{"id":"https://openalex.org/W4402586402","doi":"https://doi.org/10.1007/978-3-031-72200-4_10","title":"Simultaneously Building and\u00a0Reconciling a\u00a0Synteny Tree","display_name":"Simultaneously Building and\u00a0Reconciling a\u00a0Synteny Tree","publication_year":2024,"publication_date":"2024-09-18","ids":{"openalex":"https://openalex.org/W4402586402","doi":"https://doi.org/10.1007/978-3-031-72200-4_10"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-031-72200-4_10","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72200-4_10","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72200-4_10.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"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":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72200-4_10.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064067211","display_name":"Mathieu Gascon","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161954","display_name":"D\u00e9partement d'Informatique","ror":"https://ror.org/05y6rqs46","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210159245","https://openalex.org/I4210161954"]},{"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","FR"],"is_corresponding":false,"raw_author_name":"Mathieu Gascon","raw_affiliation_strings":["D\u00e9partement d\u2019informatique 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\u2019informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I4210161954","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/I4210161954","display_name":"D\u00e9partement d'Informatique","ror":"https://ror.org/05y6rqs46","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210159245","https://openalex.org/I4210161954"]},{"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","FR"],"is_corresponding":false,"raw_author_name":"Matt\u00e9o Delabre","raw_affiliation_strings":["D\u00e9partement d\u2019informatique 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\u2019informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I4210161954","https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041470344","display_name":"Nadia El-Mabrouk","orcid":"https://orcid.org/0000-0002-5385-1015"},"institutions":[{"id":"https://openalex.org/I4210161954","display_name":"D\u00e9partement d'Informatique","ror":"https://ror.org/05y6rqs46","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210159245","https://openalex.org/I4210161954"]},{"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","FR"],"is_corresponding":true,"raw_author_name":"Nadia El-Mabrouk","raw_affiliation_strings":["D\u00e9partement d\u2019informatique 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\u2019informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I4210161954","https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041470344"],"corresponding_institution_ids":["https://openalex.org/I4210161954","https://openalex.org/I70931966"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"127","last_page":"142"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10317","display_name":"Advanced Database Systems and Queries","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.98580002784729,"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":0.8234701156616211},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6940498352050781},{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.4654819369316101},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3231983780860901},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07973060011863708},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.07000869512557983}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8234701156616211},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6940498352050781},{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.4654819369316101},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3231983780860901},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07973060011863708},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07000869512557983},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-031-72200-4_10","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72200-4_10","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72200-4_10.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"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":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.1007/978-3-031-72200-4_10","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72200-4_10","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72200-4_10.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"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":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[{"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402586402.pdf","grobid_xml":"https://content.openalex.org/works/W4402586402.grobid-xml"},"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/W2181191890","https://openalex.org/W2287141830","https://openalex.org/W2534588987","https://openalex.org/W2607495137","https://openalex.org/W2618312940","https://openalex.org/W2799551362","https://openalex.org/W2890613572","https://openalex.org/W2940808208","https://openalex.org/W2976303698","https://openalex.org/W2995081665","https://openalex.org/W4231886136","https://openalex.org/W4252963756","https://openalex.org/W4285140022","https://openalex.org/W4391310464","https://openalex.org/W4396232166"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1969010119","https://openalex.org/W4395463268","https://openalex.org/W2626545547","https://openalex.org/W2167155214","https://openalex.org/W2124599625","https://openalex.org/W2952105401","https://openalex.org/W2347154653","https://openalex.org/W2733127495"],"abstract_inverted_index":{"Abstract":[0],"We":[1,193],"present":[2],"FullSynesth":[3,114,156,199],",":[4,21,132],"a":[5,13,23,56,61,66,90,103,123,128,160,167],"tree":[6,131],"reconciliation":[7],"algorithm":[8,176,216],"predicting":[9],"the":[10,79,83,85,96,111,120,180,188,202,215],"evolution":[11,121],"of":[12,15,58,63,74,122,125,174,182,190,205,214],"set":[14,57,62,67,124],"homologous":[16],"genomic":[17],"regions":[18],"or":[19,51],"syntenies":[20,59,101,126],"inside":[22],"species":[24,104],"tree.":[25,105],"The":[26,106,171],"considered":[27],"evolutionary":[28,93],"model":[29],"involves":[30],"segmental":[31],"events":[32],"(i.e.":[33],"acting":[34],"on":[35,117,159,195],"multiple":[36],"genes)":[37],"including":[38],"duplications":[39],"(D),":[40],"losses":[41],"(L),":[42],"synteny":[43,130,168],"fissions":[44],"and":[45,65,100,165],"transfers":[46],"possibly":[47],"going":[48],"through":[49],"unsampled":[50],"extinct":[52],"species.":[53],"Formally,":[54],"given":[55,102,127],"in":[60,154,179,187],"genomes":[64],"$$\\mathcal":[68,138],"{G}$$":[69,139],"<mml:math":[70,140],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[71,141],"<mml:mi>G</mml:mi>":[72,142],"</mml:math>":[73,143],"consistent":[75],"gene":[76,80,98,183,191],"trees":[77,99,184],"for":[78,110],"families":[81],"composing":[82],"syntenies,":[84],"problem":[86,107],"is":[87,108,115,157,177,217],"to":[88,208],"infer":[89],"most":[91],"parsimonious":[92],"history":[94],"explaining":[95],"observed":[97],"NP-hard":[109],"DL":[112],"distance.":[113],"based":[116,158],"Synesth":[118,206],"explicating":[119],"single":[129],"which":[133],"can":[134],"be":[135],"obtained":[136],"from":[137],"by":[144],"selecting":[145],"an":[146],"\u201coptimal\u201d":[147],"supertree.":[148,211],"Rather":[149],"than":[150,186],"trying":[151],"each":[152,209],"supertree":[153,169],"turn,":[155],"two-in-one":[161],"approach":[162],"simultaneously":[163],"building":[164],"reconciling":[166],".":[170,221],"running":[172,203],"time":[173,204],"this":[175],"exponential":[178],"number":[181],"rather":[185],"size":[189],"trees.":[192],"show":[194],"simulated":[196],"datasets":[197],"that":[198],"significantly":[200],"improves":[201],"applied":[207],"possible":[210],"An":[212],"implementation":[213],"available":[218],"at:":[219],"http://www.iro.umontreal.ca/~mabrouk/":[220]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
