{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T16:23:31Z","timestamp":1757780611659},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Network biology has emerged as a powerful tool to uncover the organizational properties of living systems through the application of graph theoretic approaches. However, due to limitations in underlying data models and visualization software, knowledge relating to large molecular assemblies and biologically active fragments is poorly represented.<\/jats:p>\n               <jats:p>Results: Here, we demonstrate a novel hypergraph implementation that better captures hierarchical structures, using components of elastic fibers and chromatin modification as models. These reveal unprecedented views of the biology of these systems, demonstrating the unique capacity of hypergraphs to resolve overlaps and uncover new insights into the subfunctionalization of variant complexes.<\/jats:p>\n               <jats:p>Availability and implementation: Hyperscape is available as a web application at http:\/\/www.compsysbio.org\/hyperscape. Source code, examples and a tutorial are freely available under a GNU license.<\/jats:p>\n               <jats:p>Contacts: \u00a0john.parkinson@utoronto.ca or graham.cromar@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv385","type":"journal-article","created":{"date-parts":[[2015,6,25]],"date-time":"2015-06-25T00:30:42Z","timestamp":1435192242000},"page":"3390-3391","source":"Crossref","is-referenced-by-count":9,"title":["Hyperscape: visualization for complex biological networks"],"prefix":"10.1093","volume":"31","author":[{"given":"Graham L.","family":"Cromar","sequence":"first","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Yang","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"},{"name":"2 Department of Biochemistry and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Parkinson","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 21-9830 PGCRL, 686 Bay Street, Toronto, ON, M5G 0A4, Canada,"},{"name":"2 Department of Biochemistry and"},{"name":"3 Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,6,24]]},"reference":[{"key":"2023020202314701100_btv385-B1","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1093\/bioinformatics\/btp025","article-title":"MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions","volume":"25","author":"Chautard","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202314701100_btv385-B2","doi-asserted-by":"crossref","first-page":"D235","DOI":"10.1093\/nar\/gkq830","article-title":"MatrixDB, the extracellular matrix interaction database","volume":"39","author":"Chautard","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020202314701100_btv385-B3","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/nbt1304","article-title":"Towards zoomable multidimensional maps of the cell","volume":"25","author":"Hu","year":"2007","journal-title":"Nat. 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Genet."},{"key":"2023020202314701100_btv385-B9","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":"2023020202314701100_btv385-B10","doi-asserted-by":"crossref","first-page":"4766","DOI":"10.1073\/pnas.0730882100","article-title":"Human tumstatin and human endostatin exhibit distinct antiangiogenic activities mediated by alpha v beta 3 and alpha 5 beta 1 integrins","volume":"100","author":"Sudhakar","year":"2003","journal-title":"Proc. Natl. Acad. Sci. 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