Selected Publications

2016

106 Li M, Tang Y, Wu X, et al. C-DEVA: Detection, evaluation, visualization and annotation of clusters from biological networks[J]. Biosystems, 2016, 150: 78-86.

105 Luo H, Wang J, Li M, et al. Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm[J]. Bioinformatics, 2016: btw228.

104 Peng X, Wang J, Peng W, et al. Protein–protein interactions: detection, reliability assessment and applications[J]. Briefings in Bioinformatics, 2016: bbw066.

103 Li M, Yan X, Zhao L, et al. VAliBS: A Visual Aligner for Bisulfite Sequences[C]//Bioinformatics Research and Applications: 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings. Springer, 2016, 9683: 307.

102 Li M, Chen X, Ni P, et al. Identifying Essential Proteins by Purifying Protein Interaction Networks[C]//International Symposium on Bioinformatics Research and Applications. Springer International Publishing, 2016: 106-116.

101 Wu L, Li M, Wang J, et al. Minimum steering node set of complex networks and its applications to biomolecular networks[J]. IET systems biology, 2016, 10(3): 116-123.

100 Lan W, Wang J, Li M, et al. Predicting drug–target interaction using positive-unlabeled learning[J]. Neurocomputing, 2016.

99 Chen B, Shang X, Li M, et al. Identifying individual-cancer-related genes by re-balancing the training samples[J]. 2016.

98 Zhao B, Wang J, Li M, et al. A New Method for Predicting Protein Functions From Dynamic Weighted Interactome Networks[J]. IEEE transactions on nanobioscience, 2016, 15(2): 131-139.

97 Yaseen A, Nijim M, Williams B, et al. FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information[J]. BMC Bioinformatics, 2016, 17(8): 281.

96 Li M, Liao Z, He Y, et al. ISEA: iterative seed-extension algorithm for de novo assembly using paired-end information and insert size distribution[J]. 2016.

95 Peng X, Wang J, Huan J, et al. Double-layer clustering method to predict protein complexes based on power-law distribution and protein sublocalization[J]. Journal of theoretical biology, 2016, 395: 186-193.

2015

94 Huang S Y, Li M, Wang J, et al. HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein-and Ligand-Based Approaches[J]. Journal of chemical information and modeling, 2015.

93 Peng W, Wang J, Zhao B, et al. Identification of protein complexes using weighted PageRank-Nibble algorithm and core-attachment structure[J].IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(1): 179-192.

92 Tang Y, Li M, Wang J, et al. CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks[J]. BioSystems, 2015, 127: 67-72.

91 Min Li, Ruiqing Zheng, Qi Li, Fangxiang Wu, Zhuohua Zhang. Prioritizing Disease Genes By Using Search Engine Algorithm. Current Bioinformatics,2015. Accepted.

90 Chen B, Li M, Wang J, et al. A fast and high performance multiple data integration algorithm for identifying human disease genes[J]. BMC medical genomics, 2015, 8(Suppl 3): S2.

89 Zhong J, Wang J, Peng W, et al. A feature selection method for prediction essential protein[J]. Tsinghua Science and Technology, 2015, 20(5): 491-499.

88 Li G, Li M, Wang J, et al. A Novel Method for Predicting Essential Proteins Based on Subcellular Localization, Orthology and PPI Networks[J]. Bioinformatics Research and Applications, 2015: 427.

87 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.

86 Peng W, Wang J, Cheng Y, et al. UDoNC: an algorithm for identifying essential proteins based on protein domains and protein-protein interaction networks[J]. , IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(2): 276-288.

85 Li M, Lu Y, Wang J, et al. A topology potential-based method for identifying essential proteins from PPI networks[J]. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 2015, 12(2): 372-383.

84 Junwei Luo, Jianxin Wang, Zhen Zhang, Fang-Xiang Wu, Min Li and Yi Pan. (2015). “EPGA: de novo assembly using the distributions of reads and insert size”, Bioinformatics, 31(6), 825-833.

83 Guo, X., Yu, N., Ding, X., Wang, J., & Pan, Y. (2015). DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly. Journal of Computational Biology, 22(2), 159-177.

82 Zhen Zhang, Jianxin Wang, Junwei Luo, Xiaojun Ding, Jiancheng Zhong, Jun Wang, Fang-Xiang Wu and Yi Pan. (2015). Sprites: detection of deletions from low-coverage sequencing data by re-aligning split reads, GIW 2015, ToKyo.

