{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T02:27:38Z","timestamp":1775269658740,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,9,25]],"date-time":"2017-09-25T00:00:00Z","timestamp":1506297600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["098051"],"award-info":[{"award-number":["098051"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["099202"],"award-info":[{"award-number":["099202"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https:\/\/github.com\/jameshadfield\/phandango.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx610","type":"journal-article","created":{"date-parts":[[2017,9,23]],"date-time":"2017-09-23T07:09:15Z","timestamp":1506150555000},"page":"292-293","source":"Crossref","is-referenced-by-count":521,"title":["Phandango: an interactive viewer for bacterial population genomics"],"prefix":"10.1093","volume":"34","author":[{"given":"James","family":"Hadfield","sequence":"first","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"Nicholas J","family":"Croucher","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, Imperial College London, London, UK"}]},{"given":"Richard J","family":"Goater","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"Khalil","family":"Abudahab","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"David M","family":"Aanensen","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, Imperial College London, London, UK"},{"name":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"Simon R","family":"Harris","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,9,25]]},"reference":[{"key":"2023012712232796200_btx610-B1","first-page":"199","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography","volume":"10","author":"Argim\u00f3n","year":"2016","journal-title":"Microb. Genom"},{"key":"2023012712232796200_btx610-B2","doi-asserted-by":"crossref","first-page":"e1004547","DOI":"10.1371\/journal.pgen.1004547","article-title":"Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes","volume":"10","author":"Chewapreecha","year":"2014","journal-title":"PLoS Genet"},{"key":"2023012712232796200_btx610-B3","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712232796200_btx610-B4","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1126\/science.1198545","article-title":"Rapid pneumococcal evolution in response to clinical interventions","volume":"331","author":"Croucher","year":"2011","journal-title":"Science"},{"key":"2023012712232796200_btx610-B5","author":"Lees","year":"2016"},{"key":"2023012712232796200_btx610-B6","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1093\/nar\/gkr928","article-title":"Detection of recombination events in bacterial genomes from large population samples","volume":"40","author":"Marttinen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023012712232796200_btx610-B7","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712232796200_btx610-B8","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/292\/48913057\/bioinformatics_34_2_292.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/292\/48913057\/bioinformatics_34_2_292.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:07:09Z","timestamp":1674806829000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/2\/292\/4212949"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,25]]},"references-count":8,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx610","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/119545","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1,15]]},"published":{"date-parts":[[2017,9,25]]}}}