王勇 科研简历 个人信息 姓名 : 出生日期 : 籍贯 : 性别 : 王勇 1976 年 8 月 1 日内蒙古自治区男 联系方式 地址 : 中国科学院数学与系统科学研究院应用数学所思源楼 1003 室, 北京市海淀区中关村东路 55 号, 100190. 电话 : +86-10-62616659 传真 : +86-10-62561963 电子邮件 : ywang AT amss DOT ac DOT cn 个人主页 : http://zhangroup.aporc.org/yongwang 1
简介王勇是中国科学院 (CAS) 数学与系统科学研究院 (AMSS) 应用数学所副研究员 同时也是中国科学院国家数学与交叉科学中心 (NCMIS) 的研究人员 他在 1999 年从内蒙古大学数学系的数学物理专业本科学位, 在 2002 年从大连理工大学应用数学系获得运筹学与控制论硕士学位,2005 年从中国科学院数学与系统科学研究院获得运筹学与控制论专业的理学博士学位 2005 年到 2007 年在国家信息中心 日本大阪产业大学电子情报通信系从事博士后研究工作 并于 2007 年 9 月到 2008 年 9 月在波士顿大学生物信息学计划从事访问研究 2010 年 10 月到 2011 年 4 月任日本产业技术综合研究所计算生物研究中心特别研究员 2012 年 11 月访问斯坦福大学统计系 他目前的研究兴趣是最优化理论与算法 生物信息学和系统生物学 2
教育情况 2002 2005 博士 运筹学与控制论, 中国科学院数学与系统科学研究院应用数学所. 指导教师 : 章祥荪研究员 1999 2002 硕士 运筹学与控制论, 大连理工大学应用数学系. 指导教师 : 冯恩民教授 1995 1999 本科 数学物理, 内蒙古大学数学系. 指导教师 : 戎卫东教授 博士论文指导教师 : 章祥荪研究员 博士论文题目 : 基于人工神经网络的蛋白质结构预测与分类研究 研究经历 3
2010. 3 目前副研究员, 中国科学院数学与系统科学研究院应用数学研究所. 2012.11 2013.11, 访问学者, 美国斯坦福大学. 2011.11 2011.12, 访问学者, 美国密苏里大学哥伦比亚分校. 2010.10 2011.4 特别研究员, 日本产业技术综合研究所 (AIST) 计算生物研究中 心 (CBRC). 2007. 9 2008. 9, 访问学者, 美国波士顿大学生物信息学研究中心. 2007. 6 2010. 3 助理研究员, 中国科学院数学与系统科学研究院应用数学研究所. 2005. 6 2007. 6 日本文部省奖学金资助博士后, 日本大阪市大阪产业大学电子情报通 信系. 2005.5 2005.10 博士后, 国家信息中心. 4
科研项目 2005 2007 2005 2007 2006 2008 2006 2008 2007 2009 2006 2008 2007 2009 2009 2011 2009 2011 运筹学方法在若干生物信息学重要问题研究中的应用批准号. 10471141 中国国家自然科学基金委员会 (NSFC) 基于复杂系统观点和方法论的电子政务管理研究批准号. 2005038334 中国国家博士后基金委员会生物信息学中的单体型推断模型与算法研究批准号. 60503004 中国国家自然科学基金委员会 (NSFC) 生物信息学中的若干重要问题研究中国科学院基础局基于三维结构和高通量数据的蛋白质功能标注与预测研究 NSFC-JSPS 合作研究项目, 批准号. 10711140116 国家自然科学基金委员会 (NSFC) 日本学术振兴会 (JSPS) 商业银行数据挖掘网格系统的研究与应用批准号. 70602034 中国国家自然科学基金委员会 (NSFC) 复杂网络中模块结构探测的理论与算法研究批准号. 10701080 中国国家自然科学基金委员会 (NSFC) 基因调控网络重建中的优化模型和算法研究批准号. 10801131 中国国家自然科学基金委员会 (NSFC) 最优化方法在信息技术中的应用批准号. kjcx-yw-s7 中国科学院创新方向性项目 5
2009 2011 2010 2012 2011 2012 2012 2016 2012 2015 生物分子网络中功能模块探测问题的数学模型及算法批准号. 1092011 北京市自然科学基金资助项目基于条件随机场的生物信息学研究批准号. 60970091 中国国家自然科学基金委员会 (NSFC) 基因调控网络重建的数据集成方法研究教育部留学回国人员科研启动基金复杂网络的最优化方法及在系统生物学的应用批准号. 11131009 中国国家自然科学基金委员会 (NSFC) 诱导多能干细胞的生物信息学研究批准号. 61171007 中国国家自然科学基金委员会 (NSFC) 研究兴趣 最优化理论与算法 生物信息学 系统生物学 机器学习 运筹学理论与应用 发表物 著作或章节 1. Computational Systems Biology. Luonan Chen, Xiang-Sun Zhang, Ling-Yun Wu, and Yong Wang (eds.). Proceedings of The 6th IEEE International Conference on Systems Biology (ISB 2012), Xi an, 2012. 2. Computational Systems Biology. Luonan Chen, Xiang-Sun Zhang, Ling-Yun Wu, and Yong Wang (eds.). Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), Zhuhai, 2011. 6
3. Operations Research and its Applications. Xiang-Sun Zhang, De-Gang Liu, Ling- Yun Wu, and Yong Wang (eds.). Lecture Notes in Operations Research 14, World Publishing Corporation, Beijing, 2011. 4. Computational Systems Biology. Luonan Chen, Xiang-Sun Zhang, Bairong Shen, Ling-Yun Wu, and Yong Wang (eds.). Lecture Notes in Operations Research 13, World Publishing Corporation, Beijing, 2010. 5. Operations Research and its Applications. Xiang-Sun Zhang, De-Gang Liu, Ling- Yun Wu, and Yong Wang (eds.). Lecture Notes in Operations Research 12, World Publishing Corporation, Beijing, 2010. 6. Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data, Computational Methodologies in Gene Regulatory Networks, Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009. 7. Optimization and Systems Biology. Xiang-Sun Zhang, Luonan Chen, Ling-Yun Wu and Yong Wang (eds.). Lecture Notes in Operations Research 11, World Publishing Corporation, Beijing, 2009. 8. Optimization and Systems Biology. Xiang-Sun Zhang, Luonan Chen, Ling-Yun Wu, and Yong Wang (eds.). Lecture Notes in Operations Research 9, Proceedings of the Second International Symposium of Optimization and Systems Biology, Lijiang, China, October 31 November 2, 2008. World Publishing Corporation, Beijing, 2008. (ISTP) 9. Operations Research and its Applications. Xiang-Sun Zhang, De-Gang Liu, and Yong Wang (eds.). Lecture Notes in Operations Research 8, Proceedings of the Seventh International Symposium of Operations Research and its Application, Lijiang, China, October 31 November 2, 2008. World Publishing Corporation, Beijing, 2008. (ISTP) 10. Optimization and Systems Biology, Lecture Notes in Operations Research 7 Edited by Xiang-Sun Zhang, Luonan Chen, Ling-Yun Wu, and Yong Wang. Proceedings of the First International Symposium of Optimization and Systems Biology, Beijing, China, 8-10 August, 2007. World Publishing Corporation, Beijing, 2007. (ISTP) 11. Operations Research 50 周年纪念特刊中文译本主编 : 章祥荪, 刘德刚, 章璟, 吴凌云, 王勇. 运筹与管理, 增刊, Vol. 13, 2004. 7
