{"id":"https://openalex.org/W4414874493","doi":"https://doi.org/10.1093/bioinformatics/btaf555","title":"Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series","display_name":"Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series","publication_year":2025,"publication_date":"2025-10-01","ids":{"openalex":"https://openalex.org/W4414874493","doi":"https://doi.org/10.1093/bioinformatics/btaf555","pmid":"https://pubmed.ncbi.nlm.nih.gov/41051238"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf555","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf555/64518962/btaf555.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf555/64518962/btaf555.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055271608","display_name":"Melis Gencel","orcid":"https://orcid.org/0000-0003-4762-5297"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Melis Gencel","raw_affiliation_strings":["Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098733139","display_name":"David Gagn\u00e9-Leroux","orcid":null},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"David Gagn\u00e9-Leroux","raw_affiliation_strings":["Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038098410","display_name":"Adrian W.R. Serohijos","orcid":"https://orcid.org/0000-0001-8369-982X"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Adrian W R Serohijos","raw_affiliation_strings":["Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Robert-Cedergren Center for Bioinformatics and Genomics, Universit\u00e9 de Montr\u00e9al , Montr\u00e9al, QC H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Universit\u00e9 de Montr\u00e9al Department of Biochemistry, , Montr\u00e9al, Quebec H3T 1J4,","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055271608"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29494382,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9747999906539917,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-barcoding","display_name":"DNA barcoding","score":0.7246999740600586},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5990999937057495},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4514999985694885},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.357699990272522},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.32519999146461487}],"concepts":[{"id":"https://openalex.org/C141732470","wikidata":"https://www.wikidata.org/wiki/Q1154642","display_name":"DNA barcoding","level":2,"score":0.7246999740600586},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5990999937057495},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5590999722480774},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4878999888896942},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4514999985694885},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4296000003814697},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42800000309944153},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37229999899864197},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.357699990272522},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.32519999146461487},{"id":"https://openalex.org/C79386861","wikidata":"https://www.wikidata.org/wiki/Q476697","display_name":"DNA profiling","level":3,"score":0.30379998683929443},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2773999869823456},{"id":"https://openalex.org/C2776841711","wikidata":"https://www.wikidata.org/wiki/Q856","display_name":"Barcode","level":2,"score":0.2676999866962433}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf555","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf555/64518962/btaf555.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41051238","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41051238","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11360908","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12553330","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf555","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf555","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf555/64518962/btaf555.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6926743809","display_name":null,"funder_award_id":"PJT-197783","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G7473178284","display_name":null,"funder_award_id":"RCHP0420","funder_id":"https://openalex.org/F4320320994","funder_display_name":"Canada Research Chairs"},{"id":"https://openalex.org/G8024971271","display_name":null,"funder_award_id":"RGPIN-2016-06566","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320320994","display_name":"Canada Research Chairs","ror":"https://ror.org/0517h6h17"},{"id":"https://openalex.org/F4320323175","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414874493.pdf","grobid_xml":"https://content.openalex.org/works/W4414874493.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1938292773","https://openalex.org/W1967350125","https://openalex.org/W1985561503","https://openalex.org/W1987191607","https://openalex.org/W1989004419","https://openalex.org/W2013681333","https://openalex.org/W2031581341","https://openalex.org/W2035420256","https://openalex.org/W2041579725","https://openalex.org/W2044713944","https://openalex.org/W2045825103","https://openalex.org/W2047453261","https://openalex.org/W2065220128","https://openalex.org/W2088580309","https://openalex.org/W2104895468","https://openalex.org/W2111187843","https://openalex.org/W2120474334","https://openalex.org/W2148323109","https://openalex.org/W2151887741","https://openalex.org/W2162871445","https://openalex.org/W2164232580","https://openalex.org/W2181542557","https://openalex.org/W2272802268","https://openalex.org/W2273981063","https://openalex.org/W2398299059","https://openalex.org/W2407334027","https://openalex.org/W2518349977","https://openalex.org/W2586245344","https://openalex.org/W2586386056","https://openalex.org/W2747263575","https://openalex.org/W2765922336","https://openalex.org/W2766580658","https://openalex.org/W2774216375","https://openalex.org/W2779050757","https://openalex.org/W2792874068","https://openalex.org/W2795842108","https://openalex.org/W2884347381","https://openalex.org/W2886855629","https://openalex.org/W2898222917","https://openalex.org/W2899373020","https://openalex.org/W2902451951","https://openalex.org/W2922092653","https://openalex.org/W2951197288","https://openalex.org/W3005327280","https://openalex.org/W3006915344","https://openalex.org/W3011002672","https://openalex.org/W3198643625","https://openalex.org/W3211123403","https://openalex.org/W3211222927","https://openalex.org/W4366998411","https://openalex.org/W4407244106","https://openalex.org/W4410546428","https://openalex.org/W4412150575"],"related_works":[],"abstract_inverted_index":{"Doblin":[0],"is":[1],"available":[2],"on":[3],"CRAN":[4],"(https://CRAN.R-project.org/package=doblin)":[5],"and":[6],"Github":[7],"(https://github.com/dagagf/doblin).":[8]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
