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Min Li (李敏) Professor

School of Information Science and Engineering,
Central South University,
Changsha, China 410083



Phone:(086) 139-7513-4596
Fax: +86-73188830212
Email: limin@mail.csu.edu.cn

Li min
RESEARCH INTERESTS
Bioinformatics/Systems Biology:
  • Clustering algorithms for protein-protein interaction networks
  • Algorithms for essential proteins discovery
  • Integrative analysis of molecular networks with other biological data
  • Algorithms for identifying dynamic network modules
EDUCATION
• 2012.03-2015.03, Postdoctoral Fellow, State Key Laboratory of Medical Genetics, Central South University.
• 2010.12-2011.12, Visiting Scholar (Postdoctoral Fellow), Department of Computer Science, Georgia State University.
• Ph.D. in Computer Science, Central South University, 2008.
• M.S. in Traffic Information and Control Engineering, Central South University, 2004.
• B.S. in Communication Engineering, Central South University, 2001.
EMPLOYMENT HISTORY
• 2015.09-current, Professor, School of Information Science and Engineering, Central South University.
• 2010.09-2015.08, Associate Professor, School of Information Science and Engineering, Central South University.
• 2009.09-2010.08, lecturer, School of Information Science and Engineering, Central South University.
• 2006.09-2009.08, Engineer, Modern Education Technology Center, Central South University.
• 2004.07-2006.09, Research Assistant, Modern Education Technology Center, Central South University.
RESEARCH GRANTS
[1] CoPI:National Natural Science Foundation of China (Key Program), “Foundational theory and algorithms on genome data analysis”, Grant No. 61732009 (¥2600,000), Jan. 1, 2018 ~ Dec. 31, 2022.
[2] CoPI:National Natural Science Foundation of China (Joint Research Fund for Overseas Chinese Scholars and Scholars in Hong Kong and Macao), “Randomized Matrix Decomposition Algorithms and Their Applications in Protein Structure Modeling” Grant No. 61428209 (¥180,000). Jan. 1, 2018 ~ Dec. 31, 2019.
[3] PI:The National Science Fund for Excellent Young Scholars, “Bioinformatics” Grant No. 61622213 (¥1300,000). Jan. 1, 2017 ~ Dec. 31, 2019.
[4] PI:National Natural Science Foundation of China, “Network-based essential protein discovery and its applications” Grant No. 61370024 (¥810,000). Jan. 1, 2014 ~ Dec. 31, 2017.
[5] CoPI:National Natural Science Foundation of China (Joint Research Fund for Overseas Chinese Scholars and Scholars in Hong Kong and Macao), “Network control-based drug target identifications for complex diseases” Grant No. 61428209 (¥200,000). Jan. 1, 2015 ~ Dec. 31, 2016.
[6] PI:National Natural Science Foundation of China, “Method for mining functional modules in dynamic protein interaction networks and its application” Grant No.61003124. (¥220,000). Jan. 1, 2011 ~ Dec. 31, 2013.
[7] PI:Program for New Century Excellent Talents in University. No (NCET-12-0547). Jan. 1, 2013 ~ Dec. 31, 2015.
[8] PI:Ph.D. Programs Foundation of Ministry of Education of China, “Analysis for the dynamic and modular organization of protein interaction networks”. Grant No. 20090162120073 (¥36,000). Jan. 1, 2010 ~ Dec. 31, 2012.
SELECTED PUBLICATIONS
[1] Min Li, Ruiqing Zheng, Yaohang Li, Fang-Xiang Wu, and Jianxin Wang. MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB.2017.2705143
[2] Min Li, Peng Ni, Xiaopei Chen, Jianxin Wang, and Yi Pan. Construction of refined protein interaction network for predicting essential proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB.2017.2665482
[3] Min Li, Zhongxiang Liao, Yiming He, Jianxin Wang, Junwei Luo, and Yi Pan. ISEA: iterative seed-extension algorithm for de novo assembly using paired-end information and insert size distribution. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017,14(4):916-925.
[4] Min Li, Dongyan Li, Yu Tang, FangXiang Wu, and Jianxin Wang. CytoCluster: a cytoscape plugin for cluster analysis and visualization of biological networks. Int. J. Mol. Sci. 2017, 18, 1880
[5] Min Li, Binbin Wu, XiaodongYan, Fang-Xiang Wu, Yi Pan, Jianxin Wang. PECC: correcting contigs based on paired-end read distribution. Computational Biology and Chemistry, 2017, 69:178-184.
[6] Min Li, Yu Lu, Zhibei Niu, Fangxiang Wu. United complex centrality for identification of essential proteins from PPI networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(2): 370-380.
