Wiki source for PubBioinformatics2007
===== Publications - Bioinformatics 2007 =====
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{{include page="PubBioinformaticsTOC"}}
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=== Refereed Journal Articles ===
~1) Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen.--- **[[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, 2007. --- Funding: NSFC(10631070), 973(2006CB503905)
~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 --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
~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. --- SCI; Funding: NSFC(10631070), 973(2006CB503905)
~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--- SCI; Funding: NSFC(10631070), NSFC(10701080), 973(2006CB503905)
~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--- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
~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.--- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
~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.--- SCI; Funding: NSFC(10471141), NSFC(60503004), NSFC(023101018)
~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10631070), NSFC(60503004), 973(2006CB503905)
~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. --- SCI; Funding: NSFC(10631070)
~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.--- Funding: NSFC(10471141), NSFC(60503004)
~1) Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang.--- **[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4KKFYKY-3&_user=209810&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000014439&_version=1&_urlVersion=0&_userid=209810&md5=e7b775a5ccedd64e31b43f7517f20b3e Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering]].**--- //Physica A//, 2007, 374, 483–490..--- SCI; Funding: NSFC(10471141)
=== Proceedings Articles ===
~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. --- EI
~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--- EI, ISTP; Funding: 973(2006CB503905)
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://www.springerlink.com/content/p815210h2x030wq0/ 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 --- EI, ISTP; Funding: NSFC(10701080), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), NSFC(60503004), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10471141), NSFC(60503004), 973(2006CB503905)
~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. --- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
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CategoryPublication
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{{include page="PubBioinformaticsTOC"}}
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=== Refereed Journal Articles ===
~1) Guangxu Jin, Shihua Zhang , Xiang-Sun Zhang, Luonan Chen.--- **[[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, 2007. --- Funding: NSFC(10631070), 973(2006CB503905)
~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 --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
~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. --- SCI; Funding: NSFC(10631070), 973(2006CB503905)
~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--- SCI; Funding: NSFC(10631070), NSFC(10701080), 973(2006CB503905)
~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--- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(60503004), 973(2006CB503905)
~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.--- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), 973(2006CB503905)
~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.--- SCI; Funding: NSFC(10471141), NSFC(60503004), NSFC(023101018)
~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10631070), NSFC(60503004), 973(2006CB503905)
~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. --- SCI; Funding: NSFC(10631070)
~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.--- Funding: NSFC(10471141), NSFC(60503004)
~1) Shihua Zhang, Rui-Sheng Wang, and Xiang-Sun Zhang.--- **[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4KKFYKY-3&_user=209810&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000014439&_version=1&_urlVersion=0&_userid=209810&md5=e7b775a5ccedd64e31b43f7517f20b3e Identification of Overlapping Community Structure in Complex Networks Using Fuzzy c-means Clustering]].**--- //Physica A//, 2007, 374, 483–490..--- SCI; Funding: NSFC(10471141)
=== Proceedings Articles ===
~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. --- EI
~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--- EI, ISTP; Funding: 973(2006CB503905)
~1) Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://www.springerlink.com/content/p815210h2x030wq0/ 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 --- EI, ISTP; Funding: NSFC(10701080), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), NSFC(60503004), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
~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.--- ISTP; Funding: NSFC(10471141), NSFC(60503004), 973(2006CB503905)
~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. --- ISTP; Funding: NSFC(10631070), 973(2006CB503905)
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CategoryPublication
