信息管理与信息系统专业

陈 磊

WP_20140713_006

陈磊, 男, 1982年生, 副教授, 上海市晨光学者。2010年华东师范大学博士毕业。研究方向包括图论及算法、算法设计与分析、生物信息学等。目前已主持完成科研项目5项,其中包括一项国家自然科学基金项目,一项上海市晨光计划,一项上海市教委科研创新项目。目前正承担上海市自然科学基金面上项目一项。曾获上海海事大学课题组科技奖(2010)、上海市计算机学会优秀博士论文优胜奖(2012)、上海海事大学学术论文奖三等奖(2012)、校优秀青年教师(2013)、上海海事大学ESI高被引论文奖(2014)、上海海事大学科技论文奖一等奖(2016)、校优秀教育工作者(2017)。目前共发表论文100余篇,其中以第一作者或通讯作者在SCI检索刊物上发表论文54篇,累计入选ESI高被引论文8篇。论文累计被SCI刊物论文引用1100余次,单篇最高被引用201次。

E-mail: chen_lei1@163.com 或 lchen@shmtu.edu.cn

办公地点: 信息楼212         办公电话: 021-38282825

学术兼职

1. 美国《数学评论》评论员

2. 以下刊物编委:Current Bioinformatics (SCI检索)(2016-present); Gene & Translational Bioinformatics (2016-present)

3. 以下刊物客座编委: Current Bioinformatics (SCI检索)(2016年)、BioMed Research International (SCI检索)(2013年、2014年、2015年、2016年)、Computational and Mathematical Methods in Medicine (SCI检索)(2014年、2015年)Artificial Intelligence in Medicine (SCI检索)(2016年)、 Current Proteomics (SCI检索)(2017年)、Combinatorial Chemistry & High Throughput Screening (SCI检索)(2017年)

4. 国家自然科学基金通讯评审

5. 中国计算机学会会员, 中国人工智能学会会员

主讲课程: 离散数学、数据结构、矩阵分析与应用(课件)、算法设计与分析、计算方法

目前研究兴趣: 生物大数据处理、机器学习算法在化合物功能预测和疾病相关基因预测的应用、控制集问题的算法与理论

一些常用的生物信息在线数据库

1. KEGG (Kyoto Encyclopedia of Genes and Genomes): 基因组、化学和系统功能信息的数据库

2. STRING (Search Tool for the Retrieval of Interacting Genes/Proteins): 蛋白质相互作用数据库

3. STITCH (Search Tool for Interactions of Chemicals) : 化合物和蛋白质相互作用数据库

4. DrugBank: 药物、药物作用和药物靶点知识库

5. CTD (Comparative Toxicogenomics Database): 收录了环境化学物质与基因功能之间的关系

代表论文

13.  Lei Chen, Chen Chu, Jing Lu, Xiangyin Kong, Tao Huang, Yu-Dong Cai, A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals, Molecular BioSystems, 11(9)(2015), 2541-2550.

12. Lei Chen, Chen Chu, Jing Lu, Xiangyin Kong, Tao Huang, Yu-Dong Cai, Gene Ontology and KEGG pathway enrichment analysis of a drug target-based classification system, PLoS ONE, 10(5)(2015), e0126492.

11. Lei Chen, Jing Lu, Tao Huang, Jun Yin, Lai Wei, Yu-Dong Cai, Finding candidate drugs of Hepatitis C based on chemical-chemical and chemical-protein interactions, PLoS ONE9(9)(2014), e107767.

10. Lei Chen, Jing Lu, Ning Zhang, Tao Huang, Yu-Dong Cai, A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes, Molecular BioSystems, 10(4)(2014), 868-877. (ESI highly cited paper)

9. Lei Chen, Wei-Ming Zeng, Yu-Dong Cai, Tao Huang, Prediction of metabolic pathway using graph property, chemical structure set and chemical functional group, Current Bioinformatics, 8(2)(2013), 200-207. (ESI highly cited paper)

8. Lei Chen, Jing Lu, Jian Zhang, Kai-Rui Feng, Ming-Yue Zheng, Yu-Dong Cai, Predicting chemical toxicity effects based on chemical-chemical interactions, PLoS ONE, 8(2)(2013), e56517.

