{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T18:08:28Z","timestamp":1757700508656},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN\u2019s ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data.<\/jats:p>\n               <jats:p>Availability: Source code and compiled package are freely available for download at http:\/\/apps.cytoscape.org\/apps\/kddn<\/jats:p>\n               <jats:p>Contact: \u00a0yuewang@vt.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu632","type":"journal-article","created":{"date-parts":[[2014,10,2]],"date-time":"2014-10-02T06:07:10Z","timestamp":1412230030000},"page":"287-289","source":"Crossref","is-referenced-by-count":14,"title":["KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring"],"prefix":"10.1093","volume":"31","author":[{"given":"Ye","family":"Tian","sequence":"first","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bai","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric P.","family":"Hoffman","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Clarke","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ie-Ming","family":"Shih","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Xuan","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Herrington","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical & Computer Engineering, Virginia Tech, Arlington, VA 22203, 2 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, 3 Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, 4 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057 and 5 Department of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,9,30]]},"reference":[{"key":"2023020116152446300_btu632-B1","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/1471-2164-13-356","article-title":"Beyond differential expression: the quest for causal mutations and effector molecules","volume":"13","author":"Hudson","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020116152446300_btu632-B2","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1534\/genetics.111.130724","article-title":"The rho1 GTPase acts together with a vacuolar glutathione S-conjugate transporter to protect yeast cells from oxidative stress","volume":"188","author":"Lee","year":"2011","journal-title":"Genetics"},{"key":"2023020116152446300_btu632-B3","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/nrg3552","article-title":"Integrative approaches for finding modular structure in biological networks","volume":"14","author":"Mitra","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"2023020116152446300_btu632-B4","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12918-014-0087-1","article-title":"Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks","volume":"8","author":"Tian","year":"2014","journal-title":"BMC Systems Biol."},{"key":"2023020116152446300_btu632-B5","doi-asserted-by":"crossref","DOI":"10.1145\/2147805.2147833","article-title":"Knowledge-guided differential dependency network learning for detecting structural changes in biological networks","author":"Tian","year":"2011"},{"key":"2023020116152446300_btu632-B6","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/btn660","article-title":"Differential dependency network analysis to identify condition-specific topological changes in biological networks","volume":"25","author":"Zhang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020116152446300_btu632-B7","article-title":"Learning structural changes of Gaussian graphical models in controlled experiments","author":"Zhang","year":"2010"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/287\/49011051\/bioinformatics_31_2_287.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/2\/287\/49011051\/bioinformatics_31_2_287.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:25:10Z","timestamp":1675297510000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/2\/287\/2366083"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,30]]},"references-count":7,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2015,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu632","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,15]]},"published":{"date-parts":[[2014,9,30]]}}}