吳凌雲[中國科學院數學與系統科學研究院研究員]

吳凌雲[中國科學院數學與系統科學研究院研究員]

姓名吳凌雲 中國科學院數學與系統科學研究院 研究員

教育背景

1997-09--2002-07 中國科學院數學與系統科學研究院 博士

1993-09--1997-07 武漢大學數學系 本科

工作經歷

工作簡歷

2015-04~現在, 中國科學院數學與系統科學研究院, 研究員

2007-04~2015-04,中國科學院數學與系統科學研究院, 副研究員

2005-06~2007-04,中國科學院數學與系統科學研究院, 助理研究員

2003-09~2005-06,中國科學院數學與系統科學研究院, 博士後

2002-08~2003-08,香港科技大學工業工程與工程管理系, 博士後

社會兼職

2016-10-16-今,中國運籌學會, 常務理事

2016-10-16-今,中國運籌學會, 青年工作委員會副主任

2012-10-18-今,中國運籌學會, 科普工作委員會副主任

2012-10-18-今,中國運籌學會, 理事

2011-09-01-今,中國運籌學會計算系統生物學分會, 副理事長

2010-10-01-今,運籌與管理, 編委

教授課程

生物信息學與計算系統生物學

生物信息學與系統生物學

出版信息

發表論文

(1) Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces, BMC Bioinformatics, 2017, 通訊作者

(2) NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis, BMC Systems Biology, 2017, 通訊作者

(3) Discovering cooperative biomarkers for heterogeneous complex disease diagnoses, Briefings in Bioinformatics, 2017, 通訊作者

(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, 通訊作者

(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, 通訊作者

(14) Corbi: A new R package for biological network alignment and querying, BMC Systems Biology, 2013, 通訊作者

(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, 通訊作者

(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, 通訊作者

(21) An efficient network querying method based on conditional random fields, Bioinformatics, 2011, 通訊作者

(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, 通訊作者

(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) 多階段多目標多部門應急決策模型, Emergency decision model with multiple stages, multiple objectives, and multidivisional cooperation, 系統工程理論與實踐, 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

發表著作

(1) Proceedings of 12th International Symposium on Operations Research and Its Applications, IET, 2015-08, 第 3 作者

科研活動

科研項目

( 1 ) 複雜網路中的最佳化問題及其在系統生物學中的套用, 參與, 國家級, 2012-01--2016-12

( 2 ) 動態網路生物標記識別的可計算建模與算法, 主持, 國家級, 2014-01--2016-12

( 3 ) 圖理論和算法研究及其在生物信息學中的套用, 參與, 國家級, 2017-01--2021-12

( 4 ) 癌症基因組大數據深度分析中的最佳化建模和算法研究, 參與, 國家級, 2017-01--2019-12

( 5 ) 幹細胞增殖的計算建模及其在癌症演變動力學的套用, 參與, 國家級, 2018-01--2019-12

( 6 ) 高效區塊鏈網路技術研究, 主持, 院級, 2017-08--2019-07

( 7 ) 無人倉(地狼AGV方案)最優入庫與揀選策略, 主持, 院級, 2017-12--2018-12

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