7. Lei Chen, Wei-Ming Zeng, Yu-Dong Cai, Kai-Yan Feng, Kuo-Chen Chou, Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities, PLoS ONE, 7(4)(2012), e35254. (ESI highly cited paper)

6. Lei Chen, Weiming Zeng, Changhong Lu, NP-completeness and APX-completeness of restrained domination in graphs, Theoretical Computer Science, 448(2012), 1-8.

5. Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Hai-Peng Li, Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition, BMC Bioinformatics, 11(2010), 293. (ESI highly cited paper)

4. Lei Chen, Changhong Lu, Zhenbing Zeng, Hardness results and approximation algorithms for (weighted) paired-domination in graphs, Theoretical Computer Science, 410(47-49)(2009), 5063-5071.

3. Lei Chen, Changhong Lu, Zhenbing Zeng, A linear-time algorithm for paired-domination problem in strongly chordal graphs, Information Processing Letters, 110(1)(2009), 20-23.

2. Lei Chen, Lin Lu, Kairui Feng, Wenjin Li, Jie Song, Lulu Zheng, Youlang Yuan, Zhenbin Zeng, Kaiyan Feng, Wencong Lu, Yudong Cai, Multiple classifier integration for the prediction of protein structural classes, Journal of Computational Chemistry, 30(14)(2009), 2248-2254.

1. Lei Chen, Xiaohe Shi, Xiangyin Kong, Zhenbing Zeng, Yudong Cai, Identifying protein complex using hybrid properties, Journal of Proteome Research, 8(11)(2009), 5212-5218.

其它论文

96. Quan Zou, Lei Chen, Tao Huang, Zhenguo Zhang, Yungang Xue, Machine Learning and Graph Analytics in Computational Biomedicine, Artificial Intelligence in Medicine, in press.

95. JiaRui Li, Lei Chen, ShaoPeng Wang, YuHang Zhang, XiangYin Kong, Tao Huang, Yu-Dong Cai, A computational method using the random walk with restart algorithm for identifying novel epigenetic factors, Molecular Genetics and Genomics, in press.

94. Lei Chen, Yu-Hang Zhang, Guohua Huang, ShaoPeng Wang, Tao Huang, Yu-Dong Cai, Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection, Molecular Genetics and Genomics, in press.

93. Yu-Hang Zhang, Tao Huang, Lei Chen, YaoChen Xu, Yu Hu, Lan-Dian Hu, Yudong Cai, Xiangyin Kong, Identifying and analyzing different cancer subtypes using RNA-seq data of blood platelets, Oncotarget, in press.

92. Qianwu Ni, Lei Chen, A feature and algorithm selection method for improving the prediction of protein structural classes, Combinatorial Chemistry & High Throughput Screening, in press.

91. ShaoPeng Wang, Yu-Hang Zhang, Ning Zhang, Lei Chen, Tao Huang, Yu-Dong Cai, Recognizing and predicting thioether bridges formed by lanthionine and β-methyllanthionine in lantibiotics using a random forest approach with feature selection, Combinatorial Chemistry & High Throughput Screening, in press.

90. Lei Chen, Chen Chu, Tao Huang, Mingyue Zheng, Xiangyin Kong, Yu-Dong Cai, Identification of drug-drug interactions using chemical interactions, Current Bioinformatics, in press.

89. Lei Chen, Yu-Hang Zhang, ShaoPeng Wang, YunHua Zhang, Tao Huang, Yu-Dong Cai, Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways, PLoS ONE, 12(9)(2017), e0184129.

88. Lei Chen, Jing Lu Tao Huang, Yu-Dong Cai, A computational method for the identification of candidate drugs for non-small cell lung cancer, PLoS ONE, 12(8)(2017), e0183411.