发表物 期刊论文 1. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Computational systems biology in the big data era, BMC Systems Biology, 2013, 7(Suppl 1):S1. 2. Yongcui Wang, Nai-Yang Deng, Shi-Long Chen, Yong Wang. Drug repositioning by kernel integration molecular structure, molecular activity, and phenotype data. PLoS One. in press, 2013. 3. Tao Zeng, Shao-Yan Sun, Yong Wang, and Luonan Chen. Network biomarkers reveal dys-functional gene regulations during disease progression. FEBS Journal. in revision, 2013. 4. Shao-Yan Sun, Tao Zeng, Zhi-Ping Liu, Yong Wang, and Luonan Chen. Spatiotemporal analysis of type 2 diabetes mellitus based on differential expression networks. Scientific Report, 3, 2268; DOI:10.1038/srep02268, 2013. 5. Zhong-Yuan Zhang, Yong Wang, and Yong-Yeol Ahn. Overlapping community detection in complex networks using symmetric binary matrix factorization. Physical Review E. in press, 2013. 6. Xianwen Ren, Yong Wang, Xiang-Sun Zhang, and Qi Jin. ipcc: a novel feature extraction method for accurate disease class discovery and prediction. Nucleic Acids Research. Vol. 41, No. 4, e143, 2013. 7. Zikai Wu, Yong Wang, and Luonan Chen. Network-Based Drug Repositioning Mol. BioSyst. 2013, 9 (6), 1268-1281. 8. Yongcui Wang, Nai-Yang Deng, Shi-Long Chen, Yong Wang. Network predicting drug s anatomical therapeutic chemical code. Bioinformatics, (2013) 2013 29: 1317-1324. 9. Zikai Wu, Yong Wang, and Luonan Chen. A New Framework for Repositioning Drugs by Incorporating Various Functional Information IET Systems Biology In press. 10. Junhua Zhang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang. Integrating somatic mutation, copy number variation, and gene expression data to identify mutated core modules in cancers. BMC Systems Biology In press. 11. Qiang Huang, Ling-Yun Wu, Yong Wang, and Xiang-Sun Zhang. GOMA: Functional enrichment analysis tool based on GO modules. Chinese Journal of Cancer. 32(4):195-204, 2013. 8
12. Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang, and Qi Jin. ellipsoidfn: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions Nucleic Acids Research. 2013 41: e53. 13. Ying Wang, Xiaowei Chen, Zhi-Ping Liu, Qiang Huang, Yong Wang, Derong X- u, Xiang-Sun Zhang, Runsheng Chen and Luonan Chen. De novo prediction of RNA protein interactions from sequence information, Mol. BioSyst. Mol. BioSyst., 2013, 9, 133 142. 14. Yong Wang. Bioinformatics studies on induced pluripotent stem cell, Current Bioinformatics, 2013, Vol. 8, 80 87. 15. Yu-Shu Liu, Pei-Wen Tsai, Tan-chi Fan, Yong Wang, Chia-Hung Hsieh, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan and Hao-Teng Chang, Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein, BMC Systems biology, 6:105, 2012. 16. Huijia Li, Yong Wang, Ling-Yun Wu, Junhua Zhang, and Xiang-Sun Zhang. Potts model based on a Markov process computation solves the community structure problem effectively, Phys. Rev. E, 86, 016109, 2012. 17. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Modelling biological systems from molecules to dynamical networks, BMC Systems Biology, 2012, 6(Suppl 1):S1. 18. Guanying Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto. A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats. BMC Systems Biology, 2012, 6(Suppl 1):S2. 19. Yong Wang, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, and Fan-Rong Liang. Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection. BMC Systems Biology, 2012, 6(Suppl 1):S15. 20. Xianwen Ren, Yong Wang, Jiguang Wang and Xiang-Sun Zhang A unified computational model for revealing and predicting subtle subtypes of cancers. BMC Bioinformatics, 13:70, 2012. 9
