Selected Publications (from >70 SCI papers)


1. Zhao XM, Li S. HISP: A Hybrid Intelligent Approach for Identifying Directed Signaling Pathways. Journal of Molecular Cell Biology, 2017;

2. Wang YY, Bai H, Zhang RZ, Yan H, Ning K, Zhao XM, et al. Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. Oncotarget, 2017;8 (55):93957-93968.

3. Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH. MVP: a microbe-phage interaction database. Nucleic Acids Research, 2017;doi: 10.1093/nar/gkx1124.

4. Peng S, Yang S, Su W, Zhang X, Zhang T, Liu W, Zhao XM. A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017;PP (99):1-1.

5. Xie WB, Yan H, Zhao XM, et al. EmDL: Extracting miRNA-Drug Interactions from Literature. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017;PP (99):1-1.

6. He F, Zhu G, Wang YY, Zhao XM, et al. PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-scale Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017;14(3):678-686.

7. Zhu G, Yang H, Chen X, Wu J, Zhang Y, Zhao XM. CSTEA: a webserver for the Cell State Transition Expression Atlas. Nucleic Acids Research, 2017;45 (Web Server issue).

8. Qin GM, Li RY, Zhao XM. PhosD: inferring kinase-substrate interactions based on protein domains. Bioinformatics, 2017;33(8):1197-1204.

9. Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM. GEAR: A database of Genomic Elements Associated with drug Resistance. Scientific Reports, 2017;7:44085.


10. Qin GM, Li RY, Zhao XM. Identifying disease associated miRNAs based on protein domains. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016;13(6):1027-1035.

11. Zhang XF, Ou-Yang L, Zhao XM, Yan H. Differential network analysis from cross-platform gene expression data. Scientific Reports, 2016;6:34112.

12. Lee JH, Zhao XM, Yoon I, Lee JY, et al. Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers. Cell Discovery, 2016;2:16025.

13. Zhang XD, Song J, Bork P, Zhao XM. The exploration of network motifs as potential drug targets from post-translational regulatory networks. Scientific Reports, 2016;6:20558.

14. Qin GM, Hou YB, Zhao XM. A systematic exploration of the associations between amino acid variants and post-translational modifications. Neurocomputing, 2016;206: 13-18.

15. Zhu G, Wu A, Xu XJ, Xiao PP, Lu L, Zhao XM, et al. PPIM: A Protein-Protein Interaction Database for Maize. Plant Physiology, 2016;170(2):618-26.


16. Downs CA, Kreiner L, Zhao XM, Trac P, Johnson NM, Hansen JM, Brown LA, Helms MN. Oxidized glutathione (GSSG) inhibits epithelial sodium channel activity in primary alveolar epithelial cells. American Journal of Physiology-Lung Cellular and Molecular Physiology, 2015;308(9):L943-52.

17. Zhao XM, Liu KQ, Zhu G, He F, Duval B, Richer JM, Huang DS, Jiang CJ, Hao JK, Chen L. Identifying cancer-related microRNAs based on gene expression data. Bioinformatics, 2015;31(8):1226-34.

18. Zhang X, Zhao J, Hao JK, Zhao XM, Chen L. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research, 2015;43(5):e31.

19. Wang HQ, Zheng CH, Zhao XM. jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data. Bioinformatics, 2015;31(4):572-80.


20. Wang M, Zhao XM, Tan H, Akutsu T, Whisstock J, and Song J. Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinformatics, 2014;30(1):71-80.

21. Chen WH, Zhao XM, Noort V and Bork P. Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication". PLoS Computational Biology, 2014;10(7):e1003758.

22. Zhao XM, Chen L. Network-based biomarkers for complex diseases. Journal of Theoretical Biology. 2014;362:1-2.

23. Zhao XM, Ngom A, Hao JK. Pattern recognition in bioinformatics. Neurocomputing, 2014;145:1-2.

24. Qin G, Zhao XM. A survey on computational approaches to identifying disease biomarkers based on molecular networks. Journal of theoretical biology, 2014;362:9-16.


25. Wang H, Zheng H, Azuaje F, Zhao XM. Drug-Domain Interaction Networks in Myocardial Infarction. IEEE Transactions on NanoBioscience, 2013;12(3):182-8.

26. Chen WH, Zhao XM, van Noort V, Bork P. Human monogenic disease genes have frequently functionally redundant paralogs. PLoS Computational Biology, 2013;9(5):e1003073.

27. Liu X, Zhang X, Tang WH, Chen L, Zhao XM. eFG: an electronic resource for Fusarium graminearum. Database (Oxford), 2013;2013:bat042.

28. Liu X, Liu R, Zhao XM, Chen L. Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Medical Genomics, 2013;6 Suppl 2:S8.

29. Sun C, Shi ZZ, Zhou X, Chen L, Zhao XM. Prediction of S-Glutathionylation Sites Based on Protein Sequences. PLoS ONE, 2013;8(2):e55512.

30. Zhang X, Liu K, Liu ZP, Duval B, Richer JM, Zhao XM, Hao JK, Chen L. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, 2013;29(1):106-13.