81 Junwei Luo, Jianxin Wang, Weilong Li, Zhen Zhang, Fang-Xiang Wu, Min Li and Yi Pan. (2015). “EPGA2: memory-efficien de novo assembler”, Bioinformatics, 31(24), 3988-3990.

80 Xiaojun Ding; Min Li; HaiHua Gu; XiaoQing Peng; Zhen Zhang; Fangxiang Wu, "Detecting SNP Combinations Discriminating Human Populations From HapMap Data," in NanoBioscience, IEEE Transactions on , vol.14, no.2, pp.220-228, March 2015 doi: 10.1109/TNB.2015

79 Wei Peng, Jianxin Wang, Zhen Zhang and Fang-Xiang Wu, Applications of Random Walk Model on Biological Networks, Current Bioinformatics, 2015.

78 Wei Peng, Jianxin Wang, Fang-xiang Wu and Yi Pan Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison, Algorithms for Molecular Biology, 2015

77 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 (TCBB), 2015, preprint, doi: 10.1109/TCBB.201

76 Qianghua Xiao, Jianxing Wang, Xiaoqing Peng, Fangxiang Wu, Yi Pan. Identifying essential proteins from active PPI networks constructed with dynamic gene expression[J]. BMC Genomics,2015, 16(Suppl 3):S1.

75 Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li, and Yi Pan. "Re-alignment of the unmapped reads with base quality score." BMC bioinformatics 16, no. Suppl 5 (2015):S8.

74 Xiaoqing Peng, Jianxin Wang, Jun Wang, Fang-Xiang Wu, and Yi Pan. "Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks." PloS one 10, no. 6 (2015): e0130743.

2014

73 Bihai Zhao, Jianxin Wang, Min Li, Fang-xiang Wu and YiPan. Detecting Protein Complexes Based on Uncertain Graph Model[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014, 11(3): 486-497 links

72 Bihai Zhao, Jianxin Wang, Min Li, Fang-xiang Wu, Yi Pan. Prediction of essential proteins based on overlapping essential modules, IEEE Transactions on NanoBioscience, DOI (identifier) 10.1109/TNB.2014.2337912. links

71 Bolin Chen, JianXin Wang, Min Li, and FangXiang Wu: Identifying disease causing genes by integrating multiple data sources, BMC Medical Genomics, 2014, 7(Suppl 2):S2

70 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.

69 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: links

68 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. links

67 J. Wang, J. Zhong, G. Chen, M. Li, F. Wu and Y. Pan,ClusterViz: a CytoscapeAPP for Clustering Analysis of Biological Network, IEEE/ACM Transactions onComputational Biology and Bioinformatics , DOI 10.1109/TCBB.2014.2361348,2014. links

66 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. Accpted

65 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. links

64 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 Lif links

63 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[J]. Methods, 2014,67(3):325-333. links

62 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. links

61 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. links

60 Peng, W, Wang, J, Cai, J, Chen, L, Li, M, Wu, F.-X., Improving protein function prediction using domain and protein complexes in PPI networks. BMC systems biology 2014, 8 (1), 35. links

59 Tang X, Wang J, Zhong J, Pan Y. Predicting Essential proteins based on Weighted Degree Centrality[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014, 11(2): 407 - 418 links

58 Wang J, Peng X, Peng W, Wu F.X. Dynamic protein interaction network construction and applications[J]. Proteomics, 2014, 8(4-5): 338-352. links

57 Wei Peng, Jianxin Wang, Yingjiao Cheng, Yu Lu, Fangxiang Wu and Yi Pan. UDoNC: An algorithm for identifying essential proteins based on protein domains and protein-protein interaction networks, IEEE/ACM Transactions on Computational Biology and Bioinforma links

56 Xiwei Tang, Jianxin Wang, Min Li, Yiming He, and Yi Pan.A Novel Algorithm for Mining Protein Complex from the Weighted NetworkBioMed Research International, Volume 2014 (2014), Article ID 354539, 8 pages. links

55 Xuan Guo, Jianxin Wang, and Yi Pan. DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly. Journal of Computational Biology. Accpted

54 Yu Tang, Min Li, Jianxin Wang, Yi Pan, Fang-Xiang Wu. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of biological networks. BioSystems, 2014, DOI: 10.1016/j.biosystems.2014.11.005

2013

53 Jianxin Wang*, Xiaoqing Peng, Qianghua Xiao, Min Li, 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(1): 28. links

52 Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li and 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 links

51 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 links

50 Min Li, Jianxin Wang, Huan Wang, and Yi Pan. Identification of Essential Proteins from Weighted Protein Interaction Networks. J Bioinform Comput Biol 11(3): 1341002, 2013. links

49 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.

