Wiki source for PubBioinformatics2010
===== Publications - Bioinformatics 2010 =====
----
{{include page="PubBioinformaticsTOC"}}
----
=== Books & Chapters ===
~1) Ling-Yun Wu, Xiaobo Zhou, and Stephen T. C. Wong. ---**[[http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470180935.html Computational Imaging and Modeling for System Biology]]**--- Chapter 17 in //Elements of Computational Systems Biology//, Huma M. Lodhi and Stephen H. Muggleton (Editors). John Wiley & Sons, February, 2010.
=== Refereed Journal Papers ===
~1) Yan Xu, Xiao-Bo Wang, Jun Ding, Ling-Yun Wu, and Naiyang Deng. ---**[[http://www.ncbi.nlm.nih.gov/pubmed/20085770 Lysine acetylation sites prediction using an ensemble of support vector machine classifiers]]**--- //Journal of Theoretical Biology//, 264(1):130-135, 2010.--- SCI;
~1) Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia. ---**[[http://nar.oxfordjournals.org/content/38/18/5959 Protein evolution in yeast transcription factor subnetworks]]**--- //Nucleic Acids Research//, 38(18): 5959–5969, 2010. ---SCI; Funding: NSFC(10801131, 10631070)
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/13/1616 Prediction of protein-RNA binding sites by a random forest method with combined features]]**--- //Bioinformatics//, 26(13):1616-1622, 2010.--- SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
~1) Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.biomedcentral.com/1752-0509/4/S2/S11/ Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains]]**--- //BMC Systems Biology//, 4(Suppl 2):S11.---SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
~1) Yongcui Wang, Zhixia Yang, Yong Wang, and Nai-Yang Deng. ---**[[http://www.ingentaconnect.com/content/ben/lddd/2010/00000007/00000005/011aj Computationally probing drug-protein interactions via support vector machine]]**--- //Letters In Drug Design & Discovery//, 7(5), 370-378, 2010.--- SCI;
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding, Xian-Wen Ren, and Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/y62142r517762595/fulltext.pdf Binary matrix factorization for analyzing gene expression data]]**--- // Data Mining and Knowledge Discovery//, 20(1), 28-52, 2010.--- SCI;
~1) Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu, and Xiang-Sun Zhang. ---**[[http://www.biomedcentral.com/1752-0509/4/72 An information-flow-based model with dissipation, saturation and direction for active pathway inference]]**--- //BMC Systems Biology//, 4:72, 2010.--- SCI; Funding: NSFC(60873205), 973(2006CB503905)
~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.biomedcentral.com/1471-2105/11/26 Detecting disease associated modules and prioritizing active genes based on high throughput data. ]]**--- //BMC Bioinformatics.// 11:26, 2010.--- SCI; Funding: 973(2006CB503905), NSFC(60873205, 10801131), CAS(kjcx-yw-s7)
~1) Zheng Xia, Ling-Yun Wu, Xiaobo Zhou, and Stephen TC Wong. ---**[[http://www.biomedcentral.com/qc/1752-0509/4/S2/S6 Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces.]]**--- //BMC Systems Biology//, Vol. 4, Suppl 2, S6, 2010.--- SCI;
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.biomedcentral.com/qc/1752-0509/4/S2/S1 Optimization Meets Systems Biology.]]**--- //BMC Systems Biology//, Vol. 4, Suppl 2, S1, 2010.--- SCI;
~1) Tingting Gao, Zhixia Yang, Yong Wang, Ling Jing. ---**[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-4XGBG64-1&_user=1999482&_coverDate=02%2F21%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=ed86676e176a49bb8aa4e34c74836a87&searchtype=a Identifying translation initiation sites in prokaryotes using support vector machine.]]**--- //Journal of Theoretical Biology//, Vol. 262, No. 4, 644-649, 2010.--- SCI; Funding: NSFC(10631070, 10801131)
~1) Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.springerlink.com/content/85083565w7877872/ SANA: an algorithm for sequential and non-sequential protein structure alignment]]**--- //Amino Acids//, Vol. 39, No. 2, 417-425, 2010. --- SCI; Funding: NSFC(10631070, 60503004), JSPS-NSFC (10711140116).
