{"id":"https://openalex.org/W2744549373","doi":"https://doi.org/10.3233/fi-2017-1552","title":"Species-Driven Persistent Phylogeny","display_name":"Species-Driven Persistent Phylogeny","publication_year":2017,"publication_date":"2017-08-09","ids":{"openalex":"https://openalex.org/W2744549373","doi":"https://doi.org/10.3233/fi-2017-1552","mag":"2744549373"},"language":"en","primary_location":{"id":"doi:10.3233/fi-2017-1552","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2017-1552","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038691764","display_name":"Paola Bonizzoni","orcid":"https://orcid.org/0000-0001-7289-4988"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paola Bonizzoni","raw_affiliation_strings":["DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. bonizzoni@disco.unimib.it"],"affiliations":[{"raw_affiliation_string":"DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. bonizzoni@disco.unimib.it","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043161270","display_name":"Anna Paola Carrieri","orcid":"https://orcid.org/0000-0003-2349-1896"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anna Paola Carrieri","raw_affiliation_strings":["IBM Research, UK. annapaola.carrieri@disco.unimib.it"],"affiliations":[{"raw_affiliation_string":"IBM Research, UK. annapaola.carrieri@disco.unimib.it","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059679442","display_name":"Gianluca Della Vedova","orcid":"https://orcid.org/0000-0001-5584-3089"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluca Della Vedova","raw_affiliation_strings":["DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. gianluca.dellavedova@unimib.it"],"affiliations":[{"raw_affiliation_string":"DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. gianluca.dellavedova@unimib.it","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086249420","display_name":"Raffaella Rizzi","orcid":"https://orcid.org/0000-0001-9730-7516"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Raffaella Rizzi","raw_affiliation_strings":["DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. raffaella.rizzi@unimib.it"],"affiliations":[{"raw_affiliation_string":"DISCo, Universit\u00e0 degli Studi di Milano-Bicocca, Italy. raffaella.rizzi@unimib.it","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047355764","display_name":"Gabriella Trucco","orcid":"https://orcid.org/0000-0002-5904-0969"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriella Trucco","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 degli Studi di Milano, Italy. gabriella.trucco@unimi.it"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 degli Studi di Milano, Italy. gabriella.trucco@unimi.it","institution_ids":["https://openalex.org/I189158943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038691764"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08449742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"154","issue":"1-4","first_page":"47","last_page":"63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9950000047683716,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9914000034332275,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.8860744833946228},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4647720456123352},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.418226957321167},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3217931389808655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.22584301233291626},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08246445655822754}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.8860744833946228},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4647720456123352},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.418226957321167},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3217931389808655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.22584301233291626},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08246445655822754},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3233/fi-2017-1552","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2017-1552","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},{"id":"pmh:oai:boa.unimib.it:10281/185816","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/185816","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1504581534","https://openalex.org/W1523916760","https://openalex.org/W1558924190","https://openalex.org/W1979900996","https://openalex.org/W1990061958","https://openalex.org/W2005193052","https://openalex.org/W2005915210","https://openalex.org/W2008323735","https://openalex.org/W2031170804","https://openalex.org/W2054547415","https://openalex.org/W2056113107","https://openalex.org/W2072719910","https://openalex.org/W2074507113","https://openalex.org/W2076755063","https://openalex.org/W2110570734","https://openalex.org/W2117797567","https://openalex.org/W2120854648","https://openalex.org/W2122392334","https://openalex.org/W2147849085","https://openalex.org/W2155316689","https://openalex.org/W2157751858","https://openalex.org/W2166815431","https://openalex.org/W2482614962","https://openalex.org/W2514535054","https://openalex.org/W3145128584"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2061542922","https://openalex.org/W1923231248","https://openalex.org/W2383763250","https://openalex.org/W248275141","https://openalex.org/W2518331723"],"abstract_inverted_index":{"The":[0,31,141],"perfect":[1,75,131,150,157],"phylogeny":[2,144,158,166,184],"is":[3,34,42,51,105,146],"a":[4,64,117,156,164,181,192,196],"widely":[5],"used":[6],"model":[7,145],"in":[8,21,28,46,59,96],"phylogenetics,":[9],"since":[10,155],"it":[11,77],"provides":[12],"an":[13,177],"effective":[14],"representation":[15],"of":[16,18,67,88,109],"evolution":[17],"binary":[19],"characters":[20],"several":[22],"contexts,":[23],"such":[24],"as":[25],"for":[26],"example":[27],"haplotype":[29],"inference.":[30],"model,":[32,91],"which":[33],"conceptually":[35],"the":[36,45,60,74,85,89,101,125,149,152],"simplest":[37],"among":[38],"those":[39],"actually":[40],"used,":[41],"based":[43],"on":[44],"finite":[47],"sites":[48],"assumption,":[49],"that":[50,83,188],"no":[52,160],"character":[53,169],"can":[54],"mutate":[55,172],"more":[56,94],"than":[57],"once":[58],"whole":[61],"tree.":[62],"Since":[63],"large":[65],"number":[66],"biological":[68,98],"phenomena":[69],"cannot":[70],"be":[71],"modeled":[72],"by":[73],"phylogeny,":[76,132,134,154],"becomes":[78],"important":[79],"to":[80,170,179],"find":[81],"generalizations":[82],"retain":[84],"computational":[86],"tractability":[87],"original":[90],"but":[92],"are":[93],"flexible":[95],"modeling":[97],"data":[99],"when":[100],"infinite":[102],"site":[103],"assumption":[104],"violated,":[106],"e.g.":[107],"because":[108],"back":[110,161,171],"mutations.":[111],"In":[112],"this":[113],"paper,":[114],"we":[115,123,186],"introduce":[116],"new":[118],"model\u2014called":[119],"species-driven":[120,138,142,182,197],"persistent":[121,133,139,143,153,165,183,198],"phylogeny\u2014and":[122],"study":[124],"relations":[126],"between":[127,148],"three":[128],"different":[129],"formulations:":[130],"galled":[135],"trees,":[136],"and":[137,151,163,185],"phylogeny.":[140,199],"intermediate":[147],"allows":[159,167],"mutations":[162],"each":[168],"only":[173],"once.":[174],"We":[175],"describe":[176],"algorithm":[178],"compute":[180],"prove":[187],"every":[189],"matrix":[190],"admitting":[191],"galled-tree":[193],"also":[194],"admits":[195]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}