[7] Wei Peng, Min Li*, Lu Chen, and Lusheng Wang. Predicting protein functions by using unbalanced random walk algorithm on three biological networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(2):360-369.
[8] Wei Lan, Min Li, Kaijie Zhao, Jin Liu, Fangxiang Wu, Yi Pan, Jianxin Wang*. LDAP: a web server for lncRNA-disease association prediction. Bioinformatics, 2017, 33(3): 458-460.
[9] Jin Liu, Min Li, Yi Pan, Fangxiang Wu, Xiaogang Chen, Jianxin Wang*.Classification of Schizophrenia Based on Individual Hierarchical Brain Networks Constructed From Structural MRI Images. IEEE Transactions on NanoBioscience, DOI: 10.1109/TNB.2017.2751074
[10] Lin Wu, Lingkai Tang, Min Li, Jianxin Wang, and Fang-Xiang Wu. Biomolecular Network Controllability With Drug Binding Information. IEEE Transactions on Nanobioscience. 2017, 16(5): 326-332.
[11] Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu and Yi Pan. BOSS: a novel scaffolding algorithm based on optimized scaffold graph. Bioinformatics, 2017, 33(2):169-176.
[12] Jin Liu, Min Li, Wei Lan, Fangxiang Wu, Yi Pan, Jianxin Wang. Classification of Alzheimer’s Disease Using Whole Brain Hierarchical Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics. http://dx.doi.org/10.1109/TCBB.2016.2635144
[13] Min Li, Yu Tang, Xuehong Wu, Jianxin Wang*, Fang-Xiang Wu, Yi Pan. C-DEVA: detection, evaluation, visualization and annotation of clusters from biological networks. Biosystems, 2016,150:78-86. DOI 10.1016/j.biosystems.2016.08.004
[14] Min Li, Ruiqing Zheng, Qi Li, Jianxin Wang, Fangxiang Wu, Zhuohua Zhang. Prioritizing Disease Genes by Using Search Engine Algorithm. Current Bioinformatics, 2016, 11(2): 195-202. DOI: 10.2174/1574893611666160125220905
[15] Min Li, Zhibei Niu, Xiaopei Chen, Ping Zhong*, Fang-Xiang Wu, Yi Pan. A reliable neighbor-based method for identifying essential proteins by integrating gene expressions, orthology, and subcellular localization information. TSINGHUA SCIENCE AND TECHNOLOGY, 2016, 12(6): 668-677.
[16] Gaoshi Li, Min Li*, Jianxin Wang*, Fang-Xiang Wu and Yi Pan. Predicting essential proteins based on subcellular localization, orthology and PPI networks. BMC Bioinformatics. Vol 17 Suppl, 2016. DOI: 10.1186/s12859-016-1115-5
[17] Sheng-You Huang, Min Li, Jianxin Wang, and Yi Pan. HybridDock: a hybrid protein-ligand docking protocol integrating protein- and ligand-based approaches. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00275. 2015
[18] Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu and Yi Pan. BOSS: a novel scaffolding algorithm based on optimized scaffold graph. Bioinformatics. DOI: 10.1093/bioinformatics/btw597
[19] Wei Lan, Jianxin Wang, Min Li, Jin Liu, Fangxiang Wu, Yi Pan. Predicting microRNA-disease associations based on improved microRNA and disease similarities". IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2016.2586190
[20] Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang and Yaohang Li. FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information. BMC Bioinformatics. Vol 17 Suppl, 2016. DOI: 10.1186/s12859-016-1117-3
[21] Huimin Luo, Jianxin Wang, Min Li, Junwei Luo, Xiaoqing Peng, Fangxiang Wu, Yi Pan. Drug repositioning based on comprehensive similarity measures and Bi-Random Walk algorithm. Bioinformatics. DOI: 10.1093/bioinformatics/btw228
[22] Bihai Zhao, Jianxin Wang*, Min Li*, Xueyong Li, Yaohang Li, Fang-Xiang Wu, Yi Pan. A new method for predicting protein functions from dynamic weighted interactome networks, IEEE Transactions on Nanobioscience. DOI: 10.1109/TNB.2016.2536161
[23] Jiancheng Zhong, Jianxin Wang, Xiaojun Ding, Zhen Zhang, Min Li, Fang-Xiang Wu, Yi Pan. Protein Inference from the Integration of Tandem MS Data and Interactome Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics.DOI 10.1109/TCBB.2016.2601618
[24] Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang, and Fang-Xiang Wu*. Identifying individual-cancer-related genes by re-balancing the training samples. IEEE Transactions on Nanobioscience. DOI: 10.1109/TNB.2016.2553119
[25] Wei Lan, Jianxin Wang, Min Li, Jin Liu, Yaohang Li, Fangxiang Wu, Yi Pan. Predicting drug-target interaction using positive-unlabeled learning. Neurocomputing, 2016, DOI: 10.1016/j.neucom.2016.03.080
[26] Lin Wu, Min Li, Jianxin Wang, and Fang-Xiang Wu. The minimum steering node set of complex networks and its applications to biomolecular networks. IET Systems Biology, 2016, 10(3):116-23. 2016 Jun
[27] Jianxin Wang, Min Li, Zuguo Yu. Nonlinear Science and Network Methods For Prediction Problems In Bioinformatics And Systems Biology. Current Bioinformatics. 2016, 11(2):154-155.
