===== Publications - Bioinformatics 2008 ===== ---- {{include page="PubBioinformaticsTOC"}} ---- === Refereed Journal Articles === ~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070), 973(2006CB503905) ~1) Lin Wang, Yuqing Qiu, Jiguang Wang, 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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10631070) ~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) Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen.---**[[http://www.inderscience.com/search/index.php?action=record&rec_id=21179&prevQuery=&ps=10&m=or 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. --- Funding: NSFC(60503004), NSFC(10631070), 973(2006CB503905) ~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. --- SCI; Funding: NSFC(10701080), NSFC(10631070), 973(2006CB503905) ~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//, 35(3): 627-650, 2008. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), 973(2006CB503905) ~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(10701080), NSFC(10631070), NSFC(60503004), 973(2006CB503905) ~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. --- SCI; Funding: NSFC-JSPS(10711140116), NSFC(60503004), NSFC(10631070), 973(2006CB503905) ~1) Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang.--- **[[http://www.sciencedirect.com/science/article/pii/S0378437107011557 Detecting community structure in complex networks based on a measure of information discrepancy.]]**--- //Physica A//, 2008, 387(7), 1675-1682. --- SCI; Funding: NSFC(10701080), NSFC(10631070) ~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. --- SCI; Funding: NSFC-JSPS(10711140116), 973(2006CB503905) ~1) Shu-Qin Zhang, Wai-Ki Ching, Yue Jiao, Ling-Yun Wu, and Raymond H. Chan. ---**[[http://www.scirp.org/Journal/PaperInformation.aspx?paperID=9 Construction and control of genetic regulatory networks: A multivariate Markov chain approach.]] **--- //Journal of Biomedical Science and Engineering//, Vol. 1, pp. 15-21, 2008. === 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.---EI; NSFC (10701080), NSFC(10631070), NSFC-JSPS(10711140116) ~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. ---ISTP ~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. ---ISTP; Funding: NSFC(10631070), 973(2006CB503905) ~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. ---ISTP; Funding: NSFC-JSPS(10711140116), NSFC(10631070), NSFC(60503004) ~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. ---ISTP ~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. ---ISTP; Funding: NSFC(60873205), NSFC(10631070), NSFC(60503004), NSFC(10701080) ~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. ---ISTP; Funding: NSFC(10631070), NSFC(60503004) ~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. ---ISTP; Funding: NSFC(60503004) ~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. ---ISTP; Funding: NSFC-JSPS(10711140116), NSFC(10631070), 973(2006CB503905) ~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. ---ISTP; Funding: NSFC(10631070), 973(2006CB503905) ~1) Junhua Zhang, Weihua Yue, and Xiang-Sun Zhang.--- **[[http://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 ---ISTP ~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. ---ISTP; Funding: NSFC(10801131), 973(2006CB503905) ~1) Shu-Qin Zhang, Wai-Ki Ching, Yue Jiao, Ling-Yun Wu, and Raymond H. Chan. ---**A simplified multivariate Markov chain model for the construction and control of genetic regulatory networks. **---Proceedings of the 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), pp. 569--572, Shanghai, China, 2008. ~1) Zhi-Xia Yang. --- **[[http://www.aporc.org/LNOR/9/OSB2008F07.pdf A Multi-class Algorithm Model Based on p-class Support Vector Ordinal Regression Machine]].** --- Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 54-61, World Publishing Corporation, Lijiang, 2008. ---ISTP; Funding: NSFC(10801112), NSFC(70601033), NSFC(10631070) ~1) Jun-Yan Tang, Zhi-Xia Yang. --- **[[http://www.aporc.org/LNOR/9/OSB2008F44.pdf Incorporating Gene Similarity into Support Vector Machine for Microarray Classification and Gene Selection]].** --- Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 350-357, World Publishing Corporation, Lijiang, 2008. ---ISTP; Funding: NSFC(10801112), NSFC(70601033), NSFC(10631070) ---- CategoryPublication