1. Li C#, Han J#, Yao Q#, Zou C, Xu Y, Zhang C, Shang D, Zhou L, Sun Z, Li J, Zhang Y, Yang H, Gao X*, Li X*. Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic acids research. 2013;41(9):e101.(SCI IF=8.8)[PubMed]

2. Li C, Li X*, Miao Y, Wang Q, Jiang W, Xu C, Li J, Han J, Zhang F, Gong B, Xu L. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic acids research. 2009;37(19):e131.(SCI IF=7.8) [PubMed]

3. Liu W#, Li C#, Xu Y, Yang H, Yao Q, Han J, Shang D, Zhang C, Su F, Li X, Xiao Y, Zhang F, Dai M*, Li X*. Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. Bioinformatics. 2013;29(17):2169-2177.(SCI IF=5.3) [PubMed]

4. Wu B#, Li C#, Du Z, Yao Q, Wu J, Feng L, Zhang P, Li S, Xu L*, Li E*. Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma. Sci Rep. 2014 Jun 23;4:5403.(SCI IF=5.1) [PubMed]

5. Xu J#, Li C#, Li Y, Lv J, Ma Y, Shao T, Xu L, Wang Y, Du L, Zhang Y, Jiang W, Li C, Xiao Y, Li X*. MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic acids research. 2011;39(3):825-836.(SCI IF=8.0) [PubMed]

6. Qiu F#, Xu Y#,*, Li K#, Li Z#, Liu Y#, DuanMu H, Zhang S, Chang Z, Zhou Y, Zhang R, Li C, Zhang Y, Liu M, Li X. CNVD: text mining-based copy number variation in disease database. Human mutation. 2012;33(11):E2375-81.(SCI IF=6.0) [PubMed]

7. Li F#, Xu Y#, Shang D, Yang H, Liu W, Han J, Sun Z, Yao Q, Zhang C, Ma J, Su F, Feng L, Shi X, Zhang Y, Li J, Gu Q, Li X*, Li C*. MPINet: metabolite pathway identification via coupling of global metabolite network structure and metabolomic profile. Biomed Res Int. 2014;2014:325697. [PubMed]

8. Li C#, Han J#, Shang D#, Li J, Wang Y, Zhang Y, Yao Q, Zhang C, Li K*, Li X*. Identifying disease related sub-pathways for analysis of genome-wide association studies. Gene. 2012;503(1):101-109. [PubMed]

9. Li X#*, Li C#, Shang D#, Li J, Han J, Miao Y, Wang Y, Wang Q, Li W, Wu C, Zhang Y, Li X, Yao Q. The implications of relationships between human diseases and metabolic subpathways. PLoS One. 2011;6(6):e21131. [PubMed]

10. Wu B#, Li C#, Du Z, Zhou F, Xie J, Luo L, Wu J, Zhang P, Xu L*, Li E*. Functional analysis of the mRNA profile of neutrophil gelatinaseassociated lipocalin overexpression in esophageal squamous cell carcinoma using multiple bioinformatic tools. Mol Med Rep. 2014 Oct;10(4):1800-1812. [PubMed]

11. Li C#, Shang D#, Wang Y#, Li J, Han J, Wang S, Yao Q, Wang Y, Zhang Y, Zhang C, Xu Y, Jiang W, Li X*. Characterizing the network of drugs and their affected metabolic subpathways. PLoS One. 2012;7(10):e47326. [PubMed]

12. Zhang C#, Li C#, Li J#, Han J, Shang D, Zhang Y, Zhang W, Yao Q, Han L, Xu Y, Yan W, Bao Z, You G, Jiang T*, Kang C*, Li X*. Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure. PLoS One. 2014 May 8;9(5):e96908. [PubMed]

13. Li J#, Gong B#, Chen X, Liu T, Wu C, Zhang F, Li C, Li X*, Rao S*. DOSim: an R package for similarity between diseases based on Disease Ontology. BMC bioinformatics. 2011;12:266. [PubMed]

14. Shang D#, Li C#, Yao Q#, Yang H, Xu Y, Han J, Li J, Su F, Zhang Y, Zhang C, Li D*, Li X*. Prioritizing Candidate Disease Metabolites Based on Global Functional Relationships between Metabolites in the Context of Metabolic Pathways. PLoS One. 2014 Aug 25;9(8):e104934. [PubMed]

