{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049402,"version":"3.50.1"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Searle Leadership Fund"},{"name":"Biotechnology Training Program"},{"DOI":"10.13039\/100000183","name":"Army Research Office","doi-asserted-by":"publisher","award":["W911NF-19-1-0298"],"award-info":[{"award-number":["W911NF-19-1-0298"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation Graduate Research Fellowships Program","award":["DGE-1842165"],"award-info":[{"award-number":["DGE-1842165"]}]},{"name":"National Institute of Health, National Institute of Diabetes and Digestive and Kidney Diseases","award":["R24DK110499"],"award-info":[{"award-number":["R24DK110499"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Identifying variant forms of gene clusters of interest in phylogenetically proximate and distant taxa can help to infer their evolutionary histories and functions. Conserved gene clusters may differ by only a few genes, but these small differences can in turn induce substantial phenotypes, such as by the formation of pseudogenes or insertions interrupting regulation. Particularly as microbial genomes and metagenomic assemblies become increasingly abundant, unsupervised grouping of similar, but not necessarily identical, gene clusters into consistent bins can provide a population-level understanding of their gene content variation and functional homology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed GeneGrouper, a command-line tool that uses a density-based clustering method to group gene clusters into bins. GeneGrouper demonstrated high recall and precision in benchmarks for the detection of the 23-gene Salmonella enterica LT2 Pdu gene cluster and four-gene Pseudomonas aeruginosa PAO1 Mex gene cluster among 435 genomes spanning mixed taxa. In a subsequent application investigating the diversity and impact of gene-complete and -incomplete LT2 Pdu gene clusters in 1130 S.enterica genomes, GeneGrouper identified a novel, frequently occurring pduN pseudogene. When investigated in vivo, introduction of the pduN pseudogene negatively impacted microcompartment formation. We next demonstrated the versatility of GeneGrouper by clustering distant homologous gene clusters and variable gene clusters found in integrative and conjugative elements.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GeneGrouper software and code are publicly available at https:\/\/pypi.org\/project\/GeneGrouper\/.<\/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\/btab752","type":"journal-article","created":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T07:09:25Z","timestamp":1635491365000},"page":"612-620","source":"Crossref","is-referenced-by-count":7,"title":["Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1803-3623","authenticated-orcid":false,"given":"Alexander G","family":"McFarland","sequence":"first","affiliation":[{"name":"Department of Civil and Environmental Engineering, Northwestern University , Evanston, IL 60208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nolan W","family":"Kennedy","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Northwestern University , Evanston, IL 60208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carolyn E","family":"Mills","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Northwestern University , Evanston, IL 60208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danielle","family":"Tullman-Ercek","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Northwestern University , Evanston, IL 60208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1110-0096","authenticated-orcid":false,"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[{"name":"Harvard Chan Microbiome in Public Health Center, Harvard T. 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Chan School of Public Health, Boston, MA 02115, USA"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erica M","family":"Hartmann","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, Northwestern University , Evanston, IL 60208, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,4]]},"reference":[{"key":"2023020201174155600_btab752-B1","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1038\/s41467-020-16366-7","article-title":"Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0","volume":"11","author":"Asnicar","year":"2020","journal-title":"Nat. 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