{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T16:38:23Z","timestamp":1771000703667,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2017,1,25]],"date-time":"2017-01-25T00:00:00Z","timestamp":1485302400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"FP7 Collaborative Project Microme","award":["# 222886-2"],"award-info":[{"award-number":["# 222886-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway. Thus, BioPAXViz can significantly facilitate, and contribute to, the study of metabolic pathway evolution and engineering.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>BioPAXViz has been developed as a Cytoscape app and is available at: https:\/\/github.com\/CGU-CERTH\/BioPAX.Viz. The software is distributed under the MIT License and is accompanied by example files and data. Additional documentation is available at the aforementioned GitHub repository.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw813","type":"journal-article","created":{"date-parts":[[2017,1,6]],"date-time":"2017-01-06T12:05:50Z","timestamp":1483704350000},"page":"1418-1420","source":"Crossref","is-referenced-by-count":6,"title":["BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution"],"prefix":"10.1093","volume":"33","author":[{"given":"Fotis E","family":"Psomopoulos","sequence":"first","affiliation":[{"name":"Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), Thessalonica, Greece"}]},{"given":"Dimitrios M","family":"Vitsios","sequence":"additional","affiliation":[{"name":"Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), Thessalonica, Greece"},{"name":"The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Shakuntala","family":"Baichoo","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Engineering, Faculty of Engineering, University of Mauritius, Reduit, Mauritius"}]},{"given":"Christos A","family":"Ouzounis","sequence":"additional","affiliation":[{"name":"Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), Thessalonica, Greece"},{"name":"Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada"}]}],"member":"286","published-online":{"date-parts":[[2017,1,25]]},"reference":[{"key":"2023020205025596100_btw813-B1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/bioinformatics\/btp665","article-title":"ChiBE: interactive visualization and manipulation of BioPAX pathway models","volume":"26","author":"Babur","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020205025596100_btw813-B2","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1089\/cmb.2011.0066","article-title":"Detecting highways of horizontal gene transfer","volume":"18","author":"Bansal","year":"2011","journal-title":"J. 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