{"id":"https://openalex.org/W7128549760","doi":"https://doi.org/10.1007/s00224-025-10259-2","title":"FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees","display_name":"FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees","publication_year":2026,"publication_date":"2026-02-10","ids":{"openalex":"https://openalex.org/W7128549760","doi":"https://doi.org/10.1007/s00224-025-10259-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/41684729"},"language":"en","primary_location":{"id":"doi:10.1007/s00224-025-10259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00224-025-10259-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00224-025-10259-2.pdf","source":{"id":"https://openalex.org/S4210177266","display_name":"Theory of Computing Systems","issn_l":"1432-4350","issn":["1432-4350","1433-0490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Theory of Computing Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s00224-025-10259-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064067211","display_name":"Mathieu Gascon","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":"Mathieu Gascon","raw_affiliation_strings":["D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0009-0003-8654-8375","affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","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 et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0003-4561-683X","affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125479907","display_name":"Nadia El-Mabrouk","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":true,"raw_author_name":"Nadia El-Mabrouk","raw_affiliation_strings":["D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-5385-1015","affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5125479907"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":{"value":2290,"currency":"EUR","value_usd":2890},"fwci":15.6147,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.97208001,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"70","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9111999869346619,"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":0.9111999869346619,"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":0.07750000059604645,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.007799999788403511,"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/supertree","display_name":"Supertree","score":0.9379000067710876},{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.9154000282287598},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6796000003814697},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6381000280380249},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5224999785423279},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.47029998898506165},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4350000023841858},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.4027000069618225}],"concepts":[{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.9379000067710876},{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.9154000282287598},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6796000003814697},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6381000280380249},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5224999785423279},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.47029998898506165},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4350000023841858},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4027000069618225},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3896999955177307},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36390000581741333},{"id":"https://openalex.org/C3017489831","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Running time","level":2,"score":0.3625999987125397},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.349700003862381},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3425000011920929},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.31139999628067017},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.3098999857902527},{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.299699991941452},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.29750001430511475},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2922999858856201},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.289900004863739},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2896000146865845},{"id":"https://openalex.org/C90119067","wikidata":"https://www.wikidata.org/wiki/Q43260","display_name":"Polynomial","level":2,"score":0.2727999985218048}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/s00224-025-10259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00224-025-10259-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00224-025-10259-2.pdf","source":{"id":"https://openalex.org/S4210177266","display_name":"Theory of Computing Systems","issn_l":"1432-4350","issn":["1432-4350","1433-0490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Theory of Computing Systems","raw_type":"journal-article"},{"id":"pmid:41684729","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41684729","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":"Theory of computing systems","raw_type":null},{"id":"pmh:oai:europepmc.org:11698685","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12891257","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:12891257","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12891257/","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":"Theory Comput Syst","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s00224-025-10259-2","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00224-025-10259-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00224-025-10259-2.pdf","source":{"id":"https://openalex.org/S4210177266","display_name":"Theory of Computing Systems","issn_l":"1432-4350","issn":["1432-4350","1433-0490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Theory of Computing Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6280889331","display_name":null,"funder_award_id":"335135,335893","funder_id":"https://openalex.org/F4320334841","funder_display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies"},{"id":"https://openalex.org/G7286034794","display_name":null,"funder_award_id":"RN000743","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"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":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7128549760.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1619065037","https://openalex.org/W1981037505","https://openalex.org/W1986968252","https://openalex.org/W1993092519","https://openalex.org/W2032299129","https://openalex.org/W2078109763","https://openalex.org/W2130775582","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2147873222","https://openalex.org/W2166566648","https://openalex.org/W2181191890","https://openalex.org/W2287141830","https://openalex.org/W2534588987","https://openalex.org/W2607495137","https://openalex.org/W2618312940","https://openalex.org/W2799551362","https://openalex.org/W2920034498","https://openalex.org/W2976303698","https://openalex.org/W2995081665","https://openalex.org/W3187893169","https://openalex.org/W4231886136","https://openalex.org/W4285140022","https://openalex.org/W4391310464","https://openalex.org/W4396232166"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"We":[1,187],"present":[2],"FullSynesth":[3,117,159,193],",":[4,21,135],"a":[5,13,23,56,61,66,90,103,126,131,149,163,170,181],"tree":[6,134],"reconciliation":[7],"algorithm":[8,175,210],"predicting":[9],"the":[10,79,83,85,96,114,123,196,209],"evolution":[11,124],"of":[12,15,58,63,74,125,128,184,199,208],"set":[14,57,62,67,127],"homologous":[16],"genomic":[17],"regions":[18],"or":[19,51],"syntenies":[20,59,101,129],"inside":[22],"species":[24,104],"tree.":[25,105],"The":[26,106],"considered":[27],"evolutionary":[28,93],"model":[29],"involves":[30],"segmental":[31],"events":[32],"(i.e.":[33],"acting":[34],"on":[35,120,162,189],"multiple":[36],"genes)":[37],"including":[38],"duplications":[39],"(D),":[40],"losses":[41],"(L),":[42],"synteny":[43,133,171],"fissions":[44],"and":[45,65,100,168],"transfers":[46],"possibly":[47],"going":[48],"through":[49],"unsampled":[50],"extinct":[52],"species.":[53],"Formally,":[54],"given":[55,102,130,150],"in":[60,157,177],"genomes":[64],"$$\\mathcal":[68,141],"{G}$$":[69,142],"<mml:math":[70,143],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[71,144],"<mml:mi>G</mml:mi>":[72,145],"</mml:math>":[73,146],"consistent":[75],"gene":[76,80,98,185],"trees":[77,99],"for":[78,113,180],"families":[81],"composing":[82],"syntenies,":[84],"problem":[86,107],"is":[87,108,118,160,211],"to":[88,110,202],"infer":[89],"most":[91],"parsimonious":[92],"history":[94],"explaining":[95],"observed":[97],"known":[109],"be":[111,138],"NP-hard":[112],"DL":[115],"distance.":[116],"based":[119,161],"Synesth":[121,200],"explicating":[122],"single":[132],"which":[136],"can":[137],"obtained":[139],"from":[140],"by":[147],"selecting":[148],"supertree.":[151,205],"Rather":[152],"than":[153],"trying":[154],"each":[155,203],"supertree":[156,172],"turn,":[158],"two-in-one":[164],"approach":[165],"simultaneously":[166],"building":[167],"reconciling":[169],".":[173,215],"This":[174],"runs":[176],"polynomial":[178],"time":[179,198],"fixed":[182],"number":[183],"trees.":[186],"show":[188],"simulated":[190],"datasets":[191],"that":[192],"significantly":[194],"improves":[195],"running":[197],"applied":[201],"possible":[204],"An":[206],"implementation":[207],"available":[212],"at:":[213],"https://github.com/UdeM-LBIT/FullSynesth":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2026-02-11T00:00:00"}