[28] Min Li, Yu Lu, Zhibei Niu, Fangxiang Wu. United complex centrality for identification of essential proteins from PPI networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI 10.1109/TCBB.2015.2394487 (SCI, Impact factor:1.62)
[29] Wei Peng, Min Li*, Lu Chen, and Lusheng Wang. Predicting protein functions by using unbalanced random walk algorithm on three biological networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10.1109/TCBB.2015.2394314 (SCI, Impact factor:1.62)
[30] Yu Tang, Min Li*, Jianxin Wang, Yi Pan, Fang-Xiang Wu. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of biological networks. BioSystems, 2015, 127: 67-72. DOI: 10.1016/j.biosystems.2014.11.005 (SCI, Impact factor: 1.472)
[31] Min Li, Ruiqing Zheng, Qi Li, Fangxiang Wu, Zhuohua Zhang. Prioritizing Disease Genes By Using Search Engine Algorithm. Current Bioinformatics. Accepted
[32] Xiaojun Ding, Min Li*, Haihua Gu, Zhen Zhang, and Fangxiang Wu. Detecting SNP combinations discriminating human populations from HapMap data. IEEE Transactions on Nanobioscience, DOI (identifier) 10.1109/TNB.2015.2391134, 2015. (SCI, Impact factor:1.29)
[33] Wooyoung Kim, Min Li*, Jianxin Wang, and Yi Pan, Detection of Essential Proteins in a PPI Network with Network Motif and Gene Ontology. Int. J. DataMing and Bioinformatics. Accepted
[34] Jun Ren, Jianxin Wang, Min Li, Fangxiang Wu. Discovering essential proteins based on PPI network and protein complex. Int. J. DataMing and Bioinformatics. Accepted
[35] Gamage Upeksha Ganegoda, Min Li, Weiping Wang, and Qilong Feng*. Heterogeneous Network Model to Infer Human Disease-Long Non Coding RNA Associations. IEEE Transactions on Nanobioscience, DOI (identifier) 10.1109/TNB.2015.2391133,2015. (SCI, Impact factor:1.29)
[36] Lin Wu, Yichao Shen, Min Li, and Fang-Xiang Wu. Network Output Controllability-Based Method for Drug Target Identification. IEEE Transactions on Nanobioscience. DOI (identifier) 10.1109/TNB.2015.2391175, 2015. (SCI, Impact factor:1.29)
[37] Xiaoqing Peng, Jianxing Wang, Zhen Zhang, Qianghua Xiao, Min Li, and Yi Pan. Re-alignment of the unmapped reads with base quality score. BMC Bioinformatics, 2015, 16(Suppl 5):S8
[38] Weijie Chen, Min Li*, Xuehong Wu, and Jianxin Wang. Identifying protein complexes based on the integration of PPI network and gene expression data. Int. J. Bioinformatics Research and Applications, 2015, Vol. 11, No. 1, pp.30–44.