21. Xiang-Sun Zhang, Zhenping Li, Rui-Sheng Wang, Yong Wang. A combinatorial model and algorithm for globally searching community structure in complex networks. Journal of Combinatorial Optimization, Vol. 23, No. 4, 425-442, 2012. 22. Zhi-Ping Liu, Yong Wang. Xiang-Sun Zhang, Luonan Chen. Network-based analysis of complex diseases, IET Systems Biology, 6(1): 122-133, 2012. 23. Huijia Li, Yong Wang, Ling-Yun Wu, Zhiping Liu, Luonan Chen and Xiang-Sun Zhang. Community structure detection based on Potts model and network s spectral characterization, Europhysics Letters, 97: 48005, 2012. 24. Xianyun Sun, Hanxing Zhang, Zhenying Zhang, Yong Wang, and Shaojie Li. Involvement of a helix-loop-helix transcription factor CHC-1 in CO2-mediated conidiation suppression in Neurospora crassa. Fungal Genetics and Biology, Vol. 48(12), pp. 1077-86, 2011. 25. Xianwen Ren, Yongcui Wang, Yong Wang, Nai-Yang Deng and Xiang-Sun Zhang. Improving accuracy of protein-protein interaction prediction by considering the converse problem. BMC Bioinformatics, 12:409, 2011. 26. Yongcui Wang, Nai-Yang Deng, and Yong Wang. Kernel based data fusion improves the drug-protein interaction prediction. Computational Biology and Chemistry, Vol. 35(6), pp. 353-362,2011. 27. Ruoying Chen, Wenjing Chen, Sixiao Yang, Di Wu, Yong Wang, Yingjie Tian, and Yong Shi. Rigorous assessment and integration of the sequence and structure based features to predict hot spots. BMC Bioinformatics, 12:311, 2011. 28. Ji-Guang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. NOA: a novel network ontology analysis method, Nucleic Acids Research, 39(13):e87, 2011. 29. Zhi-Ping Liu, Yong Wang. Xiang-Sun Zhang, Weimin Xia, Luonan Chen.Detecting and analyzing differentially activated pathways in brain regions of Alzheimer s disease patients, Molecular BioSystems, 7(5):1441-1452, 2011. 30. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Computational systems biology: integration of sequence, structure, network, and dynamics, BMC Systems Biology, 5(Suppl 1):S1, 2011. 31. Yongcui Wang, Yong Wang, Zhixia Yang, Nai-Yang Deng.Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context, BMC Systems Biology, 5(Suppl 1):S6, 2011. 10
32. Ruoying Chen, Zhiwang Zhang, Di Wu, Peng Zhang, Xinyang Zhang, Yong Wang, and Yong Shi Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming, Journal of Theoretical Biology, Vol. 269, pp. 174 180, 2011. 33. 陈兴, 王勇, 吴凌云, 闫桂英. 多阶段多目标多部门应急决策模型, 系统工程理论与实践, Vol. 30, No. 11, pp. 1977 1985, 2010. 34. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Prediction of protein-rna binding sites by a random forest method with combined features. Bioinformatics, Vol. 26, No. 3, pp. 1616-1622, 2010. 35. Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia. Protein evolution in yeast transcription factor subnetworks, Nucleic Acids Research, Vol. 38, No. 18, pp. 5959-5969, 2010. 36. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Optimization meets systems biology. BMC Systems Biology, Vol. 4, Suppl 2, S1, 2010. 37. Zhi-Ping Liu, Yong Wang. Xiang-Sun Zhang, Luonan Chen. Identifying dysfunctional crosstalk of pathways in various re- gions of Alzheimer s disease brains, BMC Systems Biology, Vol. 4, Suppl 2, S11, 2010. 38. Luwen Zhang, Mei Xiao, Yong Wang, Wu Zhang. Reverse engineering large-scale genetic networks: synthetic versus real data Journal of Genetics, Vol. 89, No. 1, 2010. 39. Yongcui Wang, Zhixia Yang, Yong Wang, Nai-Yang Deng. Computationally probing drug-protein interactions via support vector machine Letters In Drug Design & Discovery, Vol. 7, No. 5, pp. 370 378(9), 2010. 40. Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen. SANA: an algorithm for sequential and non-sequential protein structure alignment. Amino Acid, Vol. 39, No.2, pp.417-425, 2010. 41. Tingting Gao, Zhixia Yang, Yong Wang, Ling Jing. Identifying translation initiation sites in prokaryotes using support vector machine. Journal of Theoretical Biology, Vol. 262, No. 4, pp. 644 649, 2010. 42. Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology, 9(5), e1000521, 2009. 11
43. Xiang-Sun Zhang, Rui-Sheng Wang, Yong Wang, Ji-Guang Wang, Yu-Qing Qiu, Lin Wang, and Luonan Chen. Modularity optimization in community detection of complex networks. Europhysics Letters, 87, 38002, 2009. 44. Yong Wang, Xiang-Sun Zhang, and Yu Xia. Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Research. 37: 5943-5958, 2009. 45. Yong Wang, Xiang-Sun Zhang, and Luonan Chen. A network biology study on circadian rhythm by integrating various omics data. OMICS: A Journal of Integrative Biology, Vol 13, No.4, pp. 313-324, 2009. 46. 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., Vol. 6, No. 4, pp. 583-593, 2009. 47. Xiaojian Shao, Yingjie Tian, Lingyun Wu, Yong Wang, Ling Jing, and Naiyang Deng. Predicting DNA- and RNA-binding proteins from sequences with kernel methods, Journal of Theoretical Biology, Vol. 258, pp. 289 293, 2009. 