{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T03:06:52Z","timestamp":1767841612868,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T00:00:00Z","timestamp":1638403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003593","name":"National Council for Scientific and Technological Development","doi-asserted-by":"crossref","award":["161552\/2019-6"],"award-info":[{"award-number":["161552\/2019-6"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Funda\u00e7\u00e3o Arauc\u00e1ria (FA) [NAPI Bioinform\u00e1tica]"},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["161552\/2019-6"],"award-info":[{"award-number":["161552\/2019-6"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordination for the Improvement of Higher Education Personnel","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["304388\/2018-1"],"award-info":[{"award-number":["304388\/2018-1"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["308258\/2018-5"],"award-info":[{"award-number":["308258\/2018-5"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present TreeAndLeaf, an R\/Bioconductor package that implements a hybrid layout strategy to represent tree diagrams with focus on the leaves. The TreeAndLeaf package combines force-directed graph and tree layout algorithms using a single visualization system, allowing projection of multiple layers of information onto a graph-tree diagram. The Supplementary Information provides two case studies that use breast cancer data from epidemiological and experimental studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TreeAndLeaf is written in the R language, and is available from the Bioconductor project at http:\/\/bioconductor.org\/packages\/TreeAndLeaf\/ (version\u22651.4.2).<\/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\/btab819","type":"journal-article","created":{"date-parts":[[2021,11,30]],"date-time":"2021-11-30T22:42:43Z","timestamp":1638312163000},"page":"1463-1464","source":"Crossref","is-referenced-by-count":12,"title":["<i>TreeAndLeaf<\/i>: an R\/Bioconductor package for graphs and trees with focus on the leaves"],"prefix":"10.1093","volume":"38","author":[{"given":"Milena A","family":"Cardoso","sequence":"first","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luis E A","family":"Rizzardi","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leonardo W","family":"Kume","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clarice S","family":"Groeneveld","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheyla","family":"Trefflich","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"},{"name":"Bioinformatics Department, Federal University of Minas Gerais , Belo Horizonte 31270-901, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7357-3446","authenticated-orcid":false,"given":"Diego A A","family":"Morais","sequence":"additional","affiliation":[{"name":"Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte , Natal 59078-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1688-6155","authenticated-orcid":false,"given":"Rodrigo J S","family":"Dalmolin","sequence":"additional","affiliation":[{"name":"Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte , Natal 59078-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce A J","family":"Ponder","sequence":"additional","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5906-1498","authenticated-orcid":false,"given":"Kerstin B","family":"Meyer","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4942-8131","authenticated-orcid":false,"given":"Mauro A A","family":"Castro","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology Laboratory, Federal University of Paran\u00e1 , Curitiba 81520-260, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,2]]},"reference":[{"key":"2023020108550296000_btab819-B1","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2012-13-4-r29","article-title":"RedeR: R\/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations","volume":"13","author":"Castro","year":"2012","journal-title":"Genome Biol"},{"key":"2023020108550296000_btab819-B2","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1038\/ng.3458","article-title":"Regulators of genetic risk of breast cancer identified by integrative network analysis","volume":"48","author":"Castro","year":"2016","journal-title":"Nat. Genet"},{"key":"2023020108550296000_btab819-B3","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"Int. J. Complex Syst"},{"key":"2023020108550296000_btab819-B4","volume-title":"Global Cancer Observatory: Cancer Tomorrow","author":"Ferlay","year":"2021"},{"key":"2023020108550296000_btab819-B5","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1007\/BF03040858","article-title":"Comparison tests for dendrograms: a comparative evaluation","volume":"12","author":"Lapointe","year":"1995","journal-title":"J. Classif"},{"key":"2023020108550296000_btab819-B6","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"2023020108550296000_btab819-B7","volume-title":"R: A Language and Environment for Statistical Computing","year":"2021"},{"key":"2023020108550296000_btab819-B8","doi-asserted-by":"crossref","first-page":"131","DOI":"10.7155\/jgaa.00163","article-title":"Grid drawings of binary trees: an experimental study","volume":"12","author":"Rusu","year":"2008","journal-title":"J. Graph Algorithms Appl"},{"key":"2023020108550296000_btab819-B9","doi-asserted-by":"crossref","first-page":"e96","DOI":"10.1002\/cpbi.96","article-title":"Using ggtree to visualize data on tree-like structures","volume":"69","author":"Yu","year":"2020","journal-title":"Curr. Protoc. Bioinf"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab819\/41764807\/btab819.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/5\/1463\/49008716\/btab819.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/5\/1463\/49008716\/btab819.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:19:10Z","timestamp":1675282750000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/5\/1463\/6448224"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,12,2]]},"references-count":9,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,2,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab819","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3,1]]},"published":{"date-parts":[[2021,12,2]]}}}