{"id":"https://openalex.org/W2976303698","doi":"https://doi.org/10.1186/s13015-020-00171-4","title":"Evolution through segmental duplications and losses: a Super-Reconciliation approach","display_name":"Evolution through segmental duplications and losses: a Super-Reconciliation approach","publication_year":2020,"publication_date":"2020-05-26","ids":{"openalex":"https://openalex.org/W2976303698","doi":"https://doi.org/10.1186/s13015-020-00171-4","mag":"2976303698","pmid":"https://pubmed.ncbi.nlm.nih.gov/32508979"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-020-00171-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00171-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-020-00171-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-020-00171-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079973056","display_name":"Matt\u00e9o Delabre","orcid":"https://orcid.org/0000-0003-4561-683X"},"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":"Matt\u00e9o Delabre","raw_affiliation_strings":["D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041470344","display_name":"Nadia El-Mabrouk","orcid":"https://orcid.org/0000-0002-5385-1015"},"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":"Nadia El-Mabrouk","raw_affiliation_strings":["D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007694498","display_name":"Katharina T. Huber","orcid":"https://orcid.org/0000-0002-6368-7511"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Katharina T. Huber","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016796629","display_name":"Manuel Lafond","orcid":"https://orcid.org/0000-0002-5305-7372"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Manuel Lafond","raw_affiliation_strings":["Department of Computer Science, Universit\u00e9 de Sherbrooke, Sherbrooke, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e9 de Sherbrooke, Sherbrooke, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042929579","display_name":"Vincent Moulton","orcid":"https://orcid.org/0000-0001-9371-6435"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vincent Moulton","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012750505","display_name":"Emmanuel Noutahi","orcid":"https://orcid.org/0000-0001-5216-9703"},"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":"Emmanuel Noutahi","raw_affiliation_strings":["D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032865321","display_name":"Miguel Sauti\u00e9 Castellanos","orcid":"https://orcid.org/0000-0002-9475-5265"},"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":"Miguel Sautie Castellanos","raw_affiliation_strings":["D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique (DIRO), Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041470344"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.6022,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.83139812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.998199999332428,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.998199999332428,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9908000230789185,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9750999808311462,"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/computer-science","display_name":"Computer science","score":0.6034957766532898},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33126169443130493}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6034957766532898},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33126169443130493}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-020-00171-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00171-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-020-00171-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:32508979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32508979","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:ueaeprints.uea.ac.uk:71959","is_oa":true,"landing_page_url":null,"pdf_url":"https://ueaeprints.uea.ac.uk/id/eprint/71959/4/Published_Version.pdf","source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:05a6c52b19e1410c84176568c9e76b05","is_oa":true,"landing_page_url":"https://doaj.org/article/05a6c52b19e1410c84176568c9e76b05","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-15 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7249433","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7249433","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-020-00171-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00171-4","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-020-00171-4","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4161983461","display_name":null,"funder_award_id":"RGPIN-249834","funder_id":"https://openalex.org/F4320321487","funder_display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4449817161","display_name":null,"funder_award_id":"249834","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4713948763","display_name":null,"funder_award_id":"RGPIN-249834","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320321487","display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334841","display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies","ror":"https://ror.org/00b9f9778"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2976303698.pdf","grobid_xml":"https://content.openalex.org/works/W2976303698.