48. 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, Vol. 72, pp. 134 141, 2008. DOI: 10.1016/j.neucom.2007.12.043 49. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Bridging protein local structures and protein functions. Amino Acids, Vol. 35(3): pp. 627 650, 2008. 50. Xing-Ming Zhao, Yong Wang, Luonan Chen, and Kazuyuki Aihara. Protein domain annotation with predicted domain-domain interaction networks. Protein & Peptide Letters, Vol. 15, pp. 456 462, 2008. 51. Xing-Ming Zhao, Yong Wang, Luonan Chen, and Kazuyuki Aihara. Gene function prediction using labeled and unlabeled data. BMC Bioinformatics, 9:57, 2008. Software: AGPS (http://intelligent.eic.osaka-sandai.ac.jp/chenen/agps.htm) 52. Xing-Ming Zhao, Yong Wang, Luonan Chen, and Kazuyuki Aihara. Protein domain annotation with integration of heterogeneous information sources. Proteins: Structure, Function, and Bioinformatics, Vol. 72(1), pp. 461 473, 2008. 12
53. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Analysis of protein surface patterns by pocket similarity network. Protein & Peptide Letters, Vol. 15(5), pp. 448 455, 2008. 54. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, and Xiang-Sun Zhang. Predicting gene ontology functions from protein s regional surface structures. BMC Bioinformatics, 8:475, 2007. 55. 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. 56. Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics, 8:391, 2007. Software: CDIinfer (http://intelligent.eic.osaka-sandai.ac.jp/chenen/cdiinfer. htm) 57. Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics, Vol. 23, pp. 3056 3064, 2007. Software: TRNinfer (http://intelligent.eic.osaka-sandai.ac.jp/chenen/trninfer. htm) 58. 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, pp. 123 144, 2007. 59. 陈洛南, 王勇, 费敏锐, 刘曾荣, 从理工科视角探索系统生物学, 科技导报, Vol. 25, No. 10: 5 9, 2007. 60. Zhenping Li, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, Vol. 23(13), pp. 1631-1639, 2007. Software: MNAligner (http://zhangroup.aporc.org/bioinfo/mnaligner/) 61. Zikai Wu, Yong Wang, Enmin Feng, and Luonan Chen. A new geometrictopological method to measure protein fold similarity, Chem. Phys. Lett., Vol. 433, pp. 432 438, 2007. 13
62. Zikai Wu, Enmin Feng, Yong Wang, and Luonan Chen. Discrimination of outer membrane proteins by a new measure of information discrepancy, Protein & Peptide Lett., Vol. 14 No. 1, pp. 37 44, 2007. 63. Yu-zhen Guo, En-min Feng, and Yong Wang. Optimal HP configurations of proteins by combining local search with elastic net algorithm, Journal of Biochemical and Biophysical Methods,70 (3), pp. 335-340, 2007. 64. Yong Shi, Xinyang Zhang, Jia Wan, Yong Wang, Wei Yin, Zhiwei Cao, and Yajun Guo. Predicting the distance between antibody s interface residue and antigen and antigen class by support vector machine. Neural Comput & Applic, Vol. 16, No. 4-5, pp. 481 490, 2007. 65. Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen. Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics, Vol. 22, pp. 2413 2420, 2006. Software: GRNInfer (http://zhangroup.aporc.org/bioinfo/grninfer/) 66. 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, 6:18, 2006. Software: SAMO (http://zhangroup.aporc.org/bioinfo/samo/) 67. 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. Software: APM (http://zhangroup.aporc.org/bioinfo/apm/) 68. Yu-zhen Guo, En-min Feng, and Yong Wang. Exploration of two-dimensional HP lattice model by combining local search with elastic net algorithm, J. Chem. Phys., Vol. 125, 154102, 2006. 69. 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. 70. Ju-Liang Zhang, Yong Wang, and Xiang-Sun Zhang. Superlinearly convergent trust region method without assumption of positive definite Hessian. Journal of Optimization Theory and Application, Vol. 129, No. 1, 2006. 14
