. 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, 2004.

Revision [276]

Edited on 2005-04-29 22:37:10 by RuishengWang [Del jssc paper]
Additions:
~1) Zhen-Ping Li, Xiang-Sun Zhang and Luo-Nan Chen. Unique optimal foldings of proteins on a triangular lattice. //Applied Bioinformatics//, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Xiang-Sun Zhang. Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding. //Journal of Mathematics and System Science//, to apperar. (in Chinese)
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing. //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, 385--400, 2005.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang. 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, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. A Genetic Algorithm for the Individual Haplotyping Problem. //Proceedings of ORSC 2004//, 814-823, Global-Link Publishing Company, 2004.
~1) Yuying Zhao, Lingyun Wu, Ruisheng Wang, Zhenping Li, Xiangsun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. //Proceedings of ORSC 2004//, 824-830, Global-Link Publishing Company, 2004.
~1) Zhang Jihong, Wu Lingyun,Wang Yong,Li Zhengping and Zhang Xiangshun. 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, 2004.
~1) Zhang Xiangsun, Li Zhenping, Zhou Wenfeng. A Neural Network Algorithm for the (m,d)-Coloring Problem of a Graph. //Proceedings of ORSC 2004//, 382-389, Global-Link Publishing Company, 2004.
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, Xiang-Sun Zhang. Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Xiang Sun Zhang, Rui Sheng Wang, Ling Yun Wu, Yu-Ying Zhao and Luo Nan Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) Xiang Sun Zhang, Yong Wang, Zhong Wei Zhan, Ling-Yun Wu, 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.
Deletions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, 385--400, 2005.
~1) Li, Zhen-Ping, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. Applied Bioinformatics, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Xinag-Sun Zhang, Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding, Jornal of Mathematics and System Science, to apperar. (in Chinese)
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, Xiang-Sun Zhang, Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang, 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, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. A Genetic Algorithm for the Individual Haplotyping Problem. Proceedings of ORSC 2004, 814-823, Global-Link Publishing Company, 2004.
~1) Yuying Zhao, Lingyun Wu, Ruisheng Wang, Zhenping Li, Xiangsun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. Proceedings of ORSC 2004, 824-830, Global-Link Publishing Company, 2004.
~1) Zhang Jihong, Wu Lingyun,Wang Yong,Li Zhengping and Zhang Xiangshun. 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, 2004.
~1) Zhang Xiangsun, Li Zhenping, Zhou Wenfeng. A Neural Network Algorithm for the (m,d)-Coloring Problem of a Graph. Proceedings of ORSC 2004, 382-389, Global-Link Publishing Company, 2004.
~1) X. -S. Zhang, R. -S. Wang, L.-Y. Wu, Y.-Y., Zhao and L.-N. Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) X.-S. Zhang, Y. Wang, Z.-W. Zhan, L. -Y Wu, J. -H. 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.

Revision [275]

Edited on 2005-04-29 22:29:41 by RuishengWang [Del jssc paper]
Additions:
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. Haplotype reconstruction from SNP fragments by minimum error correction. //Bioinformatics//, doi:10.1093/ bioinformatics/ bti352, 2005.
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen. Exploring Protein's Optimal HP Configurations by Self-Organizing, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, 385--400, 2005.
~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).
Deletions:
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen, Exploring Protein's Optimal HP Configurations by Self-Organizing, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, 385--400, 2005.
~1) Xiangsun Zhang, Jihong Zhang and Lingyun Wu, A reconstruction algorithm to solve positional sequencing by hybridization, J. of Systems Science and Mathematical Sciences, vol.22, no.3, pp.258-269, 2002. (in Chinese).
~1) X.-S. Zhang, Y. Wang, Z.-W. Zhan, L. -Y Wu, J. H. Zhang, A Fast Approach Measure the Protein Structure Similarity from the Global Shape View. IAM-R003, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) R.-S. Wang, L.-Y. Wu, Z.-P. Li, X.-S. Zhang, Haplotype reconstruction from SNP fragments by minimum error correction, Bioinformatics. doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [273]

Edited on 2005-04-29 22:20:04 by RuishengWang [Del jssc paper]
Additions:
~1) R.-S. Wang, L.-Y. Wu, Z.-P. Li, X.-S. Zhang, Haplotype reconstruction from SNP fragments by minimum error correction, Bioinformatics. doi:10.1093/ bioinformatics/ bti352, 2005.
Deletions:
~1) R. -S. Wang, L. -Y. Wu, Z. -P. Li, X. -S. Zhang, Haplotype reconstruction from SNP fragments by minimum error correction, Bioinformatics. doi:10.1093/ bioinformatics/ bti352, 2005.

