{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T15:25:57Z","timestamp":1761405957806,"version":"build-2065373602"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-197783"],"award-info":[{"award-number":["PJT-197783"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"the Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"crossref","award":["RGPIN-2016-06566"],"award-info":[{"award-number":["RGPIN-2016-06566"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs Program","doi-asserted-by":"crossref","award":["RCHP0420"],"award-info":[{"award-number":["RCHP0420"]}],"id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Facult\u00e9 des \u00e9tudes sup\u00e9rieures et postdoctorales"},{"DOI":"10.13039\/501100005242","name":"Universit\u00e9 de Montr\u00e9al","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005242","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population\u2019s ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin\u2019s accuracy using lineage data from evolutionary simulations, showing that it recovers the clones\u2019 identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of Escherichia coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin\u2019s versatility allows it to be applied to lineage time-series data across different experimental setups.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Doblin is available on CRAN (https:\/\/CRAN.R-project.org\/package=doblin) and Github (https:\/\/github.com\/dagagf\/doblin).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf555","type":"journal-article","created":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T12:12:31Z","timestamp":1759320751000},"source":"Crossref","is-referenced-by-count":0,"title":["Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series"],"prefix":"10.1093","volume":"41","author":[{"given":"Melis","family":"Gencel","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","place":["Canada"]},{"name":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","place":["Canada"]}]},{"given":"David","family":"Gagn\u00e9-Leroux","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","place":["Canada"]},{"name":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","place":["Canada"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8369-982X","authenticated-orcid":false,"given":"Adrian W R","family":"Serohijos","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","place":["Canada"]},{"name":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 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