15. Li J, Li C, Han J, Zhang C, Shang D, Yao Q, Zhang Y, Xu Y, Liu W, Zhou M, Yang H, Su F, Li X*. The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. J Biomed Inform. 2014 June;49:187-197. [PubMed]

16. Chen S#, Li C#, Wu B, Zhang C, Liu C, Lin X, Wu X, Sun L, Chen B, Zhong Z*, Xu L*, Li E. Identification of differentially expressed genes and their subpathways in recurrent versus primary bone giant cell tumors. Int J Oncol. 2014 .Sep;45(3):1133-1142. [PubMed]

17. Wu B#, Luo L#, Li C, Xie J, Du Z, Wu J, Zhang P, Xu L*, Li E*. Comprehensive bioinformation analysis of the mRNA profile of fascin knockdown in esophageal squamous cell carcinoma. Asian Pacific journal of cancer prevention : APJCP. 2013;14(12):7221-7227. [PubMed]

18. Shi H, Xu J, Zhang G, Xu L, Li C, Wang L, Zhao Z, Jiang W, Guo Z*, Li X*. Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. BMC systems biology. 2013;7:101. [PubMed]

19. Zhang F#, Gao B#, Xu L, Li C, Hao D, Zhang S, Zhou M, Su F, Chen X, Zhi H, Li X*. Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast. PLoS One. 2013;8(1):e53581. [PubMed]

20. Qiao W, Cheng H, Li C, Jin H, Yang S, Li X, Zhang Y*. Identification of pathways involved in paclitaxel activity in cervical cancer. Asian Pacific journal of cancer prevention : APJCP. 2011;12(1):99-102. [PubMed]

21. Li J#, Zhang Y#, Wang Y#, Zhang C, Wang Q, Shi X, Li C, Zhang R*, Li X*. Functional combination strategy for prioritization of human miRNA target. Gene. 2014;533(1):132-141. [PubMed]

22. Wu B#, Li C#, Zhang P, Yao Q, Wu J, Han J, Liao L, Xu Y, Lin R, Xiao D, Xu L, Li E*, Li X*. Dissection of miRNA-miRNA interaction in esophageal squamous cell carcinoma. PLoS One. 2013;8(9):e73191. [PubMed]

23. Liu W, Bai X#, Liu Y#, Wang W, Han J, Wang Q, Xu Y, Zhang C, Zhang S, Li X, Ren Z, Zhang J*, Li C*. Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case. Sci Rep. 2015 Aug 19;5:13192. (SCI IF=5.5) [PubMed]

24. Feng L, Xu Y#, Zhang Y#, Sun Z, Han J, Zhang C, Yang H, Shang D, Su F, Shi X, Li S, Li C *, Li X*. Subpathway-GMir: identifying miRNA-mediated metabolic subpathways by integrating condition-specific genes, microRNAs, and pathway topologies. Oncotarget. 2015 Oct 12. doi: 10.18632/oncotarget.5341. (SCI IF=6.3) [PubMed]

25. Han J, Shi X#, Zhang Y#, Xu Y, Jiang Y, Zhang C, Feng L, Yang H, Shang D, Sun Z, Su F, Li C*, Li X*. ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis. Sci Rep. 2015 Aug 12;5:13044. doi: 10.1038/srep13044. (SCI IF=5.5) [PubMed]

26. Lv W, Wang Q#, Chen H#, Jiang Y#, Zheng J, Shi M, Xu Y, Han J, Li C *, Zhang R*. Prioritization of rheumatoid arthritis risk subpathways based on global immune subpathway interaction network and random walk strategy. Mol Biosyst. 2015 Oct 13;11(11):2986-97. [PubMed]

27. Liu W, Wang Q#, Zhao J, Zhang C, Liu Y, Zhang J, Bai X, Li X, Feng H, Liao M, Wang W*, Li C*. Integration of pathway structure information into a reweighted partial Cox regression approach for survival analysis on high-dimensional gene expression data. Mol Biosyst. 2015 Jul;11(7):1876-86. [PubMed]

28. Zhang J, Wang Y#, Shang D#, Yu F, Liu W, Zhang Y, Feng C, Wang Q, Xu Y, Liu Y, Bai X, Li X, Li C*. Characterizing and optimizing human anticancer drug targets based on topological properties in the context of biological pathways. J Biomed Inform. 2015 Apr;54:132-140. [PubMed]

29. Shang D, Yang H#, Xu Y, Yao Q, Zhou W, Shi X, Han J, Su F, Su B, Zhang C, Li C*, Li X*. A global view of network of lncRNAs and their binding proteins. Mol Biosyst. 2015 Feb;11(2):656-663. [PubMed]

30. Deng L, Xu Y, Zhang C, Yao Q, Feng L, Li C*. A network-based strategy from the global perspective for identification of risk pathways in complex diseases. Prog Biochem Biophys. 2015 Jan 15;42(3):11.