87. ShaoPeng Wang, Yu-Hang Zhang, GuoHua Huang, Lei Chen, Yu-Dong Cai, Analysis and prediction of myristoylation sites using the mRMR method, the IFS method and an extreme learning machine algorithm, Combinatorial Chemistry & High Throughput Screening, 20(2)(2017), 96-106.

86. Yemin Fang, Lei Chen, A binary classifier for prediction of the types of metabolic pathway of chemicals, Combinatorial Chemistry & High Throughput Screening, 20(2)(2017), 140-146.

85. Shiheng Lu, Yan Yan, Zhen Li, Lei Chen, Jing Yang, Yu-Hang Zhang, ShaoPeng Wang, Lin Liu, Determination of genes related to uveitis by utilization of the Random Walk with Restart algorithm on a protein-protein interaction network, International Journal of Molecular Sciences, 18(5)(2017), 1044.

84. Lei Chen, Jing Yang, Zhihao Xing, Fei Yuan, Yang Shu, YunHua Zhang, XiangYin Kong, Tao Huang, HaiPeng Li, Yu-Dong Cai, An integrated method for the identification of novel genes related to oral cancer, PLoS ONE, 12(4)(2017), e0175185.

83. Lei Chen, Yu-Hang Zhang, Guohui Lu, Tao Huang, Yu-Dong Cai, Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways, Artificial Intelligence in Medicine76(2017), 27-36.

82. Yu-Dong Cai, Qing Zhang, Yu-Hang Zhang, Lei Chen, Tao Huang, Identification of genes associated with breast cancer metastasis to bone on a protein-protein interaction network with a shortest path algorithm, Journal of Proteome Research, 16(2)(2017), 1027-1038.

81. Lili Liu, Lei Chen, Yu-Hang Zhang,  Lai Wei, Shiwen Cheng, Xiangyin Kong, Mingyue Zheng, Tao Huang, Yu-Dong Cai, Analysis and prediction of drug-drug interaction by minimum redundancy maximum relevance and incremental feature selection, Journal of Biomolecular Structure & Dynamics, 35(2)(2017), 312-329. (ESI highly cited paper)

80. Lei Chen, Baoman Wang, SaoPeng Wang, Jing Yang, Jerry Hu, ZhiQun Xie, Yuwei Wang, Tao Huang, Yu-Dong Cai, OPMSP: A computational method integrating protein interaction and sequence information for the identification of novel putative oncogenes, Protein & Peptide Letters23(12)(2016), 1081-1094.

79. Jian Zhang, Jing Yang, Tao Huang, Yang Shu, Lei Chen, Identification of novel proliferative diabetic retinopathy related genes on protein-protein interaction network, Neurocomputing, 217(2016), 63-72.  (ESI highly cited paper)

78. Yu-Hang Zhang, Chen Chu, Shaopeng Wang, Lei Chen, Jing Lu, XiangYin Kong, Tao Huang, HaiPeng Li, Yu-Dong Cai, The use of Gene Ontology term and KEGG pathway enrichment for analysis of drug half-life, PLoS ONE, 11(10)(2016), e0165496.

77. Lei Chen, Yu-Hang Zhang, Mingyue Zheng, Tao Huang, Yu-Dong Cai, Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichments for proteins and molecular fragments of compounds, Molecular Genetics and Genomics, 291(6)(2016), 2065-2079.

76. Tao Huang, Lei Chen, Jiangning Song, Mingyue Zheng, Jialiang Yang, Zhenguo Zhang, Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016, BioMed Research International, 2016(2016), 6585069.

75. Lei Chen, Yu-Hang Zhang, Quan Zou, Chen Chu, Zhiliang Ji, Analysis of the chemical toxicity effects using the enrichments of Gene Ontology terms and KEGG pathways, Biochimica et Biophysica Acta (BBA) – General Subjects, 1860(11 Part B)(2016), 2619-2626.