Revision [272]

Edited on 2005-04-29 22:19:40 by RuishengWang [Del jssc paper]
Additions:
== Technical Reports ==
Deletions:
== Technique Report ==

Revision [270]

Edited on 2005-04-29 22:19:00 by RuishengWang [Del jssc paper]
Additions:
~1) R. -S. Wang, L. -Y. Wu, Z. -P. Li, X. -S. Zhang, Haplotype reconstruction from SNP fragments by minimum error correction, Bioinformatics. doi:10.1093/ bioinformatics/ bti352, 2005.
== Technique Report ==
~1) X. -S. Zhang, R. -S. Wang, L.-Y. Wu, Y.-Y., Zhao and L.-N. Chen. Minimum conflict haplotyping from genotype data and SNP fragments. Report of Research, IAM-R001, Institute of Applied Mathematics, AMSS, CAS, 2005.
~1) X.-S. Zhang, Y. Wang, Z.-W. Zhan, L. -Y Wu, J. -H. 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.

Revision [265]

Edited on 2005-04-29 22:13:33 by YongWang [Del jssc paper]
Additions:
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang, Reconstruction of DNA sequencing by hybridization, Bioinformatics, vol.19, no.1, pp.14-21, 2003.
Deletions:
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang, Reconstruction of DNA sequencing by hybridization, Bioinformatics, vol.19, no.1, pp.14-21, 2003. (Abstract, PDF).

Revision [264]

Edited on 2005-04-29 22:12:06 by YongWang [Del jssc paper]
Additions:
== Refereed Journal Articles ==
~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen, Exploring Protein's Optimal HP Configurations by Self-Organizing, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, 385--400, 2005.
~1) Li, Zhen-Ping, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. Applied Bioinformatics, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Xinag-Sun Zhang, Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding, Jornal of Mathematics and System Science, to apperar. (in Chinese)
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, Xiang-Sun Zhang, Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang, Reconstruction of DNA sequencing by hybridization, Bioinformatics, vol.19, no.1, pp.14-21, 2003. (Abstract, PDF).
~1) Xiangsun Zhang, Jihong Zhang and Lingyun Wu, A reconstruction algorithm to solve positional sequencing by hybridization, J. of Systems Science and Mathematical Sciences, vol.22, no.3, pp.258-269, 2002. (in Chinese).
~1) X.-S. Zhang, Y. Wang, Z.-W. Zhan, L. -Y Wu, J. H. Zhang, A Fast Approach Measure the Protein Structure Similarity from the Global Shape View. IAM-R003, Institute of Applied Mathematics, AMSS, CAS, 2005.
== Proceedings Articles ==
~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. A Genetic Algorithm for the Individual Haplotyping Problem. Proceedings of ORSC 2004, 814-823, Global-Link Publishing Company, 2004.
~1) Yuying Zhao, Lingyun Wu, Ruisheng Wang, Zhenping Li, Xiangsun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. Proceedings of ORSC 2004, 824-830, Global-Link Publishing Company, 2004.
~1) Zhang Jihong, Wu Lingyun,Wang Yong,Li Zhengping and Zhang Xiangshun. 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, 2004.
~1) Zhang Xiangsun, Li Zhenping, Zhou Wenfeng. A Neural Network Algorithm for the (m,d)-Coloring Problem of a Graph. Proceedings of ORSC 2004, 382-389, Global-Link Publishing Company, 2004.
Deletions:
== Refereed Journal Articles ==

~1) Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen, A New SOM Approach for 2D HP-Model of Proteins' Structure Prediction, Submitted to RECOMB04
~1) Li, Zhen-Ping, Xiang-Sun Zhang and Luonan Chen. Unique optimal foldings of proteins on a triangular lattice. Applied Bioinformatics, accepted.
~1) Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Xinag-Sun Zhang, Research on Self-Organizing Map Algorithm for the 2-Dimensional HP Model of Protein Folding, Jornal of Mathematics and System Science, to apperar. (in Chinese)
~1) Luo-Nan Chen, Tian-Shou Zhou, Yun Tang, Xiang-Sun Zhang, Structure of Alignment of Protein by Mean Field Annealing. ICSB2003.
~1) Ji-Hong Zhang, Ling-Yun Wu and Xiang-Sun Zhang, Reconstruction of DNA sequencing by hybridization, Bioinformatics, vol.19, no.1, pp.14-21, 2003. (Abstract, PDF).
~1) Xiangsun Zhang, Jihong Zhang and Lingyun Wu, A reconstruction algorithm to solve positional sequencing by hybridization, J. of Systems Science and Mathematical Sciences, vol.22, no.3, pp.258-269, 2002. (in Chinese).

== Proceedings Articles ==

~1) Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang. A Genetic Algorithm for the Individual Haplotyping Problem. Proceedings of ORSC 2004, 814-823, Global-Link Publishing Company, 2004.
~1) Yuying Zhao, Lingyun Wu, Ruisheng Wang, Zhenping Li, Xiangsun Zhang. Haplotyping an Individual from Weighted SNPs Fragments. Proceedings of ORSC 2004, 824-830, Global-Link Publishing Company, 2004.
~1) Zhang Jihong, Wu Lingyun,Wang Yong,Li Zhengping and Zhang Xiangshun. 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, 2004.
~1) Zhang Xiangsun, Li Zhenping, Zhou Wenfeng. A Neural Network Algorithm for the (m,d)-Coloring Problem of a Graph. Proceedings of ORSC 2004, 382-389, Global-Link Publishing Company, 2004.

Revision [87]

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