Affiliation: Harbin Medical University
- Zhao Z, Li Y, Chen H, Lu J, Thompson P, Chen J, et al. PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders. BMC Med Genomics. 2014;7:71 pubmed publisher..The PD_NGSAtlas will be a valuable data resource and will enable researchers to investigate the pathophysiology and aetiology of disease in detail. The database is available at http://bioinfo.hrbmu.edu.cn/pd_ngsatlas/. ..
- Wang P, Ning S, Zhang Y, Li R, Ye J, Zhao Z, et al. Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res. 2015;43:3478-89 pubmed publisher..In summary, this study uncovered and systematically characterized global properties of human lncACTs that may have prognostic value for predicting clinical outcome in cancer patients. ..
- Zhao T, Xu J, Liu L, Bai J, Wang L, Xiao Y, et al. Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data. FEBS Lett. 2015;589:521-31 pubmed publisher..Together, we describe a method for the analysis of lncRNAs and demonstrate how integration of multi-omics data can improve understanding of lncRNAs. ..
- Li Y, Xu J, Ju H, Xiao Y, Chen H, Lv J, et al. A network-based, integrative approach to identify genes with aberrant co-methylation in colorectal cancer. Mol Biosyst. 2014;10:180-90 pubmed publisher..These results show that the network-centric method could identify novel disease biomarkers and model how oncogenic lesions mediate epigenetic changes, providing important insights into tumorigenesis. ..
- Ping Y, Deng Y, Wang L, Zhang H, Zhang Y, Xu C, et al. Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data. Nucleic Acids Res. 2015;43:1997-2007 pubmed publisher..Together, these results demonstrate integrative multi-omics data can identify driver modules and uncover their dysregulated genes, which is useful for interpreting cancer genome. ..
- Zhao H, Zhang G, Pang L, Lan Y, Wang L, Yu F, et al. 'Traffic light rules': Chromatin states direct miRNA-mediated network motifs running by integrating epigenome and regulatome. Biochim Biophys Acta. 2016;1860:1475-88 pubmed publisher..The findings form a basis for further understanding of the complicated roles of epigenetic marks on regulatory circuits. ..
- Wang P, Zhi H, Zhang Y, Liu Y, Zhang J, Gao Y, et al. miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. Database (Oxford). 2015;2015: pubmed publisher..A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge. ..
- Zhang H, Deng Y, Zhang Y, Ping Y, Zhao H, Pang L, et al. Cooperative genomic alteration network reveals molecular classification across 12 major cancer types. Nucleic Acids Res. 2017;45:567-582 pubmed publisher..In summary, our method can be effectively used to discover cancer-driving cooperative events that can be valuable clinical markers for patient stratification. ..
- Ning S, Yue M, Wang P, Liu Y, Zhi H, Zhang Y, et al. LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs. Nucleic Acids Res. 2017;45:D74-D78 pubmed publisher..LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases. ..
- Shao T, Wu A, Chen J, Chen H, Lu J, Bai J, et al. Identification of module biomarkers from the dysregulated ceRNA-ceRNA interaction network in lung adenocarcinoma. Mol Biosyst. 2015;11:3048-58 pubmed publisher..95. Our study about LDCCNet opens up the possibility of a new biological mechanism in cancer that could serve as a biomarker for diagnosis. ..
- Xu J, Feng L, Han Z, Li Y, Wu A, Shao T, et al. Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues. Nucleic Acids Res. 2016;44:9438-9451 pubmed..Analyzing ceRNA interactions during the development of multiple tissues will provideinsights in the regulation of normal development and the dysregulation of key mechanisms during pathogenesis. ..
- Yang H, Shang D, Xu Y, Zhang C, Feng L, Sun Z, et al. The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases. Sci Rep. 2017;7:6655 pubmed publisher..Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases. ..
- Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, et al. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinformatics. 2014;15:152 pubmed publisher..The database is available at http://bioinfo.hrbmu.edu.cn/LincSNP. ..
- Zhang C, Xu Y, Yang H, Xu Y, Shang D, Wu T, et al. sPAGM: inferring subpathway activity by integrating gene and miRNA expression-robust functional signature identification for melanoma prognoses. Sci Rep. 2017;7:15322 pubmed publisher..Taken together, the sPAGM model provided a framework for inferring subpathway activities and identifying functional signatures for clinical applications. ..
- Li Y, Xu J, Shao T, Zhang Y, Chen H, Li X. RNA Function Prediction. Methods Mol Biol. 2017;1654:17-28 pubmed publisher..We consider that the application of these techniques can provide valuable functional and mechanistic insights into ncRNAs, and that they are crucial steps in future functional studies. ..
- Wang H, Zheng H, Wang C, Lu X, Zhao X, Li X. Insight into HOTAIR structural features and functions as landing pads for transcription regulation proteins. Biochem Biophys Res Commun. 2017;485:679-685 pubmed publisher..The detailed architectural context could yield broad biological insights and provides a framework for comprehending lncRNA structure-function interrelationships. ..
- Ning S, Zhang J, Wang P, Zhi H, Wang J, Liu Y, et al. Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers. Nucleic Acids Res. 2016;44:D980-5 pubmed publisher..With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource. ..
- Chen L, Wang H, Zhang L, Li W, Wang Q, Shang Y, et al. Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. BMC Bioinformatics. 2010;11:392 pubmed publisher..This was extended to causal dysfunctions of some complexes maintained by several physically interacting proteins, thus coordinating several metabolic pathways that directly underlie cancer. ..