2019 Literature

Qian FC, Li XC, Guo JC, Zhao JM, Li YY, Tang ZD, Zhou LW, Zhang J, Bai XF, Jiang Y, Pan Q, Wang QY, Li EM, Li CQ, Xu LY, Lin DC. SEanalysis: a web tool for super-enhancer associated regulatory analysis. Nucleic Acids Res. 2019 Jul 2;47(W1):W248-W255. doi: 10.1093/nar/gkz302. PubMed PMID: 31028388 [PubMed]
Jiang Y, Qian F, Bai X, Liu Y, Wang Q, Ai B, Han X, Shi S, Zhang J, Li X, TangZ, Pan Q, Wang Y, Wang F, Li C. SEdb: a comprehensive human super-enhancerdatabase. Nucleic Acids Res. 2019 Jan 8;47(D1):D235-D243. doi:10.1093/nar/gky1025. PubMed PMID: 30371817 [PubMed]
Feng C, Song C, Liu Y, Qian F, Gao Y, Ning Z, Wang Q, Jiang Y, Li Y, Li M,Chen J, Zhang J, Li C. KnockTF: a comprehensive human gene expression profiledatabase with knockdown/knockout of transcription factors. Nucleic Acids Res.2019 Oct 10. pii: gkz881. doi: 10.1093/nar/gkz881. [Epub ahead of print] PubMedPMID: 31598675. [PubMed]
Zhao J, Li X, Guo J, Li M, Zhang J, Ding J, Li S, Tang Z, Qian F, Li Y, Wang Q, Li C, Li E, Xu L. ReCirc: prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays. Mol Omics. 2019 Apr 1;15(2):150-163. doi: 10.1039/c8mo00252e. Epub 2019 Mar 27. PubMed PMID: 30916068. [PubMed]
Meng Li # , Jianmei Zhao # , Xuecang Li # , Yang Chen, Chenchen Feng,Fengcui Qian, Yuejuan Liu, Jian Zhang, Jianzhong He, Bo Ai, Ziyu Ning,Wei Liu, Xuefeng Bai, Xiaole Han, Zhiyong Wu, Xiue Xu, Zhidong Tang,Qi Pan, Liyan Xu, Chunquan Li*, Qiuyu Wang* and Enmin Li*.HiFreSP: A novel high-frequency sub-pathway mining approach to identify robust prognostic gene signatures.Brief Bioinform.2019 July 27.doi: 10.1093/bib/bbz078.PMID: 31350847. [PubMed]
Ning Z#, Feng C#, Song C#, Liu W, Shang D, Li M, Wang Q, Zhao J, Liu Y, Chen J,Yu X*, Zhang J*, Li C * .Topologically inferring active miRNA-mediated subpathways toward precise cancer classification by directed random walk. Mol Oncol. 2019 Aug 13. [PubMed]

2018 Literature

Tang Z, Li X, Zhao J, Qian F, Feng C, Li Y, Zhang J, Jiang Y, Yang Y, Wang Q, Li C. TRCirc: a resource for transcriptional regulation information of circRNAs. Brief Bioinform. 2018 Sep 3. doi: 10.1093/bib/bby083. [Epub ahead of print]PubMed PMID: 30184150. [PubMed]
Feng C#, Song C#, Ning Z#, Ai B, Wang Q, Xu Y, Li M, Bai X, Zhao J, Liu Y, Li X, Zhang J*, Li C*. ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies. J Cell Mol Med. 2018 Nov 12. doi:10.1111/jcmm.13997. [Epub ahead of print] PubMed PMID: 30421585. [PubMed]
Han J*#, Liu S#, Jiang Y#, Xu C#, Zheng B, Jiang M, Yang H, Su F, Li C*, Zhang Y*.Inference of patient-specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer. J Cell Mol Med. 2018 Jul 4. doi: 10.1111/jcmm.13720. [Epub ahead of print] PubMed PMID: 29971923. [PubMed]
Zhang J, Feng C, Song C, Ai B, Bai X, Liu Y, Li X, Zhao J, Shi S, Chen X, SuX, Li C. Identification and analysis of a key long non-coding RNAs(lncRNAs)-associated module reveal functional lncRNAs in cardiac hypertrophy. JCell Mol Med. 2018 Feb;22(2):892-903. doi: 10.1111/jcmm.13376. Epub 2017 Nov 20. PubMed PMID: 29154475. [PubMed]

2017 Literature

Zhang HYang H#, Shang D#, Xu Y, Zhang C, Feng L, Sun Z, Shi X, Zhang Y, Han J, Su F, Li C*, Li X*. The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases. Sci Rep. 2017 Jul 27;7(1):6655. doi: 10.1038/s41598-017-06897-3. PubMed PMID: 28751672; PubMed Central PMCID: PMC5532316. [PubMed]
Han J#, Liu S#, Sun Z, Zhang Y, Zhang F, Zhang C, Shang D, Yang H, Su F, Xu Y, Li C*, Ren H*, Li X*. LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. Sci Rep. 2017 Apr 20;7:46566. doi: 10.1038/srep46566. PubMed PMID: 28425476; PubMed Central PMCID: PMC5397852. [PubMed]
Song C#, Zhang J#, Qi H#, Feng C, Chen Y, Cao Y, Ba L, Ai B, Wang Q, Huang W, Li C *, Sun H*. The global view of mRNA-related ceRNA cross-talks across cardiovascular diseases. Sci Rep. 2017 Aug 31;7(1):10185. doi: 10.1038/s41598-017-10547-z. PubMed PMID: 28860540; PubMed Central PMCID: PMC5579186. [PubMed]
Li C#*, Wang Q#*, Ma J#, Shi S, Chen X, Yang H, Han J*. Integrative Pathway Analysis of Genes and Metabolites Reveals Metabolism Abnormal Subpathway Regions and Modules in Esophageal Squamous Cell Carcinoma. Molecules. 2017 Sep 22;22(10). pii: E1599. doi: 10.3390/molecules22101599. PubMed PMID: 28937628. [PubMed]
Li CQ #, Huang GW#, Wu ZY#, Xu YJ, Li XC, Xue YJ, Zhu Y, Zhao JM, Li M, Zhang J, Wu JY, Lei F, Wang QY, Li S, Zheng CP, Ai B, Tang ZD, Feng CC, Liao LD, Wang SH, Shen JH, Liu YJ, Bai XF, He JZ, Cao HH, Wu BL, Wang MR, Lin DC, Koeffler HP, Wang LD, Li X*, Li EM*, Xu LY*. Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma. Oncogenesis. 2017 Feb 13;6(2):e297. doi: 10.1038/oncsis.2017.1. PubMed PMID: 28194033; PubMed Central PMCID: PMC5337622. [PubMed]

2016 Literature

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]
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]
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]
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]
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]
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]

2015 Literature

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. [PubMed]
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. [PubMed]
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. [PubMed]
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]
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]
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]
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]
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. [PubMed]
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]
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]
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]

2014 Literature

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. [PubMed]
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]
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]
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]
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]
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]

2013 Literature

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. [PubMed]
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. [PubMed]
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]

2012 Literature

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]
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]

2011 Literature

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]

2009 Literature

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. [PubMed]