{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T20:15:56Z","timestamp":1776024956048,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,22]],"date-time":"2016-11-22T00:00:00Z","timestamp":1479772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001742","name":"U.S. National Science Foundation","doi-asserted-by":"publisher","award":["IOS \u2013 1339156"],"award-info":[{"award-number":["IOS \u2013 1339156"]}],"id":[{"id":"10.13039\/501100001742","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001742","name":"U.S. National Science Foundation","doi-asserted-by":"publisher","award":["IOS \u2013 1444490"],"award-info":[{"award-number":["IOS \u2013 1444490"]}],"id":[{"id":"10.13039\/501100001742","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>FractBias is freely available as a web application at https:\/\/genomevolution.org\/CoGe\/SynMap.pl. The software is open source (MIT license) and executable with Python 2.7 or iPython notebook, and available on GitHub (https:\/\/goo.gl\/PaAtqy). Documentation for FractBias is available on CoGepedia (https:\/\/goo.gl\/ou9dt6)<\/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\/btw666","type":"journal-article","created":{"date-parts":[[2016,10,24]],"date-time":"2016-10-24T19:05:28Z","timestamp":1477335928000},"page":"552-554","source":"Crossref","is-referenced-by-count":26,"title":["FractBias: a graphical tool for assessing fractionation bias following polyploidy"],"prefix":"10.1093","volume":"33","author":[{"given":"Blake L","family":"Joyce","sequence":"first","affiliation":[{"name":"BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asher","family":"Haug-Baltzell","sequence":"additional","affiliation":[{"name":"Genetis GIDP, University of Arizona, Tucson, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean","family":"Davey","sequence":"additional","affiliation":[{"name":"BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Bomhoff","sequence":"additional","affiliation":[{"name":"BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James C","family":"Schnable","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Lyons","sequence":"additional","affiliation":[{"name":"BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA"},{"name":"Genetis GIDP, University of Arizona, Tucson, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,11,22]]},"reference":[{"key":"2023020204431157700_btw666-B1","first-page":"131","article-title":"Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants","volume":"15","author":"Freeling","year":"2012","journal-title":"Genome Stud. Mol. Genet"},{"key":"2023020204431157700_btw666-B2","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1093\/genetics\/166.2.935","article-title":"Genomic duplication, fractionation and the origin of regulatory novelty","volume":"166","author":"Langham","year":"2004","journal-title":"Genetics"},{"key":"2023020204431157700_btw666-B3","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s12042-008-9017-y","article-title":"The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids","volume":"1","author":"Lyons","year":"2008","journal-title":"Trop. Plant Biol"},{"key":"2023020204431157700_btw666-B4","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1073\/pnas.1101368108","article-title":"Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss","volume":"108","author":"Schnable","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020204431157700_btw666-B5","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/515151a","article-title":"Interactive notebooks: sharing the code","volume":"515","author":"Shen","year":"2014","journal-title":"Nature"},{"key":"2023020204431157700_btw666-B6","first-page":"1.","article-title":"Screening synteny blocks in pairwise genome comparisons through integer programming","volume":"1212","author":"Tang","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020204431157700_btw666-B7","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1534\/genetics.111.137349","article-title":"Altered patterns of fractionation and exon deletions in brassica rapa support a two-step model of paleohexaploidy","volume":"190","author":"Tang","year":"2012","journal-title":"Genetics"},{"key":"2023020204431157700_btw666-B8","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1101\/gr.4708406","article-title":"Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes","volume":"16","author":"Thomas","year":"2006","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/552\/49037940\/bioinformatics_33_4_552.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/552\/49037940\/bioinformatics_33_4_552.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:48:10Z","timestamp":1675313290000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/4\/552\/2617574"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,22]]},"references-count":8,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw666","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,15]]},"published":{"date-parts":[[2016,11,22]]}}}