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.springerlink.com/content/n5330464821r2360/ Self-organizing map of complex networks for community detection]]**---//Journal of Systems Science and Complexity//, 23(5), 931-941, 2010. --- SCI; Funding: NSFC(10631070, 60873205, 10701080), BNSFC(1092011)
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/w40345661t887670/ A linear programming model based on network flow for pathway inference]]**---//Journal of Systems Science and Complexity//, 23(5), 971-977, 2010. --- SCI; Funding: NSFC(10631070, 60873205)
~1) Junhua Zhang, Yuqing Qiu, Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/33188l5260668780/ Detecting community structure: From parsimony to weighted parsimony]]**---//Journal of Systems Science and Complexity//, 23(5), 1024-1036, 2010. --- SCI; Funding: NSFC(60873205),CAS(kjcx-yw-s7)
=== Proceedings Papers ===
~1) Zhi-Ping Liu, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.icmlc.com/program/ICMLC_proceedingsPaper.pdf Inferring gene regulatory networks from expression data with prior knowledge by linear programming. ]]**--- Proceedings of the 9th International Conference on Machine Learning and Cybernetics. pp. 3067-3072, Qingdao, China, 2010.--- EI; Funding: 973(2006CB503905), NSFC(10631070, 10801131)
~1) Yong Wang, Xiang-Sun Zhang, Katsuhisa Horimoto, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D5573108&authDecision=-203 System Identification Models for Gene Regulation System. ]]**--- Proceedings of The 29th Chinese Control Conference (CCC), pp. 6239-6244, Beijing, 2010.--- EI; Funding: NSFC(10801131)
~1) Ruisheng Wang, Zhenping Li, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D5573015&authDecision=-203 Optimization and Control of Metabolic Networks. ]]**--- Proceedings of The 29th Chinese Control Conference (CCC), pp. 6251-6255, Beijing, 2010.--- EI; Funding: NSFC(10631070,10701080,60873205)
~1) Xiaorong Yang, Xianwen Ren, Xiaobo Zhou. ---**[[http://www.aporc.org/LNOR/13/ISB2010F17.pdf Transcriptional Regulatory Network Discovery via Information Mining Approach in Rett Syndromes Study]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 109-118
~1) Zhi-Ping Liu, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/13/ISB2010F26.pdf Effects of Multiple Probesets in Affymetrix GeneChips on Identifying Differentially Expressed Genes in iPS Cells]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 187–195
~1) Jiguang Wang, Yong Wang, Xianwen Ren, Wei Guo, Luonan Chen. ---**[[http://www.aporc.org/LNOR/13/ISB2010F31.pdf Uncover the Transient Transcriptional Regulations by a Novel Sliding Window Correlation Strategy]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 235–242
~1) Jibin Qu, Michael Ng, Luonan Chen. ---**[[http://www.aporc.org/LNOR/13/ISB2010F41.pdf Constrained Subspace Clustering for Time Series Gene Expression Data]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 323–330
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/13/ISB2010F42.pdf Drug Target Identification Based on Flux Balance Analysis of Metabolic Networks]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 331–338
~1) Yu-Qing Qiu, Xing-Ming Zhao, Zikai Wu, Chaochao Wu, Rong Zeng, Luonan Chen.---**[[http://www.aporc.org/LNOR/13/ISB2010F45.pdf Network Flow Model Based Analysis of Mouse Hepatocarcinogenesis]]**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 355–362
~1) Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/12/ISORA2010F53.pdf An Optimization Model for Fuzzy Binary Clustering]].**---The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 422-432
~1) Junhua Zhang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/12/ISORA2010F60.pdf On Resolution Limit of the Modularity in Community Detection]].**---The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 492-499
----
CategoryPublication
----
{{include page="PubBioinformaticsTOC"}}
----
=== Books & Chapters ===
~1) Ling-Yun Wu, Xiaobo Zhou, and Stephen T. C. Wong. ---**[[http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470180935.html Computational Imaging and Modeling for System Biology]]**--- Chapter 17 in //Elements of Computational Systems Biology//, Huma M. Lodhi and Stephen H. Muggleton (Editors). John Wiley & Sons, February, 2010.
