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[1]Min Li*, Jie Yang, Fang-Xiang Wu, Yi Pan,Jianxin Wang*.DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. Bioinformatics. 2018. DOI: 10.1093/bioinformatics/btx821
[2]Lin Wu, Min Li, Jianxin Wang,Fang-Xiang Wu.CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. Bioinformatics, 2017. doi.org/10.1093/bioinformatics/btx764
[3]Huimin Luo, Min Li, Shaokai Wang, Quan Liu, Yaohang Li, Jianxin Wang.Computational Drug Repositioning using Low-Rank Matrix Approximation and Randomized Algorithms. Bioinformatics
[4]Min Li*, Ruiqing Zheng, Yaohang Li, Fang-Xiang Wu,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
[5]Min Li*, Peng Ni, Xiaopei Chen, Jianxin Wang,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
[6]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
[7]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
[8]Junwei Luo, Jianxin Wang, Juan Shang, Huimin Luo, Min Li, Fangxiang Wu,Yi Pan.GapReduce: a gap filling algorithm based on partitioned read sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB.2018.2789909
[9]Min Li*, Dongyan Li, Yu Tang, FangXiang Wu,Jianxin Wang.CytoCluster: a cytoscape plugin for cluster analysis and visualization of biological networks. Int. J. Mol. Sci. 2017, 18, 1880; doi:10.3390/ijms18091880
[10]Min Li*, Zhongxiang Liao, Yiming He, Jianxin Wang, Junwei Luo,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
[11]Min Li, Ping Huang, Xiaodong Yan, Lingchen Zhao, Jianxin Wang, Fang-Xiang Wu,Yi Pan.VAliBS: a visual aligner for bisulfite sequences. BMC Bioinformatics 2017 18(Suppl 12):410
[12]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
[13]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
[14]Wei Peng, Min Li*, Lu Chen,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
[15]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
[16]Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu,Yi Pan.BOSS: a novel scaffolding algorithm based on optimized scaffold graph. Bioinformatics, 2017， 33(2):169-176
[17]Jianxin Wang, Yi Pan..Guest Editors Introduction to the Special Section on ISBRA 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(2): 314-315
[18]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, 2017, 16(7): 600-608
[19]Jin Liu, Min Li, Yi Pan, Wei Lan, Ruiqing Zheng, Fang-Xiang Wu,Jianxin Wang.Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey. Complexity. Volume 2017, Article ID 8362741, 27 pages
[20]Lin Wu, Lingkai Tang, Min Li, Jianxin Wang,Fang-Xiang Wu.Biomolecular Network Controllability With Drug Binding Information. IEEE Transactions on Nanobioscience. 2017, 16(5): 326-332
[21]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. 2017, 14(6): 1399-1409
[22]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
[23]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
[24]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
[25]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
[26]Gaoshi Li, Min Li*, Jianxin Wang*, Fang-Xiang Wu,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
[27]Sheng-You Huang, Min Li, Jianxin Wang,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
[28]Junwei Luo, Jianxin Wang, Zhen Zhang, Min Li, Fang-Xiang Wu,Yi Pan..BOSS: a novel scaffolding algorithm based on optimized scaffold graph. Bioinformatics. DOI: 10.1093/bioinformatics/btw597
[29]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
[30]Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang,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
[31]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
[32]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
[33]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
[34]Bolin Chen, Xuequn Shang, Min Li, Jianxin Wang,Fang-Xiang Wu*.Identifying individual-cancer-related genes by re-balancing the training samples. IEEE Transactions on Nanobioscience. DOI: 10.1109/TNB.2016.2553119
[35]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
[36]Lin Wu, Min Li, Jianxin Wang,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
[37]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
[38]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
[39]Wei Peng, Min Li*, Lu Chen,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
[40]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
[41]Min Li, Ruiqing Zheng, Qi Li, Fangxiang Wu, Zhuohua Zhang.Prioritizing Disease Genes By Using Search Engine Algorithm. Current Bioinformatics
[42]Xiaojun Ding, Min Li*, Haihua Gu, Zhen Zhang,Fangxiang Wu..Detecting SNP combinations discriminating human populations from HapMap data. IEEE Transactions on Nanobioscience, DOI (identifier) 10.1109/TNB.2015.2391134, 2015
[43]Wooyoung Kim, Min Li*, Jianxin Wang,Yi Pan.Detection of Essential Proteins in a PPI Network with Network Motif and Gene Ontology. Int. J. DataMing and Bioinformatics
[44]Jun Ren, Jianxin Wang, Min Li, Fangxiang Wu.Discovering essential proteins based on PPI network and protein complex. Int. J. DataMing and Bioinformatics
[45]Gamage Upeksha Ganegoda, Min Li, Weiping Wang,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