74. ZhiHao Xing, Chen Chu, Lei Chen, Xiangyin Kong, The use of Gene Ontology terms and KEGG pathways for analysis and prediction of oncogenes, Biochimica et Biophysica Acta (BBA) – General Subjects, 1860(11 Part B)(2016), 2725-2734.

73. Nizhuan Wang, Weiming Zeng, Dongtailang Chen, Jun Yin, Lei Chen, A Novel Brain Networks Enhancement Model (BNEM) for BOLD fMRI Data Analysis with Highly Spatial Reproducibility, IEEE Journal of Biomedical and Health Informatics, 20(4)(2016), 1107-1119.

72. Lei Chen, Yu-Hang Zhang, Tao Huang, Yang Jiang, Mingyue Zheng, Yu-Dong Cai, Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach, Scientific Reports, 6(2016), 29849.

71. Liucun Zhu, Yu-Hang Zhang, Fangchu Su, Lei Chen, Tao Huang, Yu-Dong Cai, A shortest-path-based method for the analysis and prediction of fruit-related genes in Arabidopsis thaliana, PLoS ONE, 11(7)(2016), e0159519.

70. Lei Chen, Chen Chu, Yu-Hang Zhang, Changming Zhu, Xiangyin Kong, Tao Huang, Yu-Dong Cai, Analysis of gene expression profiles in the brain stem, cerebellum and cerebral cortex, PLoS ONE, 11(7)(2016), e0159395.

69. Guangzhong Liu, Min Liu, Daozheng Chen, Lei Chen, Jiali Zhu, Bo Zhou, Jun Gao, Predicting protein ligand binding sites with structure alignment method on Hadoop, Current Proteomics, 13(2)(2016), 113-121.

68.  Lei Chen, Yu-Hang Zhang, Tao Huang, Yu-Dong Cai, Identifying new protein phenotypic annotations by hybridizing protein-protein interactions and protein sequence similarities, Molecular Genetics and Genomics, 291(2)(2016), 913-934.

67. Lei Chen, Yu-Hang Zhang, Tao Huang, Yu-Dong Cai, Gene expression profiling gut microbiota in different races of humans, Scientific Reports, 6(2016), 23075.

66. Bi-Qing Li, Lu-Lu Zheng, Kai-Yan Feng, Le-Le Hu,  Guohua Huang, Lei Chen, Prediction of linear B-cell epitopes with mRMR feature selection and analysis, Current Bioinformatics, 11(1)(2016), 22-31.

65. You Zhou, Biqing Li, Yuchao Zhang, Lei Chen, Xiang-Yin Kong, Feature Classification and Analysis of Lung Cancer Related Genes Through Gene Ontology and KEGG pathways, Current Bioinformatics, 11(1)(2016), 40-50.

64. Lei Chen, ZhiHao Xing, Tao Huang, Yang Shu, Guohua Huang, Hai-Peng Li, Application of the shortest path algorithm for the discovery of breast cancer-related genes, Current Bioinformatics, 11(1)(2016), 51-58. (ESI highly cited paper)

63. Jing Lu, Lei Chen, Jun Yin, Tao Huang, Yi Bi, Xiangyin Kong, Mingyue Zheng, Yu-Dong Cai, Identification of new candidate drugs for lung cancer using chemical-chemical interactions, chemical-protein interactions and a K-means clustering algorithm, Journal of Biomolecular Structure & Dynamics, 34(4)(2016), 906-917.

62.  Cao Wang, Lei Chen, Changhong Lu, k-power domination in block graphs, Journal of Combinatorial Optimization, 31(2)(2016), 865-873.

61. Lei Chen, Jing Yang, Xiangyin Kong, Lin Lu, Yu-Dong Cai, Mining for novel tumor suppressor genes using a shortest path approach, Journal of Biomolecular Structure & Dynamics, 34(3)(2016), 664-675.