=== Refereed Journal Papers ===
~1) Yan Xu, Xiao-Bo Wang, Jun Ding, Ling-Yun Wu, and Naiyang Deng. ---**[[http://www.ncbi.nlm.nih.gov/pubmed/20085770 Lysine acetylation sites prediction using an ensemble of support vector machine classifiers]]**--- //Journal of Theoretical Biology//, 264(1):130-135, 2010.--- SCI;
~1) Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia. ---**[[http://nar.oxfordjournals.org/content/38/18/5959 Protein evolution in yeast transcription factor subnetworks]]**--- //Nucleic Acids Research//, 38(18): 5959–5969, 2010. ---SCI; Funding: NSFC(10801131, 10631070)
~1) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/13/1616 Prediction of protein-RNA binding sites by a random forest method with combined features]]**--- //Bioinformatics//, 26(13):1616-1622, 2010.--- SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
~1) Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.biomedcentral.com/1752-0509/4/S2/S11/ Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains]]**--- //BMC Systems Biology//, 4(Suppl 2):S11.---SCI; Funding: NSFC(10631070, 60873205), 973(2006CB503905)
~1) Yongcui Wang, Zhixia Yang, Yong Wang, and Nai-Yang Deng. ---**[[http://www.ingentaconnect.com/content/ben/lddd/2010/00000007/00000005/011aj Computationally probing drug-protein interactions via support vector machine]]**--- //Letters In Drug Design & Discovery//, 7(5), 370-378, 2010.--- SCI;
~1) Zhong-Yuan Zhang, Tao Li, Chris Ding, Xian-Wen Ren, and Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/y62142r517762595/fulltext.pdf Binary matrix factorization for analyzing gene expression data]]**--- // Data Mining and Knowledge Discovery//, 20(1), 28-52, 2010.--- SCI;
~1) Xianwen Ren, Xiaobo Zhou, Ling-Yun Wu, and Xiang-Sun Zhang. ---**[[http://www.biomedcentral.com/1752-0509/4/72 An information-flow-based model with dissipation, saturation and direction for active pathway inference]]**--- //BMC Systems Biology//, 4:72, 2010.--- SCI; Funding: NSFC(60873205), 973(2006CB503905)
~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.biomedcentral.com/1471-2105/11/26 Detecting disease associated modules and prioritizing active genes based on high throughput data. ]]**--- //BMC Bioinformatics.// 11:26, 2010.--- SCI; Funding: 973(2006CB503905), NSFC(60873205, 10801131), CAS(kjcx-yw-s7)
~1) Zheng Xia, Ling-Yun Wu, Xiaobo Zhou, and Stephen TC Wong. ---**[[http://www.biomedcentral.com/qc/1752-0509/4/S2/S6 Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces.]]**--- //BMC Systems Biology//, Vol. 4, Suppl 2, S6, 2010.--- SCI;
~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.biomedcentral.com/qc/1752-0509/4/S2/S1 Optimization Meets Systems Biology.]]**--- //BMC Systems Biology//, Vol. 4, Suppl 2, S1, 2010.--- SCI;
~1) Tingting Gao, Zhixia Yang, Yong Wang, Ling Jing. ---**[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-4XGBG64-1&_user=1999482&_coverDate=02%2F21%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=ed86676e176a49bb8aa4e34c74836a87&searchtype=a Identifying translation initiation sites in prokaryotes using support vector machine.]]**--- //Journal of Theoretical Biology//, Vol. 262, No. 4, 644-649, 2010.--- SCI; Funding: NSFC(10631070, 10801131)
~1) Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.springerlink.com/content/85083565w7877872/ SANA: an algorithm for sequential and non-sequential protein structure alignment]]**--- //Amino Acids//, Vol. 39, No. 2, 417-425, 2010. --- SCI; Funding: NSFC(10631070, 60503004), JSPS-NSFC (10711140116).