48 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. links

47 Qianghua Xiao, Jianxin Wang*, Xiaoqing Peng, Fangxiang Wu. Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles. Proteome Science, 2013, 11(Suppl 1): S20. links

46 Qingfeng Chen, Wei Lan, Jianxin Wang. Mining Featured Patterns of MiRNA Interaction Based on Sequence and Structure Similarity. 2013,10(2):415-422. links

45 Tang X, Feng Q, Wang J, et al. Clustering based on multiple biological information: approach for predicting protein complexes[J]. IET systems biology, 2013, 7(5): 223-230. links

44 Wang J, Peng W, Wu F X. Computational approaches to predicting essential proteins: a survey[J]. PROTEOMICS-Clinical Applications, 2013, 7(1-2): 181-192. links

43 Wang J, Peng X, Li M, Pan Y. Construction and application of dynamic protein interaction network based on time course gene expression data[J]. Proteomics, 2013, 13(2): 301-312. links

42 Wenjun Lin, Jianxin Wang*, Wen-Jun Zhang, Fang-Xiang Wu, An unsupervised machine learning method for assessing quality of tandem mass spectra, BMC Proteome Science, 10 (Suppl 1), S12. links

41 Zhong J, Wang J, Peng W, et al. Prediction of essential proteins based on gene expression programming[J]. BMC genomics, 2013, 14(4): 1-8. links

2012

40 Ding X, Wang W, Peng X, et al. Mining protein complexes from PPI networks using the minimum vertex cut[J]. Tsinghua Science and Technology, 2012, 17(6): 674-681. links

39 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. links

38 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. links

37 Jianxin Wang, Min Li, Huan Wang, Yi Pan. Identification of essential proteins based on edge clustering coefficient[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, 9(4): 1070-1080. links

36 Jianxin Wang, Yuannan Huang, Fang-Xiang Wu, and Yi Pan. Symmetry Compression Method for Discovering Network Motifs, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, 9(6):1776-1789. links

35 Li M, Wu X, Wang J, Pan Y. Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data[J]. BMC bioinformatics, 2012, 13(1): 109. links

34 Li-Ping Tian, Jianxin Wang, Fang-Xiang Wu. Robust and Global Delay-dependent Stability for Genetic Regulatory Networks with Parameter Uncertainties, IEEE Transaction on Nanobioscience, 2012, 11(3):251-258. links

33 M Li, H Zhang, J Wang, Y Pan. A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data[J]. BMC systems biology, 2012, 6 (1): 15. links

32 W Peng, J Wang, W Wang, Q Liu, FX Wu, Y Pan. Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks[J]. BMC systems biology, 2012, 6 (1): 87. links

2011

31 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. links

30 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 links

29 Jianxin Wang, Min Li, Jian'er Chen and Yi Pan. A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks[J]. IEEE/ACM Transactions onComputational Biology and Bioinformatics, 2011, 8(3): 607-620. links

28 Jun Ren, Jianxin Wang*, Min Li, Fangxiang Wu, Discovering essential proteins based on PPI network and protein complex. International Journal of DataMing and Bioinformatics, Accepted.

27 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 , 2011,35: 143-150 links

26 Wei Peng, Jianxin Wang*, Lu Chen, Jiancheng Zhong, Zhen Zhang and Yi Pan, Predicting protein functions by using unbalanced Bi-random walk algorithm on protein-protein interaction network and functional interrelationship network, Current Protein & Peptide links

25 Wooyoung Kim, Min Li, Jianxin Wang, Yi Pan. Biological Network Motif Detection and Evaluation. BMC Systems Biology 2011, 5(Suppl 3):S5 links

24 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 links

2010

23 Jianxin Wang*, Binbin Liu, Min Li, Yi Pan. Identifying protein complexes from interaction networks based on clique percolation and distance restriction. BMC Genomics, 2010,11 (Suppl.2):S10. links

22 Jianxin Wang, Binbin Liu, Min Li and Yi Pan. Identifying protein complexes from interaction networks based on clique percolationand distance restraction. BMC Genomics, Volume 11, Suppl 2, S10, Nov. 2010 links

21 Jianxin Wang, Min Li, Youping Deng, Yi Pan. Recent advances in clustering methods for protein interaction networks[J]. BMC genomics, 2010, 11(Suppl 3): S10. links