71. 香勇, 彭春, 潘建军, 王勇, 施克仁. 混频相控阵聚焦特征的研究. 压电与声光, Vol. 28, No.1, pp. 113 116, 2006. 72. 詹钟炜, 王勇, 吴凌云, 章祥荪. 政府网站评估 DEA 模型. 运筹与管理, Vol. 15, No. 4, pp. 97 102, 2006. 73. Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang, Shihua Zhang, and Xiang-Sun Zhang. Comparison of protein structures by multi-objective optimization. Genome Informatics, Vol. 16, No. 2, pp. 114 124, 2005. 74. 王勇, 詹钟炜, 吴凌云, 章祥荪. 改进的自组织映射 (SOM) 蛋白质折叠算法和计算实现, 系统科学与数学, Vol. 25, No. 4, 2005. 75. Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, and Ling-Yun Wu. Exploring protein s optimal HP configurations by self-organizing. Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, pp. 305 320, 2005. 76. Zhen-Ping Li, Yong Wang, Yu-Ying Zhao, and Xiang-Sun Zhang. Haplotype inference and mating graphs. Applied Mathematics Journal of Chinese Universities (Series A), Vol. 19, Supplement, pp. 567 576, 2004. 77. 戴家权, 王勇, 冯恩民. 油气资源勘探与开发的综合优化模型及算法, 工程数学学报, Vol. 21, No. 3, pp. 307 311, 2004. 78. 戴家权, 王勇, 冯恩民. 油气资源勘探与开发的不确定性分析及最优策略研究, 系统工程理论与实践, Vol. 24, No. 1, pp. 35 40, 2004. 79. Ju-Liang Zhang, Yong Wang.A new trust region method for nonlinear equations. Mathematical Method of operational research, Vol. 58, No. 3, pp. 283 298, 2003. 80. 贺晓霞, 高钟毓, 王勇. 图像处理技术在球形转子质量不平衡测量中的应用, 中国图像图形学报, Vol. 8 (A), spec. 2003. 81. 冯恩民, 王勇. 三维地史数值模拟及其系统辨识, 高校应用数学学报 A 辑, Vol.18, No.2, 171 178, 2003. 82. 戴家权, 王勇, 冯恩民, 金之钧, 庞雄奇. 深盆气分布范围预测的优化模型 算法及应用, 运筹与管理, Vol.12, No.3, pp. 1 4, 2003. 83. 戴家权, 王勇, 冯恩民, 金之钧, 庞雄奇. 深盆气成藏机理及动态分布的定量研究, 石油学报, Vol. 24, No. 1, pp. 39 43, 2003. 15
84. En-Min Feng, Yong Wang. On the use of ABS algorithm in the modeling of oil deposit. Ricerca Operativa (Optimization and Decision Sciences), 31(98/100), pp. 87 107, 2001, Fascicolo 98. 发表物 会议论文 1. Yuzhen Guo, Yong Wang. Predicting the non-compact conformation of amino acid sequence by particle swarm optimization.proceedings of The 7th International Conference on Systems Biology (ISB 2013), 119 122, 2013. 2. Jibin Qu, Jinxia Zhang, Chenyang Huang, Baogui Xie, Yong Wang, Xiang-Sun Zhang. A novel discretization method for processing digital gene expression profiles. Proceedings of The 7th International Conference on Systems Biology (ISB 2013), 134 138, 2013. 3. Xinxin Wang, Duren Zhana, Chao Zhang, Lin Chen, Yong Wang. Clinical Data Analysis Reveals Three Subytpes of Gastric Cancer. Proceedings of The 6th IEEE International Conference on Systems Biology (ISB 2012), 316 321, 2012. 4. Junhua Zhang, Shihua Zhang, Yong Wang, Junfei Zhao, Xiang-Sun Zhang. Identifying Mutated Core Modules in Glioblastoma by Integrative Network Analysis. Proceedings of The 6th IEEE International Conference on Systems Biology (ISB 2012), 305 310, 2012. 5. Zikai Wu, Yong Wang, Luonan Chen. A New Method to Identify Repositioned Drugs for Prostate Cancer. Proceedings of The 6th IEEE International Conference on Systems Biology (ISB 2012), 281 285, 2012. 6. Duren Zhana, Yong Wang, Shigeru Saito, Katsuhisa Horimoto. Inferring Gene Regulatory Network for Cell Reprogramming. Proceedings of The 31th Chinese Control Conference (CCC), pp. 7437-7442, Anhui, 2012. 7. Yong Wang, Qiao-Feng Wu, Chen Chen, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, Fan-Rong Liang. Identifying Biomarkers for Acupuncture Treatment via an Optimization Model. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 319 326, 2011. 8. Ji-Bin Qu, Xiang-Sun Zhang, Ling-Yun Wu, Yong Wang, Luonan Chen. Detecting Coherent Local Patterns from Time Series Gene Expression Data by a Temporal Biclustering Method. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 399 404, 2011. 16
9. Guanying Piao, Bangguo Qian, Shigeru Saito, Zhi-Ping Liu, Tao Zeng, Yong Wang, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto. Phenotype-Difference Oriented Identification of Molecular Functions for Diabetes Progression in Goto-Kakizaki Rat. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 111 116, 2011. 10. Yu-Shu Liu, Chung-Hsaio Chao, Hao-Teng Chang, Yong Wang, Margaret Dah-Tsyr Chang, Tun-Wen Pai. Comparative Genomics Revealed a Novel DNA-Binding Regulatory Protein Involved in Homologous Recombination in Bacteria. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 137 143, 2011. 11. Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto. Identification of Master Regulator Candidates for Diabetes Progression in Goto-Kakizaki Rat by a Computational Procedure. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 197 202, 2011. 12. Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang. A Linear Programming Model for Identifying Non-Redundant Biomarkers Based on Gene Expression Profiles. Proceedings of The 5th IEEE International Conference on Systems Biology (ISB 2011), 249 254, 2011. 13. Yong Wang, Jiguang Wang, Chen Chen, Xiang-Sun Zhang. A Regularized Optimization Model for Community Identification in Complex Networks, Lecture Notes in Operations Research, 14, pp. 147 156, World Publishing Corporation, Beijing, 2011. 