%0 Journal Article %1 Zhang2011DDN %A Zhang, Bai %A Tian, Ye %A Jin, Lu %A Li, Huai %A Shih, Ie-Ming %A Madhavan, Subha %A Clarke, Robert %A Hoffman, Eric P. %A Xuan, Jianhua %A Hilakivi-Clarke, Leena %A Wang, Yue %D 2011 %J Bioinformatics %K differential-analysis networks %N 7 %P 1036--1038 %R 10.1093/bioinformatics/btr052 %T DDN: a caBIG® analytical tool for differential network analysis %U http://dx.doi.org/10.1093/bioinformatics/btr052 %V 27 %X Summary: Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG® 's In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.Availability: The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htmContact: yuewang@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.

@article{Zhang2011DDN, abstract = {Summary: Differential dependency network ({DDN}) is a {caBIG}® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under {caBIG}® 's In Silico Research Centers of Excellence ({ISRCE}) Program, {DDN} enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. {DDN} also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, {CytoDDN}, to integrate network analysis and visualization {seamlessly.Availability}: The Java and {MATLAB} source code can be downloaded at the authors' web site {http://www.cbil.ece.vt.edu/software.htmContact}: {yuewang@vt.eduSupplementary} information: Supplementary data are available at Bioinformatics online.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Zhang, Bai and Tian, Ye and Jin, Lu and Li, Huai and Shih, Ie-Ming and Madhavan, Subha and Clarke, Robert and Hoffman, Eric P. and Xuan, Jianhua and Hilakivi-Clarke, Leena and Wang, Yue}, biburl = {https://www.bibsonomy.org/bibtex/2334d98751f72541f88ffd58ef152bbe6/karthikraman}, citeulike-article-id = {8789018}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btr052}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/early/2011/02/03/bioinformatics.btr052.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/early/2011/02/03/bioinformatics.btr052.full.pdf}, citeulike-linkout-3 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065688/}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/21296752}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=21296752}, day = 1, doi = {10.1093/bioinformatics/btr052}, interhash = {7759793b03012990804866dda75a90f6}, intrahash = {334d98751f72541f88ffd58ef152bbe6}, issn = {1367-4811}, journal = {Bioinformatics}, keywords = {differential-analysis networks}, month = apr, number = 7, pages = {1036--1038}, pmcid = {PMC3065688}, pmid = {21296752}, posted-at = {2011-02-09 08:41:45}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {{DDN}: a {caBIG}® analytical tool for differential network analysis}, url = {http://dx.doi.org/10.1093/bioinformatics/btr052}, volume = 27, year = 2011 }