60. Bing Niu, Zhihao Xing, Manman Zhao, Haizhong Huo, Guohua Huang, Fuxue Chen, Qiang Su, Yin Lu, Meng Wang, Jing Yang, Lei Chen, Ling Tang, Linfeng Zheng, Study of drug-drug combinations based on molecular descriptors and physicochemical properties, Combinatorial Chemistry & High Throughput Screening, 19(2)(2016), 153-160.

59. Lei Chen, Chen Chu, Kaiyan Feng, Predicting the types of metabolic pathway of compounds using molecular fragments and sequential minimal optimization, Combinatorial Chemistry & High Throughput Screening, 19(2)(2016), 136-143.

58. Lei Chen, Yuhang Zhang, Jian Zhang, Tao Huang, Yang Shu, Yu-Dong Cai, Identification of candidate genes related to renal carcinoma using protein interactions and structures, Proceedings of The World Congress on Engineering 2015, Vol I, 577-581, July 1-3, 2015, London, U.K.

57. Lei Chen, Tao Huang, Chuan Lu, Lin Lu, Dandan Li, Machine Learning and Network Methods for Biology and Medicine, Computational and Mathematical Methods in Medicine, 2015(2015), 915124.

56. Lei Chen, Jing Yang, Tao Huang, Xiangyin Kong, Yu-Dong Cai, The use of chemical-chemical interaction and chemical structure to identify new candidate chemicals related to lung cancer, PLoS ONE, 10(6)(2015), e0128696.

55. Yu-Dong Cai, Tao Huang, Lei Chen, Bing Niu, Application of Systems Biology and Bioinformatics Methods in Biochemistry and Biomedicine 2014, BioMed Research International, 2015(2015), 568607.

54. Lei Chen, Chen Chu, Tao Huang, Xiangyin Kong,Yu-Dong Cai, Prediction and analysis of cell-penetrating peptides using pseudo amino acid composition and random forest models, Amino Acids, 47(7)(2015), 1485-1493.

53. Lei Chen, Changhong Lu, Zhenbing Zeng, Graphs with unique minimum paired-dominating sets, Ars Combinatoria, 119(2015), 177-192.

52. Tao Huang, Lei Chen, Mingyue Zheng, Jiangning Song, Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Diseas, BioMed Research International, 2015(2015), 760765.

51. Pei-Wei Zhang, Lei Chen, Tao Huang, Ning Zhang, Xiang-Yin Kong, Yu-Dong Cai, Classifying Ten Types of Major Cancers Based on Reverse Phase Protein Array Profiles, PLoS ONE, 10(3)(2015), e0123147.

50. Lei Chen, Chen Chu, Xiangyin Kong, Tao Huang, Yu-Dong Cai, Discovery of new candidate genes related to brain development using protein interaction information, PLoS ONE, 10(1)(2015), e0118003.

49. Lei Chen, Chen Chu, Xiangyin Kong, Guohua Huang, Tao Huang, Yu-Dong Cai, A hybrid computational method for the discovery of novel reproduction-related genes, PLoS ONE, 10(3)(2015), e0117090.

48. Lei Chen, Jing Lu, Xiaomin Luo, Kai-Yan Feng, Prediction of drugs’ target group by integrating information of chemical-chemical similarities and chemical-chemical/protein connections, Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics, 1844(1)(2014), 207-213.

47. Jing Yang, Lei Chen, Xiangyin Kong, Tao Huang, Yu-Dong Cai, Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway, PLoS ONE, 9(9)(2014), e107202.

46. Ning Zhang, You Zhou, Tao Huang, Yu-Chao Zhang, Bi-Qing Li, Lei Chen, Yu-Dong Cai, Discriminating between Lysine Sumoylation and Lysine Acetylation using mRMR Feature Selection and Analysis, PLoS ONE, 9(9)(2014), e107464.