14. Xianwen Ren, Yong Wang, Xiang-Sun Zhang. A Flexible Convex Optimization Model for Semi-supervised Clustering with Instance level Constraints, Lecture Notes in Operations Research, 14, pp. 178 185, World Publishing Corporation, Beijing, 2011. 15. Yong Wang,Katsuhisa Horimoto, Luonan Chen. An Integrated Pipeline for Gene Regulatory Network Inference. Proceedings of The 30th Chinese Control Conference (CCC), pp. 6593-6598, Yantai, 2011. 16. Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang. An Optimization Model for Fuzzy Binary Clustering. Lecture Notes in Operations Research, 13, pp. 422 432, World Publishing Corporation, Beijing, 2010. 17
17. Jiguang Wang, Yong Wang, Xianwen Ren, Wei Guo, Luonan Chen. Uncover the Transient Transcriptional Regulations by a Novel Sliding Window Correlation Strategy. Lecture Notes in Operations Research, 12, pp. 235 242, World Publishing Corporation, Beijing, 2010. 18. Yong Wang, Xiang-Sun Zhang, Katsuhisa Horimoto, Luonan Chen. System Identification Models for Gene Regulation System. Proceedings of The 29th Chinese Control Conference (CCC), pp. 6239-6244, Beijing, 2010. 19. Ji-Guang Wang, Lin Wang, Yu-Qing Qiu, Yong Wang, and Xiang-Sun Zhang, A Constrained Optimization Method for Community Detection. Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 142 150, World Publishing Corporation, Beijing, 2009. 20. Biao-Bin Jiang, Ji-Guang Wang, Jing-Fa Xiao, and Yong Wang. Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction Networks. Optimization and Systems Biology, Lecture Notes in Operations Research, 11, pp. 319 328, World Publishing Corporation, Beijing, 2009. 21. Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, and Luonan Chen. Dynamically dysfunctional protein interactions in the development of Alzheimer s disease. 2009 IEEE International Conference on Systems, Man, and Cybernetics. 22. Yong Wang and Yu Xia, Condition specific subnetwork identification using an optimization model, Optimization and Systems Biology, Lecture Notes in Operations Research, 9, pp. 329 336, World Publishing Corporation, Beijing, 2008. 23. Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, and 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, pp. 119 130, 2007. 24. 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. 25. Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang, and Luonan Chen. Establishing protein functional linkage in a systematic way, Optimization and Systems Biolo- 18
gy, Lecture Notes in Operations Research, 7, pp. 75-88, World Publishing Corporation, Beijing, 2007. 26. Zikai Wu, Yong Wang, Enmin Feng, and Luonan Chen, Assessing distance measures for protein structure comparison. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 324-331, World Publishing Corporation, Beijing, 2007. 27. Zhenping Li, Rui-Sheng Wang, and Yong Wang. A quadratic programming model for political districting problem. Optimization and Systems Biology, Lecture Notes in Operations Research, 7, pp. 427-435, World Publishing Corporation, Beijing, 2007. 28. 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. 29. 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, Lecture Notes in Bioinformatics, Vol. 4115, pp. 551-561, 2006. 30. 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.) 172 175, Springer-Verlag, Berlin, 2006. 31. 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. Lecture Notes in Computer Science, Vol. 3959. pp. 505 514, Springer-Verlag, 2006. 32. Zikai Wu, Yong Wang, En-Min Feng, and Jin-Cheng Zhao. Protein structure comparison based on a measure of information discrepancy. Lecture Notes in Computer Science, Vol. 3959. pp. 515 527, Springer-Verlag, 2006. 33. Zhenping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen. Alignment of protein interaction networks by integer quadratic programming. Proceedings of the 28th IEEE EMBS Annual International Conference New York City, USA, Aug 30-Sept 3, pp. 5527 5530, 2006. 34. 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 19
