===== Publications - Bioinformatics 2011 ===== ---- {{include page="PubBioinformaticsTOC"}} ---- === Books & Chapters === ~1) Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen. ---**[[http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470505192.html Computational Models for Condition-Specific Gene and Pathway Inference]]**--- Chapter 30 in //Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications//, Mourad Elloumi and Albert Y. Zomaya (Editors). John Wiley & Sons, January, 2011. ~1) Ling-Yun Wu. ---**[[http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470505192.html Haplotype Inference Models and Algorithms]]**--- Chapter 36 in //Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications//, Mourad Elloumi and Albert Y. Zomaya (Editors). John Wiley & Sons, January, 2011. ~1) Zhong-Yuan Zhang --- **Nonnegative Matrix Factorization: Models, Algorithms and Applications.** --- Chapter in //Data Minming: Foundations and Intelligent Paradigms 2//, in press, 2011. === Refereed Journal Papers === ~1) Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. ---**[[http://bioinformatics.oxfordjournals.org/content/27/22/3173 An Efficient Network Querying Method Based on Conditional Random Fields.]] **---//Bioinformatics//, 27 (22): 3173-3178, 2011. doi: 10.1093/bioinformatics/btr524. ---SCI; Funding: NSFC(60970091, 60873205), CAS(kjcx-yw-s7) ~1) Guangxu Jin, Changhe Fu, Hong Zhao, Kemi Cui, Jenny Chang, Stephen T.C. Wong --- **[[http://www.ncbi.nlm.nih.gov/pubmed/22108825 A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy.]] **--- //Cancer Res//, doi:10.1158/0008-5472.CAN-11-2333, 2011. ~1) Guangxu Jin, Hong Zhao, Xiaobo Zhou, Stephen T.C. Wong --- **[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117391/?tool=pubmed An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.]] **--- //Bioinformatics//, 27(13):i310-6, 2011. ~1) Jiguang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Luonan Chen, and Xiang-Sun Zhang --- **[[http://nar.oxfordjournals.org/content/early/2011/05/04/nar.gkr251.abstract?etoc NOA: a novel Network Ontology Analysis method.]] **--- //Nucleic Acids Research//, 39(13):e87, 2011. ---SCI; Funding: NSFC(60873205, 10801131, 60970091), CAS(kjcs-yw-s7) ~1) Shihua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou --- **[[http://bioinformatics.oxfordjournals.org/content/27/13/i401.short?rss=1 A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.]]** ---//Bioinformatics (ISMB2011)//, 27:i401-i409, 2011. ---SCI; Funding: NSFC(11001256), CAS(kjcs-yw-s7) ~1) Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang --- **[[http://www.biomedcentral.com/1752-0509/5/S1/S11 Two-stage flux balance analysis of metabolic networks for drug target identification.]] **--- //BMC Systems Biology//, 5(Suppl 1):S11, 2011. ---SCI; Funding: NSFC(10631070, 60873205, 10701080) ~1) Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang, Weiming Xia and Luonan Chen. ---**[[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c0mb00325e Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients]].**---//Molecular Biosystems//, 7(5):1441-1452, 2011. ~1) Yong Wang, Xiang-Sun Zhang, and Luonan Chen --- **[[http://www.biomedcentral.com/1752-0509/5/S1/S1 Computational systems biology: integration of sequence, structure, network, and dynamics.]] **--- //BMC Systems Biology//, 5(Suppl 1):S1, 2011 ~1) Yongcui Wang, Yong Wang, Zhixia Yang, Nai-Yang Deng --- **[[http://www.biomedcentral.com/1752-0509/5/S1/S6 Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context.]] **--- //BMC Systems Biology//, 5(Suppl 1):S6, 2011. ---SCI; Funding: NSFC(10801131, 10801112, 10971223, 11071252) ~1) Ruoying Chen, Zhiwang Zhang, Di Wu, Peng Zhang, Xinyang Zhang, Yong Wang, and Yong Shi. ---**[[http://www.sciencedirect.com/science/article/pii/S0022519310005552 Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming.]] **--- //Journal of Theoretical Biology//, Vol. 269, pp. 174--180, 2011. ~1) Xianwen Ren, Yongcui Wang, Yong Wang, Nai-Yang Deng and Xiang-Sun Zhang. ---**[[http://www.biomedcentral.com/1471-2105/12/409 Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation]]**--- BMC Bioinformatics 12:409, 2011. ---SCI; Funding: NSFC(60873205, 10801131, 10631070, 10971223, 11071252), CAS(kjcx-yw-s7) === Proceedings Papers === ~1) Jun-Fei Zhao, Jiguang Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F15.pdf A SVC-based Method to Detect Multi-scalar Noisy Communities in Complex Networks]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 133-143 ~1) Yong Wang, Jiguang Wang, Chen Chen, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F17.pdf A Regularized Optimization Model for Community Identification in Complex Networks]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 147-156 ~1)Hong-Wei Liu.