45. Jian Zhang, ZhiHao Xing, Mingming Ma, Ning Wang, Yu-Dong Cai, Lei Chen, Xun Xu, Gene Ontology and KEGG enrichment analyses of gene related to age-related macular degeneration, BioMed Research International, 2014(2014), 450386.

44. Yu-Dong Cai, Tao Huang, Lei Chen, Shan Gao, Ning Zhang, Novel computational methods and tools in biomedicine and biopharmacy, Computational and Mathematical Methods in Medicine, 2014(2014), 127515.

43. Tianlong Ren, Weiming Zeng, Nizhuan Wang, Lei Chen, Chenglin Wang, A novel approach for fMRI data analysis based on the combination of sparse approximation and affinity propagation clustering, Magnetic Resonance Imaging, 32(6)(2014), 736-746.

42. Jing Lu, Guohua Huang, Hai-Peng Li, Kai-Yan Feng, Lei Chen, Ming-Yue Zheng, Yu-Dong Cai, Prediction of cancer drugs by chemical-chemical interactions, PLoS ONE9(2)(2014), e87791.

41. Guohua Huang, Yuchao Zhang, Lei Chen, Ning Zhang, Tao Huang, Yu-Dong Cai, Prediction of multi-type of membrane protein in human by an integrated approach, PLoS ONE, 9(3)(2014), e93553.

40. Lei Chen, Wei-Ming Zeng, A two-step similarity-based method for prediction of drug’s target group, Protein & Peptide Letters, 20(3)(2013), 364-370.

39. Yang Jiang, Tao Huang, Lei Chen, Yu-Fei Gao, Yudong Cai and Kuo-Chen Chou, Signal propagation in protein interaction network during colorectal cancer progression, BioMed Research International, 2013(2013), 287019.

38. Bi-Qing Li, Jin You, Lei Chen, Jian Zhang, Ning Zhang, Tao Huang, Xiang-Yin Kong, Yu-Dong Cai, Identification of lung-cancer-related genes with the shortest path approach in a protein-protein interaction network, BioMed Research International, 2013(2013), 267375.

37. Weiren Cui, Lei Chen, Tao Huang, Qian Gao, Min Jiang, Ning  Zhang, Lulu Zheng, Kaiyan Feng, Yudong Cai , Hongwei Wang, Computationally identifying virulence factors based on KEGG pathways, Molecular BioSystems, 9(6)(2013), 1447-1452.

36. Nizhuang Wang, Weiming Zeng, Lei Chen, SACICA: A sparse approximation coefficients based ICA model for functional magnetic resonance imaging data analysis, Journal of Neuroscience Methods, 216(1)(2013), 49-61.

35. Bi-Qing Li, Bing Niu, Lei Chen, Ze-Jun Wei, Tao Huang, Min Jiang, Jing Lu, Ming-Yue Zheng, Xiang-Yin Kong, Yu-Dong Cai, Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network, PLoS ONE, 8(6)(2013), e65207.

34.  Shengnan Yao, Weiming Zeng, Nizhuan Wang, Lei Chen, Validating the Performance of Once Decomposition for fMRI Analysis Using ICA with Automatic Target Generation Process, Magnetic Resonance Imaging, 31(6)(2013), 970-975.

33. Zhen Li, Bi-Qing Li, Min Jiang, Lei Chen, Jian Zhang, Lin Liu, Tao Huang, Prediction and Analysis of retinoblastoma related genes through Gene Ontology and KEGG, BioMed Research International, 2013(2013), 304029.

32. Lei Chen, Tao Huang, Jian Zhang, Ming-Yue Zheng, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Prediction of drugs side effect based on chemical-chemical interactions and protein-chemical interactions, BioMed Research International, 2013(2013), 485034.

31. Lei Chen, Bi-Qing Li, Ming-Yue Zheng, Jian Zhang, Kai-Yan Feng, Yu-Dong Cai, Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways, BioMed Research International, 2013(2013), 723780.