Research and Its Applications, Lecture Notes in Operations Research, 5, pp. 276-284, World Publishing Corporation, Beijing, 2005. 35. Ji-Hong Zhang, Ling-Yun Wu, Yong Wang, Zhen-Ping Li, and Xiang-Sun Zhang. A statistical method based on Markov chain for optimal reconstruction of haplotype from genotype data with SNP. Symposium of 7th Academic Communication Meeting of Operations Research of China. Proceedings of ORSC 2004, pp. 1268 1278, Global-Link Publishing Company, 2004. 36. 詹钟炜, 王勇, 吴凌云, 章祥荪. 基于 DEA 的电子政务评估研究. 中国运筹学会第七届学术交流会论文集, 348 354, Global-Link Publishing Company, 2004. 37. 冯恩民, 张军, 王锡禄, 王勇, 换热网络综合问题中的布局优化, 中国运筹学会第六届学术交流会论文集,Global-Link Publishing Company, 2004. 科研活动 1. Program Committee, Trilateral Symposium on Systems and Synthetic Biology (TriSys 2013), November 7 9, Hongkong, 2013. 2. Program Committee, The Tenth International Conference on Intelligent Computing (ICIC 2014), 3-6 August, Taiyuan, China, 2014 3. Program Committee, The Twelfth Asia Pacific Bioinformatics Conference, 17-19 January, Shanghai, China, 2014 4. Program Committee, IEEE Bioinformatics and Biomedicine (BIBM), October 4-7,2013 in Philadelphia, PA, 2013. 5. Program committee, The 12th International Conference on Bioinformatics of the Asia- Pacific Bioinformatics Network (InCoB2013), Sept 20-22, Taicang, China, 2013. 6. Program Committee, The 1st International Conference on Health Information Science (HIS 2012), April 8-10, Beijing,China, 2012. 7. Workshop on Transcriptomics and Epigenomics, Institute for Pure and Applied Mathematics (IPAM). October 25-28, 2011. 8. Mini-Workshop on Cancer Genomics, Institute for Pure and Applied Mathematics (I- PAM). October 31 - November 1, 2011. 9. Program Committee, The Second International Workshop on Integrative Data Analysis in Systems Biology (IDASB) in BIBM2011, Atlanta, Georgia, USA, Nov. 12 15, 2011. 20
10. Chair of Invitation Session on Systems Biology, The 30th Chinese Control Conference (CCC2011), Yantai, China, July 22 24, 2011. 11. Program Committee, ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB) on August 1 3, 2011 in Chicago, Illinois, USA. 12. Program Committee, The Seventh International Conference on Intelligent Computing (ICIC2011) on August 11 14, 2011 in Zhengzhou, China. 13. Program Committee, Workshop on Computational Proteomics in BIBM2010, HongKong, China, Dec. 18 21, 2010. 14. Program Committee, Workshop on Integrative Data Analysis in Systems Biology in BIBM2010, HongKong, China, Dec. 18 21, 2010. 15. 邀请报告, 北京生命科学论坛第八次会议, 数学与生物学交叉应用研究学术研讨会, 北京, 中国, 2010 年 7 月 16 日. 16. Organizing Committee, The 9th International Symposium on Operations Research and Its Applications (ISORA 2010), Chengdu, China, Aug. 20-24, 2010. 17. Organizing Committee, The 4th International Conference on Computational Systems Biology (ISB 2010), Suzhou, China, Sept. 9 11, 2010. 18. Co-Chair of Invitation Session on Systems Biology, The 29th Chinese Control Conference(CCC2010), Beijing, China, July 29 31, 2010. 19. 邀请报告, 第二届反演问题计算方法及其应用国际会议, 北京, 中国, 2010 年 7 月 12 日. 20. Program Committee, IEEE International Conference on Bioinformatics & Biomedicine (BIBM), HongKong, China, Dec. 19 22, 2010. 21. Local Organizing Committee, The 21th International Conference on Genome Informatics(GIW2010), December 16 18, 2010, Hangzhou, China. 22. invited speaker, Kavil Institute for Theoretical Physics China program on Emergent behaviour of biomolecular ensembles and networks, July 2010, Beijing, China 23. Organizing Committee, Trilateral Symposium on Systems and Synthetic Biology 2010, October 2 4, Tokyo, Japan, 2010. 24. Invited visitor, Department of Mathematics, The Chinese University of Hong Kong, 18 25 April 2010, HongKong, China. 21
25. Invited speaker, Sino-German Workshop on Computational systems biology approaches for cancer research and biomarker discovery, 11 15 January 2010, Hangzhou, China 26. Invited speaker, Workshop on biological network in Computational Biology Research Center of AIST, 10-11 December 2009, Tokyo, Japan 27. Program Committee, The 2010 Third International Conference on Life System Modeling and Simulation (LSMS), Shanghai, China, Sept. 17 20, 2010. 28. Program Committee, The 2009 International Conference on Optimization and Systems Biology (OSB), Zhangjiajie, China, Sept. 20 22, 2009. 29. Invited Speaker, Trilateral Symposium on Systems and Synthetic Biology 2009, August 13-15, Seoul, Korea, 2009. 30. Visiting Osaka University, Kyoto University, and Osaka Sangyo University. July 5 July 18, 2009 31. Invited Speaker, 复杂网络 生物信息学及其他科学问题研讨会, 2009 年 6 月 25 日, 北京, 2008. 