---**[[http://www.aporc.org/LNOR/14/ISORA2011F06.pdf A Non-monotone Adaptive Trust Region Algorithm For Nonlinear Equations]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 67-74 ~1)Zhenping Li, Xianman Hu.---**[[http://www.aporc.org/LNOR/14/ISORA2011F18.pdf The Team Orienteering Problem with Capacity Constraint and Time Window]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 157-163 ~1)Xianwen Ren, Yong Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F21.pdf A Flexible Convex Optimization Model for Semi-supervised Clustering with Instance-level Constraints]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 178-185 ~1)Hong-Wei Liu.---**[[http://www.aporc.org/LNOR/14/ISORA2011F23.pdf Linear Programming for Portfolio Selection Based on Fuzzy Decision-Making Theory]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 195-202 ~1)Jin-Shan Li, San-qiang Wang, Jia-Rong Gao.---**[[http://www.aporc.org/LNOR/14/ISORA2011F28.pdf Consumer’s Optimal Choice on lp Commodity]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 234-241 ~1)Shoujun Xu, Jiguang Wang, Junhua Zhang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F40.pdf Multiple Resolution Community Structure Analysis]].**--- The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 334-349 ~1)Yong-Cui Wang, Xian-Wen Ren, Chun-Hua Zhang, Nai-Yang Deng, Xiang-Sun Zhang.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033124 Evaluating the Denoising Techniques in Protein-Protein Interaction Prediction]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 78-83 ~1) Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033143 Protein Interaction Prediction for Mouse PDZ Domains Using Dipeptide Composition Features]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 129-132 ~1) Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033155 Identification of Master Regulator Candidates for Diabetes Progression in Goto-Kakizaki Rat by a Computational Procedure]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 197-202 ~1) Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033161 A Linear Programming Model for Identifying Non-Redundant Biomarkers Based on Gene Expression Profiles]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 249-254 ~1) Yong Wang, Qiao-Feng Wu, Chen Chen, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, Fan-Rong Liang.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033172 Identifying Biomarkers for Acupuncture Treatment via an Optimization Model]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 319-326 ~1) Junhua Zhang, Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033175 A Dynamical Method to Extract Communities Induced by Low or Middle-degree Nodes]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 340-344 ~1) Qiang Huang, Ling-Yun Wu, Ji-Bin Qu, Xiang-Sun Zhang.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033177 Analyzing Time-Course Gene Expression Data Using Profile-State Hidden Markov Model]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 351-355 ~1) Chen Chen, Jun-Fei Zhao, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033181 Inferring Domain-Domain Interactions Using an Extended Parsimony Model]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 385-389 ~1) Ji-Bin Qu, Xiang-Sun Zhang, Ling-Yun Wu, Yong Wang, Luonan Chen.---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6033184 Detecting Coherent Local Patterns from Time Series Gene Expression Data by a Temporal Biclustering Method]].**---2011 IEEE International Conference on Systems Biology (ISB), pp. 399-404 ~1) Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K.K. Leung, Xiang-Sun Zhang, Stephen K.W. Tsui and Luonan Chen. ---**[[http://doc.aporc.org/wiki/MTBPPI Inferring protein-protein interactions based on sequences and interologs in Mycobacterium tuberculosis]]. **--- Leture Notes in Bioinformatics, 6840: pp. 91-96, 2011 ---- CategoryPublication