[46]Lin Wu, Yichao Shen, Min Li,Fang-Xiang Wu.Network Output Controllability-Based Method for Drug Target Identification. IEEE Transactions on Nanobioscience. DOI (identifier) 10.1109/TNB.2015.2391175, 2015
[47]Xiaoqing Peng, Jianxing Wang, Zhen Zhang, Qianghua Xiao, Min Li,Yi Pan.Re-alignment of the unmapped reads with base quality score. BMC Bioinformatics, 2015, 16(Suppl 5):S8
[48]Weijie Chen, Min Li*, Xuehong Wu,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
[49]Min Li, Ruiqing Zheng, Hanhui Zhang, Jianxin Wang,Yi Pan.Effective identification of essential proteins based on priori knowledge, network topology and gene expressions. Methods,2014,67(3):325-333
[50]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
[51]Min Li, Weijie Chen, Jianxin Wang, Fang-Xiang Wu,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
[52]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
[53]Min Li, Qi Li, Gamage Upeksha Ganegoda, Jianxin Wang, FangXiang Wu,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
[54]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
[55]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
[56]Junwei Luo, Jianxin Wang , Zhen Zhang, Fang-Xiang Wu, Min Li,Yi Pan..EPGA: de novo assembly using the distributions of reads and insert size. Bioinformatics, doi:10.1093/bioinformatics/btu762, 2014
[57]Xiwei Tang, Jianxin Wang, Min Li, Yiming He,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
[58]Bihai Zhao, Jianxin Wang, Min Li, Fang-xiang Wu,Yi Pan.Detecting Protein Complex Based on Uncertain Graph Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014, 11(3): 486-497
[59]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
[60]Bolin Chen, JianXin Wang, Min Li,FangXiang Wu.Identifying disease genes by integrating multiple data sources, BMC Medical Genomics, 2014, 7(Suppl 2):S2
[61]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
[62]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
[63]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
[64]Jin Liu, Min Li, Jianxin Wang*, Fangxiang Wu, Tianming Liu,Yi Pan.Survey of MRI-Based Brain Tumor Segmentation Methods. TSINGHUA SCIENCE AND TECHNOLOGY, 2014, 19(6):578-595
[65]Min Li, Xuehong Wu, Yi Pan,Jianxin Wang*.hF-measure: a new measurement for evaluating clusters from protein interaction networks, PROTEOMICS, 2013, 13(2):291-300
[66]Min Li, Jianxin Wang, Huan Wang,Yi Pan.Identification of Essential Proteins from Weighted Protein Interaction Networks. J Bioinform Comput Biol 2013, 11(3): 1341002,
[67]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
[68]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
[69]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
[70]Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li,Yi Pan.An effective method for re？ning predicted protein complexes based on protein activity and the mechanism of protein complex formation. BMC Systems Biology, 2013, 7:28
[71]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
[72]Min Li, Hanhui Zhang, Jianxin Wang,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
[73]Min Li, Xuehong Wu, Jianxin Wang,Yi Pan.Towards the identification of protein Complexes and Functional Modules by integrating PPI network and gene expression data. BMC Bioinformatics, 2012, 13:109
[74]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
[75]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
[76]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
[77]Min Li, Jianxin Wang, Xiang Chen, Huan Wang,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
[78]Jianxin Wang, Min Li*, Jian’er Chen,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
[79]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
[80]Wooyoung Kim, Min Li*, Jianxin Wang, Yi Pan.Biological Network Motif Detection and Evaluation. BMC Systems Biology 2011, 5(Suppl 3):S5
[81]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
[82]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
[83]Min Li, Jianxin Wang, Jianer Chen, Zhao Cai,Gang Chen.Identifying the Overlapping Complexes in Protein Interaction Networks:Int. J. DataMing and Bioinformatics, 2010, 4(1):91
[84]Min Li, Jianxin Wang, Jianer Chen, Zhao Cai,Gang Chen.Identifying the Overlapping Complexes in Protein Interaction Networks.[J]:Int. J. DataMing and Bioinformatics, 2010, 4(1):91
[85]Jianxin Wang, Min Li*, Youping Deng, Yi Pan.Recent Advances in Clustering Methods for Protein Interaction Networks.[J]:BMC Genomics 2010, 11(Suppl 3),2010
[86]Jianxin Wang, Binbin Liu, Min Li*,Yi Pan.Identifying protein complexes from interaction networks based on clique percolation and distance restriction.[J]:BMC Genomics, Volume 11, Suppl 2, S10.,2008
[87]Min Li, Jianxin Wang, Jian’er Chen,Yi Pan.Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient.[J]:Lecture Notes in Bioinformatics 5542, 75-86,2008
[88]Min Li, Jian’er Chen, Jianxin Wang, Bin Hu,Gang Chen..Modifying the DPClus algorithm for identifying protein complexes based on new topological structures.[J]:BMC Bioinformatics, 2008, 9:398.,2008
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