31. Zhang C, Li C#, Xu Y#, Feng L, Shang D, Yang X, Han J, Sun Z, Li Y*, Li X*. Integrative analysis of lung development-cancer expression associations reveals the roles of signatures with inverse expression patterns. Mol Biosyst. 2015 May; PubMed [PubMed]

32. Han J, Li C#, Yang H#, Xu Y, Zhang C, Ma J, Shi X, Liu W, Shang D, Yao Q, Zhang Y, Su F, Feng L, Li X*. A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways. Journal of the Royal Society Interface. 2015 Jan 6;12(102):20140937. [PubMed]

33. Chen X, Wang Y, Wang P, Lian B, Li C, Wang J, Li X, Jiang W. Systematic Analysis of the Associations between Adverse Drug Reactions and Pathways. Biomed Res Int. 2015;2015:670949. [PubMed]

34. Zhang Y, Liu W, Xu Y, Li C, Wang Y, Yang H, Zhang C, Su F, Li Y*, Li X*. Identification of subtype specific miRNA-mRNA functional regulatory modules in matched miRNA-mRNA expression data: multiple myeloma as a case. Biomed Res Int. 2015 Mar 19;2015:501262. [PubMed]

35. Yao Q#, Xu Y#, Yang H, Shang D, Zhang C, Zhang Y, Sun Z, Shi X, Feng L, Han J, Su F, Li C *, Li X*. Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network. Sci Rep. 2015 Nov 24;5:17201. [PubMed]

36. Song C#, Zhang J#, Liu Y, Pan H, Qi HP, Cao YG, Zhao JM, Li S, Guo J, Sun HL*, Li CQ*. Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy. Oncotarget. 2016 Mar 8;7(10):10827-40. [PubMed]

37. Feng C#, Zhang J#, Li X#, Ai B, Han J, Wang Q, Wei T, Xu Y, Li M, Li S, Song C, Li C*. Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. Sci Rep. 2016 Sep 14;6:33262. [PubMed]

38. Li S, Xu Y, Sun Z, Feng L, Shang D, Zhang C, Shi X, Han J, Su F, Yang H, Zhao J, Song C, Zhang Y, Li C*, Li X*. Identification of a lncRNA involved functional module for esophageal cancer subtypes. Mol Biosyst. 2016 Aug 19. PubMed [PubMed]

39. Zhao J#, Li X#,Yao Q#, Li M, Zhang J, Ai B, Liu W, Wang Q, Feng C, Liu Y, Bai X, Song C, Li S, Li E, Xu L*, Li C*. RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method. Oncotarget. 2016 Aug 5. [PubMed]

40. Shi X#, Xu Y#, Zhang C, Feng L, Sun Z, Han J, Su F, Zhang Y*, Li C*, Li X*. Subpathway-LNCE: Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies. Oncotarget. 2016 Sep 13. PubMed [PubMed]

41. Han J#, Liu S#, Zhang Y#, Xu Y, Jiang Y, Zhang C, Li C*, Li X*. MiRSEA: Discovering the pathways regulated by dysfunctional MicroRNAs. Oncotarget. 2016 Jul 26. PubMed PMID: [PubMed]

42. Guo JC, Li CQ, Wang QY, Zhao JM, Ding JY, Li EM*, Xu LY*. Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature. Mol Biosyst. 2016 Sep 23. PubMed [PubMed]

43. Zou HY, Lv GQ, Dai LH, Zhan XH, Jiao JW, Liao LD, Zhou TM, Li CQ, Wu BL, Xu LY*, Li EM*. A truncated splice variant of human lysyl oxidase-like 2 promotes migration and invasion in esophageal squamous cell carcinoma. Int J Biochem Cell Biol. 2016 Jun;75:85-98. [PubMed]

© 2016.Harbin Medical University Chunquan Li Lab