{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T23:56:45Z","timestamp":1706831805787},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The extraction of targeted subnetworks is a powerful way to identify functional modules and pathways within complex networks. Here, we present SubNet, a Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes. Designed with a graphical user-friendly interface, SubNet combines four different extraction methods, which offer the possibility to interrogate a biological network according to the question investigated. Of note, we developed a method based on the highly successful Google PageRank algorithm to extract the subnetwork using the node centrality metric, to which possible node weights of the selected genes can be incorporated.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.zdzlab.org\/1\/subnet.html<\/jats:p>\n               <jats:p>Contact: \u00a0zhengdong.zhang@einstein.yu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt430","type":"journal-article","created":{"date-parts":[[2013,8,15]],"date-time":"2013-08-15T08:23:32Z","timestamp":1376555012000},"page":"2509-2511","source":"Crossref","is-referenced-by-count":10,"title":["SubNet: a Java application for subnetwork extraction"],"prefix":"10.1093","volume":"29","author":[{"given":"Quanwei","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA"}]},{"given":"Zhengdong D.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,13]]},"reference":[{"key":"2023012810465848000_btt430-B1","first-page":"573","article-title":"An approximate solution for the Steiner problem in graphs","volume":"24","author":"Takahashi","year":"1980","journal-title":"Math. Japonica"},{"key":"2023012810465848000_btt430-B2","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1006\/jagm.1995.1029","article-title":"A nearly best-possible approximation algorithm for node-weighted Steiner trees","volume":"19","author":"Klein","year":"1995","journal-title":"J. Algorithms"},{"key":"2023012810465848000_btt430-B4","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1093\/bioinformatics\/btq105","article-title":"Pathway discovery in metabolic networks by subgraph extraction","volume":"26","author":"Faust","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810465848000_btt430-B5","article-title":"The PageRank citation ranking: bringing order to the Web","volume-title":"Technical report","author":"Page","year":"1999"},{"key":"2023012810465848000_btt430-B6","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/BF01386390","article-title":"A note on two problems in connexion with graphs","volume":"1","author":"Dijkstra","year":"1959","journal-title":"Numer. Math."},{"key":"2023012810465848000_btt430-B7","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1002\/zamm.19290090206","article-title":"Praktische Verfahren der Gleichungsaufl\u00f6sung","volume":"9","author":"von Mises","year":"1929","journal-title":"Z. Angew. Math. Mech."},{"key":"2023012810465848000_btt430-B8","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012810465848000_btt430-B9","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res."},{"key":"2023012810465848000_btt430-B10","doi-asserted-by":"crossref","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","article-title":"BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks","volume":"21","author":"Maere","year":"2005","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/19\/2509\/48892634\/bioinformatics_29_19_2509.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/19\/2509\/48892634\/bioinformatics_29_19_2509.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T10:47:13Z","timestamp":1674902833000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/19\/2509\/190443"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8,13]]},"references-count":9,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2013,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt430","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,10,1]]},"published":{"date-parts":[[2013,8,13]]}}}