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://www.springerlink.com/content/n5330464821r2360/ Self-organizing map of complex networks for community detection]]**---//Journal of Systems Science and Complexity//, 23(5), 931-941, 2010. --- SCI; Funding: NSFC(10631070, 60873205, 10701080), BNSFC(1092011)
~1) Xianwen Ren, Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/w40345661t887670/ A linear programming model based on network flow for pathway inference]]**---//Journal of Systems Science and Complexity//, 23(5), 971-977, 2010. --- SCI; Funding: NSFC(10631070, 60873205)
~1) Junhua Zhang, Yuqing Qiu, Xiang-Sun Zhang. ---**[[http://www.springerlink.com/content/33188l5260668780/ Detecting community structure: From parsimony to weighted parsimony]]**---//Journal of Systems Science and Complexity//, 23(5), 1024-1036, 2010. --- SCI; Funding: NSFC(60873205),CAS(kjcx-yw-s7)
=== Proceedings Papers ===
~1) Zhi-Ping Liu, Xiang-Sun Zhang and Luonan Chen. ---**[[http://www.icmlc.com/program/ICMLC_proceedingsPaper.pdf Inferring gene regulatory networks from expression data with prior knowledge by linear programming. ]]**--- Proceedings of the 9th International Conference on Machine Learning and Cybernetics. pp. 3067-3072, Qingdao, China, 2010.--- EI; Funding: 973(2006CB503905), NSFC(10631070, 10801131)
~1) Yong Wang, Xiang-Sun Zhang, Katsuhisa Horimoto, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D5573108&authDecision=-203 System Identification Models for Gene Regulation System. ]]**--- Proceedings of The 29th Chinese Control Conference (CCC), pp. 6239-6244, Beijing, 2010.--- EI; Funding: NSFC(10801131)
~1) Ruisheng Wang, Zhenping Li, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D5573015&authDecision=-203 Optimization and Control of Metabolic Networks. ]]**--- Proceedings of The 29th Chinese Control Conference (CCC), pp. 6251-6255, Beijing, 2010.--- EI; Funding: NSFC(10631070,10701080,60873205)
~1) Xiaorong Yang, Xianwen Ren, Xiaobo Zhou. ---**[[http://www.aporc.org/LNOR/13/ISB2010F17.pdf Transcriptional Regulatory Network Discovery via Information Mining Approach in Rett Syndromes Study]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 109-118
~1) Zhi-Ping Liu, Xiang-Sun Zhang. ---**[[http://www.aporc.org/LNOR/13/ISB2010F26.pdf Effects of Multiple Probesets in Affymetrix GeneChips on Identifying Differentially Expressed Genes in iPS Cells]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 187–195
~1) Jiguang Wang, Yong Wang, Xianwen Ren, Wei Guo, Luonan Chen. ---**[[http://www.aporc.org/LNOR/13/ISB2010F31.pdf Uncover the Transient Transcriptional Regulations by a Novel Sliding Window Correlation Strategy]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 235–242
~1) Jibin Qu, Michael Ng, Luonan Chen. ---**[[http://www.aporc.org/LNOR/13/ISB2010F41.pdf Constrained Subspace Clustering for Time Series Gene Expression Data]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 323–330
~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/13/ISB2010F42.pdf Drug Target Identification Based on Flux Balance Analysis of Metabolic Networks]].**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 331–338
~1) Yu-Qing Qiu, Xing-Ming Zhao, Zikai Wu, Chaochao Wu, Rong Zeng, Luonan Chen.---**[[http://www.aporc.org/LNOR/13/ISB2010F45.pdf Network Flow Model Based Analysis of Mouse Hepatocarcinogenesis]]**---The Fourth International Conference on Computational Systems Biology (ISB2010), pp. 355–362
~1) Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/12/ISORA2010F53.pdf An Optimization Model for Fuzzy Binary Clustering]].**---The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 422-432
~1) Junhua Zhang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/12/ISORA2010F60.pdf On Resolution Limit of the Modularity in Community Detection]].**---The Ninth International Symposium on Operations Research and Its Applications (ISORA’10), pp. 492-499
----
CategoryPublication