30. Lei Chen, Bi-Qing Li, Kai-Yan Feng, Predicting biological functions of protein complexes using graphic and functional features, Current Bioinformatics, 8(5)(2013), 545-551.

29. Ning Zhang, Shan Gao, Lei Chen and Jishou Ruan, Using Multitask Learning Methods to Investigate Signal Peptides and Signal Anchors, Current Bioinformatics, 8(5)(2013), 533-538.

28. Min Jiang, Yukang Chen, Yuchao Zhang, Lei Chen, Ning Zhang, Tao Huang, Yu-Dong Cai, XiangYin Kong, Identification of Hepatocellular Carcinoma Related Genes with k-th Shortest Paths in a Protein-Protein Interaction Network, Molecular BioSystems, 9(11)(2013), 2720-2728.

27. Tao Zhang, Min Jiang, Lei Chen, Bing Niu, Yudong Cai,  Prediction of gene phenotypes based on GO and KEGG pathway enrichment scores, BioMed Research International, 2013(2013), 870795.

26. Yu-Fei Gao, Lei Chen, Guo-Hua Huang, Tao Zhang, Kai-Yan Feng, Hai-Peng Li, Yang Jiang, Prediction of drugs target groups based on ChEBI ontology, BioMed Research International, 2013(2013), 132724.

25. Jian Zhang, Min Jiang, Fei Yuan, Kai-Yan Feng, Yu-Dong Cai, Xun Xu, Lei Chen, Identification of age-related macular degeneration related genes by applying shortest path algorithm in protein-protein interaction network, BioMed Research International, 2013(2013), 523415.

24. Yu-Dong Cai, Tao Huang, Lei Chen, Bin Niu, Application of Systems Biology and Bioinformatics Methods in Biochemistry and Biomedicine, BioMed Research International, 2013(2013), 651968.

23. Lei Chen, Yu-Dong Cai, Xiao-He Shi, Tao Huang, Analysis of metabolic pathway using hybrid properties, Protein & Peptide Letters, 19(1)(2012), 99-107.

22. Tao Huang, Yu-Dong Cai, Lei Chen, Lele Hu, Xiang-Yin Kong, Yi-Xue Li, Kuo-Chen Chou, Selection of Reprogramming Factors of Induced Pluripotent Stem Cells Based on the Protein Interaction Network and Functional Profiles, Protein & Peptide Letters, 19(1)(2012), 113-119.

21. Tao Huang, Jian Zhang, Zhong-Ping Xu, Le-Le Hu, Lei Chen, Jian-Lin Shao, Lei Zhang, Xiang-Yin Kong, Yu-Dong Cai, Kuo-Chen Chou, Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches, Biochimie, 94(4)(2012), 1017-1025.

20. Nizhuan Wang, Weiming Zeng, Lei Chen, A Fast-FENICA method on resting state fMRI data, Journal of Neuroscience Methods, 209(1)(2012), 1-12.

19. Bi-Qing Li, Le-Le Hu, Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Prediction of protein domain with mRMR feature selection and analysis, PLoS ONE, 7(6)(2012), e39308.

18. Peng Gao, Qing-Ping Wang, Lei Chen, Tao Huang, Prediction of human genes’ regulatory functions based on protein-protein interaction network, Protein & Peptide Letters, 19(9)(2012), 910-916.

17. Bi-Qing Li, Kai-Yan Feng , Lei Chen, Tao Huang, Yu-Dong Cai, Prediction of protein-protein interaction sites by Random Forest algorithm with mRMR and IFS, PLoS ONE, 7(8)(2012), e43927.

16. Lei Chen, Changhong Lu, Zhenbing Zeng, Vertices in all minimum paired-dominating set of block graphs, Journal of Combinatorial Optimization, 24(3)(2012), 176-191.

15. Yu-Fei Gao, Lei Chen, Yu-Dong Cai, Kai-Yan Feng, Tao Huang, Yang Jiang, Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins, PLoS ONE, 7(9)(2012), e45944.