[39] Min Li, Ruiqing Zheng, Hanhui Zhang, Jianxin Wang, and Yi Pan. Effective identification of essential proteins based on priori knowledge, network topology and gene expressions. Methods,2014,67(3):325-333. (SCI, Impact factor:4.159) ESI Top1%
[40] Min Li, Yu Lu, Jianxin Wang, Fang-Xiang Wu, Yi Pan. A topology potential-based method for identifying essential proteins from PPI networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI 10.1109/TCBB.2014.2361350, 2014
[41] Min Li, Weijie Chen, Jianxin Wang, Fang-Xiang Wu, and Yi Pan. Identifying dynamic protein complexes based on gene expression profiles and PPI Networks. BioMed Research International. Volume 2014 (2014), Article ID 375262, 10 pages. (SCI, Impact factor:2.88)
[42] Min Li, Jiayi Zhang, Qing Liu, Jianxin Wang, Fang-Xiang Wu. Prediction of disease-related genes based on weighted tissue-specific network by using DNA methylation. BMC Medical Genomics, 2014, 7(Suppl 2):S4. (SCI, Impact factor:3.91)
[43] Min Li, Qi Li, Gamage Upeksha Ganegoda, Jianxin Wang, FangXiang Wu, and Yi Pan. Prioritization of orphan disease-causing genes using topological feature and GO similarity between proteins in interaction networks. SCIENCE CHINA Life Sciences. Sci China Life Sci, 2014, 57:1064–1071. (SCI, Impact factor:1.512)
[44] Qiling Li, Min Li, Li Ma, Wenzhi Li, Xuehong Wu, Jendai Richards, Guoxing Fu, Wei Xu, Tameka Bythwood, Xu Li, Jianxin Wang, Qing Song. A Method to Evaluate Genome-wide Methylation in Archival Formalin-fixed, Paraffin-embedded Ovarian Epithelial Cells. Plos ONE, 2014, 9(8): e104481. (SCI, Impact factor:4.159)
[45] Bolin Chen, Min Li, Jianxin Wang, Fang-Xiang Wu. Disease gene identification by using graph kernels and Markov random fields. Sci China Life Sci, 2014, 57(11): 1054-1063. (SCI, Impact factor:1.512)
[46] Junwei Luo, Jianxin Wang , Zhen Zhang, Fang-Xiang Wu, Min Li, and Yi Pan. EPGA: de novo assembly using the distributions of reads and insert size. Bioinformatics, doi:10.1093/bioinformatics/btu762, 2014. (SCI, Impact factor: 4.621)
[47] Xiwei Tang, Jianxin Wang, Min Li, Yiming He, and Yi Pan. A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search. BioMed Research International, Volume 2014 (2014), Article ID 354539, 8 pages. (SCI, Impact factor:2.88)
[48] Bihai Zhao, Jianxin Wang, Min Li, Fang-xiang Wu and Yi Pan. Detecting Protein Complex Based on Uncertain Graph Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014, 11(3): 486-497. (SCI, Impact factor:1.62)
[49] Bihai Zhao, Jianxin Wang, Min Li,, Fang-xiang Wu, Yi Pan. Prediction of essential proteins based on overlapping essential modules. IEEE Transactions on Nanobioscience, 2014,13(4):1-10. (SCI, Impact factor:1.29)
[50] Bolin Chen, JianXin Wang, Min Li, and FangXiang Wu: Identifying disease genes by integrating multiple data sources, BMC Medical Genomics, 2014, 7(Suppl 2):S2. (SCI, Impact factor:3.91)
[51] Gamage Upeksha Ganegoda, JianXin Wang , Fang-Xiang Wu, Min Li. Prediction of disease genes using tissue-specified gene-gene network. BMC Systems Biology, 2014, 8(Suppl 3):S3.(SCI, Impact factor:2.982)
[52] Wei Peng, Jianxin Wang, Juan Cai, Lu Chen, Min Li, Fangxiang Wu. Improving protein function prediction using domain and protein complexes in PPI networks. BMC Systems Biology, 2014,8:35 (SCI, Impact factor:2.982)
[53] Jianxin Wang, Jiancheng Zhong, Gang Chen, Min Li, Yi Pan. ClusterViz: a Cytoscape APP for Clustering Analysis of Biological Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI 10.1109/TCBB.2014.2361348, 2014.
[54] Jin Liu, Min Li, Jianxin Wang*, Fangxiang Wu, Tianming Liu, and Yi Pan. A Survey of MRI-Based Brain Tumor Segmentation Methods. TSINGHUA SCIENCE AND TECHNOLOGY, 2014, 19(6):578-595.