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W74509308","https://openalex.org/W1137980060","https://openalex.org/W1517959117","https://openalex.org/W1523193919","https://openalex.org/W1527695627","https://openalex.org/W1619065037","https://openalex.org/W1974745849","https://openalex.org/W1978858440","https://openalex.org/W1981037505","https://openalex.org/W1985348819","https://openalex.org/W1987811475","https://openalex.org/W1993092519","https://openalex.org/W2004575303","https://openalex.org/W2011167904","https://openalex.org/W2029036185","https://openalex.org/W2043950637","https://openalex.org/W2056239531","https://openalex.org/W2074302571","https://openalex.org/W2078109763","https://openalex.org/W2079384285","https://openalex.org/W2082782088","https://openalex.org/W2099181176","https://openalex.org/W2102669784","https://openalex.org/W2103141682","https://openalex.org/W2103849916","https://openalex.org/W2106882534","https://openalex.org/W2120836981","https://openalex.org/W2124105487","https://openalex.org/W2126062220","https://openalex.org/W2130640131","https://openalex.org/W2130775582","https://openalex.org/W2131148812","https://openalex.org/W2131944877","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2133090982","https://openalex.org/W2135281627","https://openalex.org/W2144653577","https://openalex.org/W2152207030","https://openalex.org/W2152404552","https://openalex.org/W2156815152","https://openalex.org/W2157360426","https://openalex.org/W2159545652","https://openalex.org/W2161192208","https://openalex.org/W2166106146","https://openalex.org/W2311203695","https://openalex.org/W2340667260","https://openalex.org/W2561675875","https://openalex.org/W2569585400","https://openalex.org/W2607495137","https://openalex.org/W2618312940","https://openalex.org/W2890613572","https://openalex.org/W2940808208","https://openalex.org/W2949124547","https://openalex.org/W4213205621","https://openalex.org/W4231886136","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Abstract":[0],"The":[1],"classical":[2],"gene":[3,14,22,114,134,147],"and":[4,16,80,125,166,192,219],"species":[5],"tree":[6,135],"reconciliation,":[7],"used":[8],"to":[9,90,116,172,196],"infer":[10],"the":[11,19,43,59,68,106,154,183,207,213,226],"history":[12,76],"of":[13,21,61,77,86,93,111,119,128,156,206,223],"gain":[15],"loss":[17,81,193],"explaining":[18],"evolution":[20,27],"families,":[23],"assumes":[24],"an":[25,168,197],"independent":[26],"for":[28,36,49,122,180,212],"each":[29],"family.":[30],"While":[31],"this":[32],"assumption":[33],"is":[34,46,164],"reasonable":[35],"genes":[37,50],"that":[38,142,153,178],"are":[39,56],"far":[40],"apart":[41],"in":[42,73,182],"genome,":[44],"it":[45],"not":[47],"appropriate":[48],"grouped":[51],"into":[52],"syntenic":[53],"blocks,":[54],"which":[55,71],"more":[57],"plausibly":[58],"result":[60],"a":[62,75,84,91,97,112,117,129,158,221],"concerted":[63],"evolution.":[64],"Here,":[65],"we":[66,104,176],"introduce":[67],"Super-Reconciliation":[69,130],"problem":[70,110,155],"consists":[72],"inferring":[74],"segmental":[78,123,190],"duplication":[79,191],"events":[82],"(involving":[83],"set":[85,92,118],"neighboring":[87],"genes)":[88],"leading":[89],"present-day":[94],"syntenies":[95],"from":[96],"single":[98,113],"ancestral":[99],"one.":[100],"In":[101,137],"other":[102],"words,":[103],"extend":[105],"traditional":[107],"Duplication-Loss":[108,214],"reconciliation":[109],"tree,":[115],"trees,":[120],"accounting":[121,179],"duplications":[124],"losses.":[126],"Existency":[127],"depends":[131,145],"on":[132,146,216,225],"individual":[133],"consistency.":[136,149],"addition,":[138],"ignoring":[139],"rearrangements":[140,181],"implies":[141],"existency":[143],"also":[144],"order":[148],"We":[150,201],"first":[151],"show":[152,177],"reconstructing":[157],"most":[159],"parsimonious":[160],"Super-Reconciliation,":[161],"if":[162],"any,":[163],"NP-hard":[165],"give":[167,220],"exact":[169,198],"exponential-time":[170],"algorithm":[171,211],"solve":[173],"it.":[174],"Alternatively,":[175],"evolutionary":[184],"model,":[185],"but":[186],"still":[187],"only":[188],"minimizing":[189],"events,":[194],"leads":[195],"polynomial-time":[199],"algorithm.":[200],"finally":[202],"assess":[203],"time":[204,210],"efficiency":[205],"former":[208],"exponential":[209],"model":[215],"simulated":[217],"datasets,":[218],"proof":[222],"concept":[224],"opioid":[227],"receptor":[228],"genes.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
