{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:13:27Z","timestamp":1783556007775,"version":"3.55.0"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01HG010040"],"award-info":[{"award-number":["R01HG010040"]}]},{"name":"National Institute of Health","award":["U01HG010961"],"award-info":[{"award-number":["U01HG010961"]}]},{"name":"National Institute of Health","award":["T15LM007092"],"award-info":[{"award-number":["T15LM007092"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed pangene, a computational tool to identify gene orientation, gene order, and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented as a walk in the graph. It additionally finds subgraphs, which we call bibubbles, that capture gene content changes. Applied to the human pangenome, pangene identifies known gene-level variations and reveals complex haplotypes that are not well studied before. Pangene also works with high-quality bacterial pangenome and reports similar numbers of core and accessory genes in comparison to existing tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code at https:\/\/github.com\/lh3\/pangene; prebuilt pangene graphs can be downloaded from https:\/\/zenodo.org\/records\/8118576 and visualized at https:\/\/pangene.bioinweb.org<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae456","type":"journal-article","created":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T21:55:37Z","timestamp":1721685337000},"source":"Crossref","is-referenced-by-count":33,"title":["Exploring gene content with pangene graphs"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4874-2874","authenticated-orcid":false,"given":"Heng","family":"Li","sequence":"first","affiliation":[{"name":"Department of Data Science, Dana-Farber Cancer Institute , Boston, MA 02215, United States"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215, Unites States"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9108-3328","authenticated-orcid":false,"given":"Maximillian","family":"Marin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215, Unites States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3871-5760","authenticated-orcid":false,"given":"Maha R","family":"Farhat","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215, Unites States"},{"name":"Pulmonary and Critical Care Medicine, Massachusetts General Hospital , Boston, MA 02114, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,23]]},"reference":[{"key":"2024072922460269700_btae456-B1","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/ng.2334","article-title":"Structural haplotypes and recent evolution of the human 17q21.31 region","volume":"44","author":"Boettger","year":"2012","journal-title":"Nat Genet"},{"key":"2024072922460269700_btae456-B2","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.tcs.2015.10.021","article-title":"Linear-time superbubble identification algorithm for genome assembly","volume":"609","author":"Brankovic","year":"2016","journal-title":"Theor Comput. 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