[55] Min Li, Xuehong Wu, Yi Pan, and Jianxin Wang*. hF-measure: a new measurement for evaluating clusters from protein interaction networks, PROTEOMICS, 2013, 13(2):291-300.(SCI, Impact factor: 4.505)
[56] Min Li, Jianxin Wang, Huan Wang, and Yi Pan. Identification of Essential Proteins from Weighted Protein Interaction Networks. J Bioinform Comput Biol 2013, 11(3): 1341002,(SCI, Impact factor: 0.931)
[57] Jun Ren, Jianxin Wang, Min Li, Lusheng Wang. Identifying protein complexes based on density and modularity in Protein-Protein Interaction Network. BMC Systems Biology. 2013, 7(Suppl 4):S12
[58] Qiling Li, Ting Kang, Xiaohua Tian, Yamin Ma, Min Li, Jendai Richards, Tameka Bythwood, Yueling Wang, Xu Li, Dong Liu,Li Ma, Qing Song. Multimeric Stability of Human C-reactive Protein in Archived Specimens. PLoS ONE, 2013, 8(3): e58094.(SCI, Impact factor: 4.351)
[59] Jianxin Wang, Xiaoqing Peng, Min Li, Yi Pan. Construction and application of dynamic protein interaction network based on time course gene expression data. PROTEOMICS, 2013, 13(2):301-312.(SCI, Impact factor: 4.505)
[60] Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li and Yi Pan. An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation. BMC Systems Biology, 2013, 7:28(SCI, Impact factor:3.57)
[61] Murtada Khalafallah Elbashir, Yu Sheng, Jianxin Wang, Fangxiang Wu, Min Li. Predicting Beta-turns in Protein Using Kernel Logistic Regression. BioMed Research International. Volume 2013 (2013), Article ID 870372, 9 pages.
[62] Min Li, Hanhui Zhang, Jianxin Wang, and Yi Pan. A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data, BMC Systems Biology, 2012, 6:15.(SCI, Impact factor:3.57)
[63] Min Li, Xuehong Wu, Jianxin Wang, and Yi Pan. Towards the identification of protein Complexes and Functional Modules by integrating PPI network and gene expression data. BMC Bioinformatics, 2012, 13:109(SCI, Impact factor: 3.03)
[64] Jianxin Wang, Min Li, Huan Wang, Yi Pan. Identification of Essential Proteins Based on Edge Clustering Coefficient. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, 9(4):1070-1080.(SCI, Impact factor: 2.28)
[65] Jianxin Wang, Gang Chen, Binbin Liu, Min Li, Yi Pan, Identifying Protein Complexes from Interactome Based on Essential Proteins and Local Fitness Method, IEEE Transactions on Nanobioscience, 2012, 11(4):324-335. (SCI, Impact factor:1.67)
[66] Jianxin Wang, Jun Ren, Min Li, Fangxiang Wu. Identification of hierarchical and overlapping functional modules in PPI networks. IEEE Transactions on NanoBioscience 2012, 11(4):386-393.
[67] Min Li, Jianxin Wang, Xiang Chen, Huan Wang and Yi Pan. A local average connectivity-based method for identifying essential proteins from the network level. Computational Biology and Chemistry 35 (2011), pp. 143-150 (SCI, Impact factor:1.37
[68] Jianxin Wang, Min Li*, Jian’er Chen and Yi Pan. A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8(3):607-620.(SCI, Impact factor: 2.28)
[69] Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li*, Gang Chen, Yi Pan: A comparison of the functional modules identified from time course and static PPI network data. BMC Bioinformatics, 2011, 12:339(SCI, Impact factor:3.49)
[70] Wooyoung Kim, Min Li*, Jianxin Wang, Yi Pan. Biological Network Motif Detection and Evaluation. BMC Systems Biology 2011, 5(Suppl 3):S5(SCI, Impact factor:3.57)
[71] Jianxin Wang, Gang Chen, Min Li, Yi Pan. Integration of Breast Cancer Gene Signatures based on Graph Centrality. BMC Systems Biology 2011, 5(Suppl 3):S10(SCI, Impact factor:3.57)
[72] Ziyang Chen, Zhao Cai, Min Li*, Binbin Liu. Using search engine technology for protein function prediction. Int. J. Bioinformatics Research and Applications, 2011,7(1): 101-113.
[73] Min Li, Jianxin Wang, Jianer Chen, Zhao Cai, and Gang Chen. Identifying the Overlapping Complexes in Protein Interaction Networks. Int. J. DataMing and Bioinformatics, 2010, 4(1):91-108. (SCI, Impact factor: 0.667)
[74] Jianxin Wang, Min Li*, Youping Deng, Yi Pan. Recent Advances in Clustering Methods for Protein Interaction Networks. BMC Genomics 2010, 11(Suppl 3):S10. doi:10.1186/1471-2164-11-S3-S10(SCI, Impact factor:3.76)
[75] Jianxin Wang, Binbin Liu, Min Li* and Yi Pan. Identifying protein complexes from interaction networks based on clique percolation and distance restriction. BMC Genomics, Volume 11, Suppl 2, S10.
[76] Min Li, Jianxin Wang, Jian’er Chen and Yi Pan. Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. Lecture Notes in Bioinformatics 5542, 75-86
[77] Min Li, Jian’er Chen, Jianxin Wang, Bin Hu, and Gang Chen. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics, 2008, 9:398. (SCI, Impact factor: 3.03)

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