{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T14:58:53Z","timestamp":1785855533160,"version":"3.56.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T00:00:00Z","timestamp":1564617600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U01HL137183-01"],"award-info":[{"award-number":["1U01HL137183-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5U54HG007990"],"award-info":[{"award-number":["5U54HG007990"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000888","name":"W. 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Keck Foundation","doi-asserted-by":"publisher","award":["DT06172015"],"award-info":[{"award-number":["DT06172015"]}],"id":[{"id":"10.13039\/100000888","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT201535\/Z\/16\/Z"],"award-info":[{"award-number":["WT201535\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT108749\/Z\/15\/Z"],"award-info":[{"award-number":["WT108749\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Compared to traditional haploid reference genomes, graph genomes are an efficient and compact data structure for storing multiple genomic sequences, for storing polymorphisms or for mapping sequencing reads with greater sensitivity. Further, graphs are well-studied computer science objects that can be efficiently analyzed. However, their adoption in genomic research is slow, in part because of the cognitive difficulty in interpreting graphs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present an intuitive graphical representation for graph genomes that re-uses well-honed techniques developed to display public transport networks, and demonstrate it as a web tool.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code: \u00a0https:\/\/github.com\/vgteam\/sequenceTubeMap.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Demonstration<\/jats:title>\n                  <jats:p>https:\/\/vgteam.github.io\/sequenceTubeMap\/.<\/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\/btz597","type":"journal-article","created":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T11:10:22Z","timestamp":1564139422000},"page":"5318-5320","source":"Crossref","is-referenced-by-count":67,"title":["Sequence tube maps: making graph genomes intuitive to commuters"],"prefix":"10.1093","volume":"35","author":[{"given":"Wolfgang","family":"Beyer","sequence":"first","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam M","family":"Novak","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenn","family":"Hickey","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Chan","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Tan","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedict","family":"Paten","sequence":"additional","affiliation":[{"name":"UC Santa Cruz Genomics Institute"},{"name":"Department of Biomolecular Engineering, University of California , Santa Cruz, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R","family":"Zerbino","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,1]]},"reference":[{"key":"2023013108412119600_btz597-B1","volume-title":"Mr. Beck\u2019s Underground Map","author":"Garland","year":"1994"},{"key":"2023013108412119600_btz597-B2","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/nbt.4227","article-title":"Variation graph toolkit improves read mapping by representing genetic variation in the reference","volume":"36","author":"Garrison","year":"2018","journal-title":"Nat. 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