基本信息
吴凌云  男  博导  中国科学院数学与系统科学研究院
电子邮件: lywu@amss.ac.cn
通信地址: 北京市海淀区中关村东路55号
邮政编码: 100190
部门/实验室:应用数学研究所

招生信息

   
招生专业
070105-运筹学与控制论
120120-管理运筹学
081203-计算机应用技术
招生方向
运筹学及其应用
优化与决策
数据挖掘与生物信息计算

教育背景

1997-09--2002-07   中国科学院数学与系统科学研究院   博士
1993-09--1997-07   武汉大学数学系   本科

工作经历

   
工作简历
2015-04~现在, 中国科学院数学与系统科学研究院, 研究员
2007-04~2015-04,中国科学院数学与系统科学研究院, 副研究员
2005-06~2007-04,中国科学院数学与系统科学研究院, 助理研究员
2003-09~2005-06,中国科学院数学与系统科学研究院, 博士后
2002-08~2003-08,香港科技大学工业工程与工程管理系, 博士后
社会兼职
2016-10-16-今,中国运筹学会, 常务理事
2016-10-16-今,中国运筹学会, 青年工作委员会副主任
2012-10-18-今,中国运筹学会, 科普工作委员会副主任
2012-10-18-今,中国运筹学会, 理事
2011-09-01-今,中国运筹学会计算系统生物学分会, 副理事长
2010-10-01-今,运筹与管理, 编委

教授课程

生物信息学与计算系统生物学
生物信息学与系统生物学

出版信息

   
发表论文
(1) Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces, BMC Bioinformatics, 2017, 通讯作者
(2) NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis, BMC Systems Biology, 2017, 通讯作者
(3) Discovering cooperative biomarkers for heterogeneous complex disease diagnoses, Briefings in Bioinformatics, 2017, 通讯作者
(4) iSulf-Cys: prediction of S-sulfenylation sites in proteins with physicochemical properties of amino acids, PLoS ONE, 2016, 第 3 作者
(5) Mal-Lys: prediction of lysine malonylation sites in proteins integrated sequence-based features with mRMR feature selection, Scientific Reports, 2016, 第 4 作者
(6) Cancer stem cells display extremely large evolvability: alternating plastic and rigid networks as a potential mechanism, Seminars in Cancer Biology, 2015, 第 4 作者
(7) iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity, Scientific Reports, 2015, 第 4 作者
(8) Enrichment set cover problem, The Proceedings of 12th International Symposium on Operations Research and Its Applications, 2015, 通讯作者
(9) Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity, Journal of Theoretical Biology, 2015, 第 4 作者
(10) iNitro-Tyr: Prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition, PLOS ONE, 2014, 第 4 作者
(11) Discovery of co-occurring driver pathways in cancer, BMC Bioinformatics, 2014, 第 2 作者
(12) iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition, PLOS ONE, 2013, 第 3 作者
(13) GOMA: Functional enrichment analysis tool based on GO modules, Chinese Journal of Cancer, 2013, 通讯作者
(14) Corbi: A new R package for biological network alignment and querying, BMC Systems Biology, 2013, 通讯作者
(15) Efficient methods for identifying mutated driver pathways in cancer, Bioinformatics, 2012, 第 3 作者
(16) Potts model based on a Markov process computation solves the community structure problem effectively, Physical Review, 2012, 第 3 作者
(17) Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection, BMC Systems Biology, 2012, 第 4 作者
(18) CNetA: Network alignment by combining biological and topological features, Proceedings of the 6th IEEE International Conference on Systems Biology (ISB), 2012, 通讯作者
(19) Community structure detection based on Potts model and network’s spectral characterization, Europhysics Letters, 2012, 第 3 作者
(20) NOA: a novel network ontology analysis method, Nucleic Acids Research, 2011, 通讯作者
(21) An efficient network querying method based on conditional random fields, Bioinformatics, 2011, 通讯作者
(22) Analyzing time-course gene expression data using profile-state hidden Markov model, Proceedings of the 5th IEEE International Conference on Systems Biology (ISB), 2011, 通讯作者
(23) 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, 第 3 作者
(24) Prediction of protein-RNA binding sites by a random forest method with combined features, Prediction of protein-RNA binding sites by a random forest method with combined features, Bioinformatics, 2010, 第 2 作者
(25) An information-flowbased model with dissipation, saturation and direction for active pathway inference, An information-flowbased model with dissipation, saturation and direction for active pathway inference, BMC Systems Biology, 2010, 第 3 作者
(26) Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces, Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces, BMC Systems Biology, 2010, 第 2 作者
(27) SANA: an algorithm for sequential and non-sequential protein structure alignment, SANA: an algorithm for sequential and non-sequential protein structure alignment, Amino Acids, 2010, 第 2 作者
(28) 多阶段多目标多部门应急决策模型, Emergency decision model with multiple stages, multiple objectives, and multidivisional cooperation, 系统工程理论与实践, 2010, 第 3 作者
(29) Lysine acetylation sites prediction using an ensemble of support vector machine classifiers, Lysine acetylation sites prediction using an ensemble of support vector machine classifiers, Journal of Theoretical Biology, 2010, 第 4 作者
(30) DEA with weight constraints for evaluation of work safety supervision, DEA with weight constraints for evaluation of work safety supervision, Lecture Notes in Operations Research, 2010, 第 2 作者
(31) Conditional random pattern algorithm for LOH inference and segmentation, Conditional random pattern algorithm for LOH inference and segmentation, Bioinformatics, 2009, 第 1 作者
(32) Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs, Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs, Protein Engineering, Design, and Selection, 2009, 第 2 作者
(33) Evaluating protein similarity from coarse structures, Evaluating protein similarity from coarse structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 第 2 作者
(34) Self-organizing map approaches for the haplotype assembly problem, Self-organizing map approaches for the haplotype assembly problem, Mathematics and Computers in Simulation, 2009, 第 1 作者
(35) Predicting DNA and RNA-binding proteins from sequences with kernel methods, Predicting DNA and RNA-binding proteins from sequences with kernel methods, Journal of Theoretical Biology, 2009, 第 3 作者
(36) Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays, Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arrays, PLoS ONE, 2009, 第 4 作者
发表著作
(1) Proceedings of 12th International Symposium on Operations Research and Its Applications, IET, 2015-08, 第 3 作者