32. Invited Speaker, A network biology study on circadian rhythm, Westlake International conference on Personalized Medicine, May 29, 2009, HangZhou, China. 33. Program Committee, The 2009 International Conference on Intelligent Computing (I- CIC), Ulsan, Korea, September 16 19, 2009. 34. Poster, Recovering Gene Regulations by Optimization Model, Asia Pacific Bioinformatics Conference (APBC2009), Beijing, China. 35. Invited Speaker, 第八届系统控制前沿科学问题研讨会 系统生物学, 2008 年 12 月 12-13 日, 北京, 2008. 36. Visiting Osaka University, Kyoto University, and Osaka Sangyo University. November 17 December 7, 2008 37. Program Committee, The 2008 International Conference on Optimization and Systems Biology (OSB), Lijiang, China, October 31 November 3, 2008. 38. Program Committee, The 2008 International Conference on Intelligent Computing (I- CIC), Shanghai, China, September 15 18, 2008. 39. Invited Speaker, Biological Network Comparison: Problems and Challenges, Systems Biology Summer School of Shanghai University, Aug. 10, 2007, Shanghai, China. 22
40. Invited Speaker, Establishing protein functional linkage in a systematic way, Systems biology workshop, Mar. 10, 2007, Suzhou, China. 41. Program Committee, The 2007 International Conference on Optimization and Systems Biology (OSB), Beijing, China, August 7 9, 2007. 42. Program Committee, The 2007 International Conference on Intelligent Computing (I- CIC), Qingdao, China, August 21 24, 2007. 43. Program Committee, The 2nd International Conference on Life System Modeling and Simulation (LSMS), Shanghai, China, September 14 17, 2007. 44. Poster, Whole-Genome Functional Linkage Network Construction in the Domain Level by Probabilistic Model, GIW2006, Yokohama, Japan. 45. Invited Speaker, Inferring gene regulatory network form multiple datasets, WICB2006, Nov. 11-14,2006, Hefei, China. 46. Poster, Inferring Protein Network by Multiple Domain Interactions, ICSB2006, Yokohama, Japan. 47. Oral Speaker, Supervised inference of gene regulatory network by linear programming, ICIC2006, Kunming, China. 48. Oral Speaker, Exploring the classification of protein structures on geometric patterns by neural networks, ISSN2006, Chengdu, China. 49. Oral Speaker, Automatic classification of protein structure based on convex hull representation, TAMC2006, Beijing, China. 50. Poster, Inferring Protein Interaction Network by Boosting Algorithm, GIW2005, Yokohama, Japan. 51. Invited Speaker, Protein Structure Prediction by SOM Approach, PhD candidate research seminar of Department of Mathematics, Tsinghua University, Beijing, China. 期刊编委 Associate Editor of American Journal of Digestive Disease Associate Editor of BMC Research Notes (BioMed Central s open access journal) Associate Editor of The Open Information Systems Journal Academic Editor of PeerJ journal 23
期刊特刊编辑 Co-editor, Methods, Special Issue on Computational Systems Biology, 2013. Co-editor, Journal of Theoretical Biology, Special Issue on Network Biomarker 2013. Co-editor, BMC Systems Biology, Special Issue on Computational Systems Biology, 2009, 2010, 2011, 2012. Co-editor, IET Systems Biology, Special Issue on Optimization and Systems Biology, Volume 3, Issue 6, 2009. Co-editor of BMC Bioinformatics, Special issue on genomic informatics. 期刊审稿 Nucleic Acids Research Bioinformatics Briefs in Bioinformatics Cancer letters Proteins: Structure, Function, and Bioinformatics IET Systems Biology BMC Systems Biology BMC Bioinformatics PLoS Computaitonal Biology Evolutionary Bioinformatics Algorithmic International Journal of Computer Mathematics Mathematical Biosciences IEEE/ACM Transactions on Computational Biology and Bioinformatics Protein Engineering, Design, and Selection Journal of Theoretical Biology 24
Frontiers of Electrical and Electronic Engineering in China Molecules Journal of Convergence Information Technology International Journal of Knowledge Discovery in Bioinformatics IEEE Transactions on Circuits and Systems I. 应用数学学报 系统科学与数学 运筹学报 运筹与管理 获奖情况 1997, 内蒙古大学一等奖学金. 1998, 内蒙古大学二等奖学金. 1998, 光华奖学金. 1999, 宝钢奖学金. 2004, 中国科学院管理 决策与信息系统重点实验室优秀奖 2004, 中国科学院数学与系统科学研究院院长奖学金特等奖 2008, 中国科学院数学与系统科学研究院突出科研成果奖 2010, Best Poster Award received in the 21st International Conference on Genome Informatics (GIW2010) for An integrated gene regulatory network inference pipeline by Yong Wang, Katsuhisa Horimoto, and Luonan Chen. 25