20 Jun Ren, Jianxin Wang*, Jianer Chen, Min Li, Gang Chen. An Agglomerate Algorithm for Mining Overlapping and Hierarchical Functional Modules in Protein Interaction Networks. Proc. 6th International Symposium on Bioinformatics Research and Applications (ISB links

19 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. links

18 Minzhu Xie, Jianxin Wang*, Jianer Chen, Jingli Wu and Xucong Liu. Computational Models and Algorithms for the Single Individual Haplotyping Problem, Current Bioinformatics, 5(1): 18-28, 2010. links

2009

17 Jingli Wu, Jianxin Wang*, Jian'er Chen. A parthenogenetic algorithm for single individual SNP haplotyping. Engineering Applications of Artificial Intelligence, 22(3): 401-406, 2009. links

16 Jingli Wu, Jianxin Wang*, Jianer Chen. A Practical Algorithm for Multiplex PCR Primer Set Selection. International Journal of Bioinformatics Research and Applications (IJBRA), 5(1): 38-49, 2009. links

15 Min Li, Jianxin Wang*, Jianer Chen, Yi Pan. Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient. Proc. 5th International Symposium on Bioinformatics Research and Applications (ISBRA 2009), links

2008

14 Jianxin Wang*, De Yang. UPNT: Uniform Projection and Neighbourhood Thresholding Method for Motif Discovery. International Journal of Bioinformatics Research and Applications (IJBRA), 4(1): 96-106, 2008. links

13 Jianxin Wang*, Zhao cai, Min li. An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks. Proc. 2008 International Conference on BioMedical Engineering and Informatics (BMEI2008), pp. 62-69, 2008. links

12 Jia-yang Peng, Lu-ming Yang, Jian-xin Wang, Zheng Liu, Ming Li: An Efficient Algorithm for Detecting Closed Frequent Subgraphs in Biological Networks. BMEI 2008:677-681 links

11 Jingli Wu, Jianxin Wang*, Jianer Chen. A Particle Swarm Optimization Algorithm Based on Optimal Result Set for Haplotyping a Single Individual. Proc. 2008 International Conference on BioMedical Engineering and Informatics (BMEI2008), pp. 395-399, 2008. links

10 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[J]. BMC bioinformatics, 2008, 9(1): 398. links

9 Min Li, Jianxin Wang*, Jianer Chen. A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks. Proc. 2008 International Conference on BioMedical Engineering and Informatics (BMEI2008), pp.3-7, 2008. links

8 Min Li'Jianxin Wang*, Jianer Chen. A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks. Proc. of Fourth International Symposium on Bioinformatics Research and Applications (ISBRA2008), pp. 208-219, 2008. links

7 Minzhu Xie, Jianer Chen, Jianxin Wang, Research on Parameterized Algorithms of the Individual Haplotyping Problem, Journal of Bioinformatics and Computational Biology, 2007, 5(3): 785-816, Imperial College Press. links

6 Minzhu Xie, Jianxin Wang*, Jian'er Chen. An Practical Exact Algorithm for the Individual Haplotyping Problem MEC. Proc. 2008 International Conference on BioMedical Engineering and Informatics (BMEI2008), pp.72-76, 2008. links

5 Minzhu Xie, Jianxin Wang*, Jianer Chen. A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors. ISBM2008, Bioinformatics, 2008, 24(13): 1105-1113. links

4 Minzhu Xie, Jianxin Wang, Jianer Chen, A Model of Higher Accuracy for the Individual Haplotyping Problem Based on Weighted SNP Fragments and Genotype with Errors'ISMB2008'Bioinformatics, i105-i113 links

3 Minzhu Xie, Jianxin Wang, Jianer Chen, A Practical Exact Algorithm for the Individual Haplotyping Problem MEC/GI. COCOON 2008, Dalian, China, June 27-29, 2008, Proceedings. Lecture Notes in Computer Science 5092 Springer 2008: 342-351 links

2 Minzhu Xie, Jianxin Wang, Jianer Chen, A Practical Parameterized Algorithm for the Individual Haplotyping Problem MLF, Proceeding of Theory and Applications of Models of Computation (TAMC2008), LNCS 4978, pp.82-93, 2008. links

1 Minzhu Xie, Jianxin Wang, Wei Zhou, Jianer Chen, A Practical Parameterized Algorithm for Weighted Minimum Letter Flips Model of the Individual Haplotyping Problem, FAW2008, Changsha, China, June 19-21, 2008, Proceeedings. Lecture Notes in Computer Science links

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