科研活动

   
科研项目
( 1 ) 复杂网络中的优化问题及其在系统生物学中的应用, 参与, 国家级, 2012-01--2016-12
( 2 ) 动态网络生物标记识别的可计算建模与算法, 主持, 国家级, 2014-01--2016-12
( 3 ) 图理论和算法研究及其在生物信息学中的应用, 参与, 国家级, 2017-01--2021-12
( 4 ) 癌症基因组大数据深度分析中的优化建模和算法研究, 参与, 国家级, 2017-01--2019-12
( 5 ) 干细胞增殖的计算建模及其在癌症演变动力学的应用, 参与, 国家级, 2018-01--2019-12
( 6 ) 高效区块链网络技术研究, 主持, 院级, 2017-08--2019-07
( 7 ) 无人仓(地狼AGV方案)最优入库与拣选策略, 主持, 院级, 2017-12--2018-12
参与会议
   

合作情况

   
项目协作单位
   

指导学生

已指导学生

孙端辰  博士研究生  070105-运筹学与控制论  

现指导学生

王灿  博士研究生  070105-运筹学与控制论  

张丽华  博士研究生  070105-运筹学与控制论  

赵越  博士研究生  070105-运筹学与控制论  

彭鑫   硕士研究生  070105-运筹学与控制论  

张国维  博士研究生  1201Z1-管理运筹学  

黄孝鹏  博士研究生  070105-运筹学与控制论  

李淼  硕士研究生  070105-运筹学与控制论  

叶心函   硕士研究生  070105-运筹学与控制论  

高永航  硕士研究生  070105-运筹学与控制论  

张驰浩  博士研究生  070105-运筹学与控制论  

王旭  博士研究生  1201Z1-管理运筹学