{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:33:36Z","timestamp":1785198816284,"version":"3.55.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,24]],"date-time":"2019-01-24T00:00:00Z","timestamp":1548288000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871026"],"award-info":[{"award-number":["11871026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61402190"],"award-info":[{"award-number":["61402190"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61602309"],"award-info":[{"award-number":["61602309"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61532008"],"award-info":[{"award-number":["61532008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei province","doi-asserted-by":"crossref","award":["2018CFB521"],"award-info":[{"award-number":["2018CFB521"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei province","doi-asserted-by":"crossref","award":["CCNU18TS026"],"award-info":[{"award-number":["CCNU18TS026"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100017622","name":"Shenzhen Research and Development program","doi-asserted-by":"crossref","award":["JCYJ20170817095210760"],"award-info":[{"award-number":["JCYJ20170817095210760"]}],"id":[{"id":"10.13039\/501100017622","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Natural Science Foundation of SZU","award":["2017077"],"award-info":[{"award-number":["2017077"]}]},{"name":"and Hong Kong Research Grants Council","award":["C1007\u201315G"],"award-info":[{"award-number":["C1007\u201315G"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>To identify biological network rewiring under different conditions, we develop a user-friendly R package, named DiffNetFDR, to implement two methods developed for testing the difference in different Gaussian graphical models. Compared to existing tools, our methods have the following features: (i) they are based on Gaussian graphical models which can capture the changes of conditional dependencies; (ii) they determine the tuning parameters in a data-driven manner; (iii) they take a multiple testing procedure to control the overall false discovery rate; and (iv) our approach defines the differential network based on partial correlation coefficients so that the spurious differential edges caused by the variants of conditional variances can be excluded. We also develop a Shiny application to provide easier analysis and visualization. Simulation studies are conducted to evaluate the performance of our methods. We also apply our methods to two real gene expression datasets. The effectiveness of our methods is validated by the biological significance of the identified differential networks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R package and Shiny app are available at https:\/\/github.com\/Zhangxf-ccnu\/DiffNetFDR.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz051","type":"journal-article","created":{"date-parts":[[2019,1,20]],"date-time":"2019-01-20T12:07:11Z","timestamp":1547986031000},"page":"3184-3186","source":"Crossref","is-referenced-by-count":17,"title":["DiffNetFDR: differential network analysis with false discovery rate control"],"prefix":"10.1093","volume":"35","author":[{"given":"Xiao-Fei","family":"Zhang","sequence":"first","affiliation":[{"name":"Central China Normal University Department of Statistics, School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, , Wuhan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le","family":"Ou-Yang","sequence":"additional","affiliation":[{"name":"Shenzhen University Department of Electronic Engineering, Guangdong Key Laboratory of Intelligent Information Processing and Shenzhen Key Laboratory of Media Security, , Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Yang","sequence":"additional","affiliation":[{"name":"Wuhan Number 1 Hospital Department of Respiratory Medicine, , Wuhan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohua","family":"Hu","sequence":"additional","affiliation":[{"name":"Drexel University Department of Information Science, College of Computing and Informatics, , Philadelphia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Yan","sequence":"additional","affiliation":[{"name":"City University of Hong Kong Department of Electronic Engineering, , Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,1,24]]},"reference":[{"key":"2023062711313421700_btz051-B1","author":"Chang","year":"2017"},{"key":"2023062711313421700_btz051-B2","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1111\/rssb.12033","article-title":"The joint graphical lasso for inverse covariance estimation across multiple classes","volume":"76","author":"Danaher","year":"2014","journal-title":"J. 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