14. Tao Huang, Zhong-Ping Xu, Lei Chen, Yu-Dong Cai, Xiangyin Kong, Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and Virus-Host Interaction Network, PLoS ONE, 6(3)(2011), e17291.

13. Tao Huang, Lei Chen, Xiao-Jun Liu, Yu-Dong Cai, Predicting triplet of transcription factor – mediating enzyme – target gene by functional profiles, Neurocomputing, 74(17)(2011), 3677-3681.

12. Tao Huang, Lei Chen, Yu-Dong Cai, Classification and analysis of regulatory pathway using graph property, biochemical and physicochemical property, and functional property, PLoS ONE, 6(9)(2011), e25297.  (ESI highly cited paper)

11. Lei Chen, Changhong Lu, Zhenbing Zeng, Labelling algorithms for paired-domination problems in block and interval graphs, Journal of Combinatorial Optimization, 19(4)(2010), 457-470.

10. Lei Chen, Ziliang Qian, Kaiyan Feng, Yudong Cai, Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity, Journal of Computational Chemistry, 31(8)(2010), 1766-1776.

9. ZhiSong He, Tao Huang XiaoHe Shi, LeLe Hu, Lei Chen, Fang Liu, Kai Wang, TieQiao Wen, XiangYin Kong, Yudong Cai, Computational Analysis of Protein Tyrosine Nitration, The Fourth International Conference on Computational Systems Biology (ISB2010), 35-42.

8. Lei Chen, Tao Huang, Xiao-He Shi, Yu-Dong Cai, Kuo-Chen Chou, Analysis of protein pathway network using hybrid properties, Molecules, 15(11)(2010), 8177-8192.

7. Yu-Dong Cai, Lin Lu, Lei Chen, Jian-Feng He, Predicting subcellular location of proteins using integrated-algorithm method, Molecular Diversity, 14(3)(2010), 551-558.

6. Lei Chen, Zhi-Song He, Tao Huang, Yu-Dong Cai, Using compound similarity and functional domain composition for prediction of drug-target interaction networks, Medicinal Chemistry, 6(6)(2010), 388-395.

5. Lei Chen, Changhong Lu, Zhenbing Zeng, Distance paired-domination problems on subclasses of chordal graphs, Theoretical Computer Science, 410(47-49)(2009), 5072-5081.

4. Lei Chen, Ziliang Qian, Yudong Cai, Zhenbing Zeng, Wencong Lu, Prediction of compounds’ biological function (metabolic pathway) based on compound similarity, 4th IAPR International Conference on Pattern Recognition in Bioinformatics, Supplementary Proceedings, P08.

3. CHEN Lei, LU Chang-hong, ZENG Zhen-bing, Constructive characterizations of (γ_p, γ)- and (γ_p, γ_pr)-trees, Applied Mathematics-A Journal of Chinese  Universities Series B, 23(4)(2008), 475-480.

2. Chen Lei, Lu Changhong, Ye Yongsheng, On the Number of Increasing Paths in Labeled Cycles and Stars, Applied Mathematics-A Journal of Chinese Universities Series B, 22(1)(2007), 1-6.

1. Changhong Lu, Lei Chen, Mingqing Zhai, Extremal problems on consecutive L(2, 1)-labelling, Discrete Applied Mathematics, 155(10)(2007), 1302-1313.

已毕业硕士研究

1. 谢瑜, 2013年9月-2015年6月, 毕业论文题目:花授粉算法的改进及其在集成学习算法中的应用

2. 程时稳,2014年9月-2016年6月,毕业论文题目:基于机器学习的药物新功能预测方法研究 (发表两篇SCI检索论文)

3. 倪前武,2015年9月-2017年6月,毕业论文题目:融合特征选择的分类算法选择性集成方法研究 (发表一篇SCI检索论文)

在读硕士研究生

1. 崔浩,2016年9月入学

2. 刘涛,2017年9月入学

3. 赵贤,2017年9月入学