31. Wang J, Hu F, Cheng H, Zhao XM, Wen T. A systems biology approach to identifying the signaling network regulated by Rho-GDI-γ during neural stem cell differentiation, Molecular BioSystems, 2012;8(11):2916-23.

32. Wang M, Zhao XM, Takemoto K, Xu H, Li Y, Akutsu T, Song J. FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model, PLoS ONE, 2012;7(8):e43847.

33. Liu KQ, Liu ZP, Hao JK, Chen L, Zhao XM. Identifying dysregulated pathways in cancers from pathway interaction networks, BMC Bioinformatics, 2012;13:126.

34. Liu X, Liu ZP, Zhao XM, Chen L. Identifying disease genes and module biomarkers by differential interactions, Journal of the American Medical Informatics Association : JAMIA, 2012;19(2):241-8.

35. Wang YY, Nacher JC, Zhao XM. Predicting drug targets based on protein domains, Molecular BioSystems, 2012;8(5):1528-34.

36. Wang YY, Xu KJ, Song J, Zhao XM. Exploring drug combinations in genetic interaction network, BMC Bioinformatics, 2012;13 Suppl 7:S7.

37. Zhang X, Zhao XM, He K, Lu L, Cao Y, Liu J, Hao JK, Liu ZP, Chen L. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information, Bioinformatics, 2012;28(1):98-104.


38. Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. Prediction of drug combinations by integrating molecular and pharmacological data, PLOS Computational Biology, 2011;7(12):e1002323.

39. Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. Drug discovery in the age of systems biology: the rise of computational approaches for data integration, Current Opinion in Biotechnology. 2012;23(4):609-16.

40. Sapkota A, Liu X, Zhao XM, Cao Y, Liu J, Liu ZP, Chen L. DIPOS: database of interacting proteins in Oryza sativa, Molecular BioSystems, 2011;7(9):2615-21.


41. Tang X, Zhang ZY, Zhang WJ, Zhao XM, Li X, Zhang D, Liu QQ, Tang WH. Global Gene Profiling of Laser-Captured Pollen Mother Cells Indicates Molecular Pathways and Gene Subfamilies Involved in Rice Male Meiosis, Plant Physiology, 2010;154(4):1855-70.

42. Liu X, Tang WH, Zhao XM, Chen L. A network approach to predict pathogenic genes for Fusarium graminearum, PLoS ONE, 2010;5(10). pii: e13021.

43. Xia JF, Zhao XM, Song J, Huang DS. APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility, BMC Bioinformatics, 2010;11:174.

44. Wu Z, Zhao XM, Chen L. A Systems biology approach to identify effective cocktail drugs, BMC Systems Biology (OSB2009 special issue), 2010;4 Suppl 2:S7.

45. Sun C, Zhao XM, Tang W, Chen L. FGsub: Fusarium graminearum protein subcellular localization prediction from primary structures, BMC Systems Biology (OSB2009 special issue), 2010;4 Suppl 2:S12.

46. Zhao XM, Cheung YM, Huang DS. Analysis of Gene Expression Data Using RPEM Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate, International Journal of Pattern Recognition and Artificial Intelligence, 2010;24(4): 651-666.

47. Zhao XM, Chen L, Aihara K. A discriminative approach to identifying domain-domain interactions from protein-protein interactions, Proteins, 2010;78(5):1243-53.


48. Zhao XM, Zhang XW, Tang WH, Chen L. FPPI: Fusarium graminearum protein-protein interaction database, Journal of Proteome Research, 2009;8(10):4714-21.

49. Zhao XM, Wang RS, Chen L, Aihara K. Automatic modeling of signaling pathways by network flow model, Journal of Bioinformatics and Computational Biology, 2009;7(2):309-22.


50. Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming, Nucleic Acids Research, 2008;36(9):e48.

51. Zhao XM, Wang Y, Chen L, Aihara K. Gene function prediction using labeled and unlabeled data, BMC Bioinformatics, 2008;9:57.

52. Zhao XM, Li X, Chen L, Aihara K. Protein classification with imbalanced data, Proteins, 2008;70(4):1125-32.

53. Zhao XM, Wang Y, Chen L, Aihara K. Protein domain annotation with integration of heterogeneous information sources, Proteins, 2008;72(1):461-73.

54. Zhao XM, Chen L, Aihara K. Protein function prediction with high-throughput data, Amino Acids, 2008;35(3):517-30.


55. Zhao XM, Du JX, Wang HQ, Zhu Y, Li Y. A new technique for selecting features from protein sequences, International Journal of Pattern Recognition and Artificial Intelligence, 2006;20(2): 271-283.

56. Huang DS, Zhao XM , Huang GB, Cheung YM. Classifying protein sequences using hydropathy blocks, Pattern Recognition, 2006;39: 2293-2300.


57. Zhao XM, Cheung YM, Huang DS. A novel approach to extracting features from motif content and protein composition for protein sequence classification, Neural Networks, 2005;18(8):1019-28.

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