{"id":"https://openalex.org/W4396232166","doi":"https://doi.org/10.3390/a17050186","title":"Synesth: Comprehensive Syntenic Reconciliation with Unsampled Lineages","display_name":"Synesth: Comprehensive Syntenic Reconciliation with Unsampled Lineages","publication_year":2024,"publication_date":"2024-04-29","ids":{"openalex":"https://openalex.org/W4396232166","doi":"https://doi.org/10.3390/a17050186"},"language":"en","primary_location":{"id":"doi:10.3390/a17050186","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17050186","pdf_url":"https://www.mdpi.com/1999-4893/17/5/186/pdf?version=1715323425","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/17/5/186/pdf?version=1715323425","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":true,"raw_author_name":"Matt\u00e9o Delabre","raw_affiliation_strings":["D\u00e9partement d\u2019Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, 2920 Chemin de la Tour, Montr\u00e9al, QC H3T 1J4, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d\u2019Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, 2920 Chemin de la Tour, Montr\u00e9al, QC H3T 1J4, Canada","institution_ids":["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/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\u2019Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, 2920 Chemin de la Tour, Montr\u00e9al, QC H3T 1J4, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d\u2019Informatique et de Recherche Op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al, 2920 Chemin de la Tour, Montr\u00e9al, QC H3T 1J4, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041470344","https://openalex.org/A5079973056"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":1.8905,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.84516955,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"17","issue":"5","first_page":"186","last_page":"186"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12496","display_name":"Color perception and design","score":0.8605999946594238,"subfield":{"id":"https://openalex.org/subfields/3207","display_name":"Social Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T12496","display_name":"Color perception and design","score":0.8605999946594238,"subfield":{"id":"https://openalex.org/subfields/3207","display_name":"Social Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.5145115852355957},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4925604462623596},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30352455377578735},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1756466031074524},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08101561665534973},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07985302805900574}],"concepts":[{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.5145115852355957},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4925604462623596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30352455377578735},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1756466031074524},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08101561665534973},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07985302805900574}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/a17050186","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17050186","pdf_url":"https://www.mdpi.com/1999-4893/17/5/186/pdf?version=1715323425","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:0a8b7cf87c52420eaa201210652f2ad3","is_oa":true,"landing_page_url":"https://doaj.org/article/0a8b7cf87c52420eaa201210652f2ad3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 17, Iss 5, p 186 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/a17050186","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a17050186","pdf_url":"https://www.mdpi.com/1999-4893/17/5/186/pdf?version=1715323425","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G155333359","display_name":null,"funder_award_id":"335893","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2313135192","display_name":null,"funder_award_id":"335893","funder_id":"https://openalex.org/F4320334841","funder_display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies"},{"id":"https://openalex.org/G3581799995","display_name":null,"funder_award_id":"RN000743","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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396232166.pdf","grobid_xml":"https://content.openalex.org/works/W4396232166.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1960535846","https://openalex.org/W1986968252","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2135281627","https://openalex.org/W2135894797","https://openalex.org/W2148231054","https://openalex.org/W2149582283","https://openalex.org/W2287141830","https://openalex.org/W2607495137","https://openalex.org/W2618312940","https://openalex.org/W2890613572","https://openalex.org/W2940808208","https://openalex.org/W2976303698","https://openalex.org/W2995081665","https://openalex.org/W3158735354","https://openalex.org/W3187893169","https://openalex.org/W4206099351","https://openalex.org/W4220893675","https://openalex.org/W4391271052"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","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/W2082860237"],"abstract_inverted_index":{"We":[0,54,184],"present":[1],"Synesth,":[2],"the":[3,43,56,71,124,149,162,174],"most":[4],"comprehensive":[5],"and":[6,28,49,64,106,156,165],"flexible":[7],"tool":[8],"for":[9,14,38,130,147,178,196],"tree":[10,48],"reconciliation":[11,62,181],"that":[12,41,172],"allows":[13,37],"events":[15,30],"on":[16,19],"syntenies":[17],"(i.e.,":[18],"sets":[20],"of":[21,59,74,85,90,92,101,123,151,159,173,202],"multiple":[22],"genes),":[23],"including":[24],"duplications,":[25],"transfers,":[26],"fissions,":[27],"transient":[29],"going":[31],"through":[32],"unsampled":[33],"species.":[34],"This":[35,168],"model":[36,63],"building":[39],"histories":[40,76,87,114],"explicate":[42],"inconsistencies":[44],"between":[45],"a":[46,80,98,152,200],"synteny":[47,164],"its":[50],"associated":[51,67],"species":[52,166],"tree.":[53],"examine":[55],"combinatorial":[57],"properties":[58],"this":[60,107],"extended":[61],"study":[65],"various":[66],"parsimony":[68],"problems.":[69],"First,":[70],"infinite":[72],"set":[73,84,100,201],"explicatory":[75],"is":[77],"reduced":[78],"to":[79,97,134,191],"finite":[81],"but":[82],"exponential":[83],"Pareto-optimal":[86,102,193],"(in":[88],"terms":[89],"counts":[91],"each":[93,131],"event":[94,103,112,117],"type),":[95],"then":[96],"polynomial":[99],"count":[104],"vectors,":[105],"eventually":[108],"ends":[109],"with":[110,141,182],"minimum":[111],"cost":[113,118,150],"given":[115],"an":[116,142],"function.":[119],"An":[120],"inductive":[121],"characterization":[122],"solution":[125],"space":[126],"using":[127],"different":[128],"algebras":[129],"granularity":[132],"leads":[133],"efficient":[135],"dynamic":[136],"programming":[137],"algorithms,":[138],"ultimately":[139],"ending":[140],"O(mn)":[143],"time":[144,169],"complexity":[145,170],"algorithm":[146],"computing":[148],"minimum-cost":[153],"history":[154],"(m":[155],"n:":[157],"number":[158],"nodes":[160],"in":[161,199],"input":[163],"trees).":[167],"matches":[171],"fastest":[175],"known":[176],"algorithms":[177],"classical":[179],"gene":[180],"transfers.":[183],"show":[185],"how":[186],"Synesth":[187],"can":[188],"be":[189],"applied":[190],"infer":[192],"evolutionary":[194],"scenarios":[195],"CRISPR-Cas":[197],"systems":[198],"bacterial":[203],"genomes.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
