{"id":"https://openalex.org/W3166605709","doi":"https://doi.org/10.1142/s0219720021400126","title":"Comparing the topology of phylogenetic network generators","display_name":"Comparing the topology of phylogenetic network generators","publication_year":2021,"publication_date":"2021-12-01","ids":{"openalex":"https://openalex.org/W3166605709","doi":"https://doi.org/10.1142/s0219720021400126","mag":"3166605709","pmid":"https://pubmed.ncbi.nlm.nih.gov/34895114"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720021400126","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720021400126","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Remie Janssen","orcid":null},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Remie Janssen","raw_affiliation_strings":["Delft University of Technology, Delft Institute of Applied Mathematics, Mekelweg 4, 2628 CD, Delft, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft University of Technology, Delft Institute of Applied Mathematics, Mekelweg 4, 2628 CD, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":null,"display_name":"Pengyu Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pengyu Liu","raw_affiliation_strings":["Simon Fraser University, Department of Mathematics, 8888 University Drive, Burnaby, BC V5A 1S6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Department of Mathematics, 8888 University Drive, Burnaby, BC V5A 1S6, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9771,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.74300358,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"06","first_page":"2140012","last_page":"2140012"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7666000127792358,"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":0.7666000127792358,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.17319999635219574,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.01119999960064888,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.8727999925613403},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8622000217437744},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.585099995136261},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.5828999876976013},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.539900004863739},{"id":"https://openalex.org/keywords/reticulate","display_name":"Reticulate","score":0.5027999877929688},{"id":"https://openalex.org/keywords/reticulate-evolution","display_name":"Reticulate evolution","score":0.4690999984741211},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.45179998874664307},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"Horizontal gene transfer","score":0.44130000472068787}],"concepts":[{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.8727999925613403},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8622000217437744},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.585099995136261},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.5828999876976013},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.539900004863739},{"id":"https://openalex.org/C2780432395","wikidata":"https://www.wikidata.org/wiki/Q21149008","display_name":"Reticulate","level":2,"score":0.5027999877929688},{"id":"https://openalex.org/C2778727739","wikidata":"https://www.wikidata.org/wiki/Q18434417","display_name":"Reticulate evolution","level":4,"score":0.4690999984741211},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.45179998874664307},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.44130000472068787},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.421999990940094},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.414900004863739},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.41110000014305115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4097000062465668},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.40450000762939453},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.39980000257492065},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.3799000084400177},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.3774000108242035},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36910000443458557},{"id":"https://openalex.org/C98722961","wikidata":"https://www.wikidata.org/wiki/Q7189436","display_name":"Phylogenetic diversity","level":4,"score":0.34549999237060547},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33980000019073486},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.33320000767707825},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.30250000953674316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29440000653266907},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.28870001435279846},{"id":"https://openalex.org/C2874115","wikidata":"https://www.wikidata.org/wiki/Q17099562","display_name":"Persistent homology","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2777000069618225},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.27649998664855957},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2728999853134155},{"id":"https://openalex.org/C176771619","wikidata":"https://www.wikidata.org/wiki/Q7189434","display_name":"Phylogenetic comparative methods","level":4,"score":0.2662000060081482},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.2547999918460846}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720021400126","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720021400126","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:34895114","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34895114","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:tudelft.nl:uuid:c17e2052-8b27-4c29-b152-d6d651f43255","is_oa":false,"landing_page_url":"http://resolver.tudelft.nl/uuid:c17e2052-8b27-4c29-b152-d6d651f43255","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5653627373","display_name":"Encoding, reconstructing and comparing complex evolutionary scenarios","funder_award_id":"639.072.602","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320319880","display_name":"Government of Canada","ror":"https://ror.org/010q4q527"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1549202508","https://openalex.org/W1700611987","https://openalex.org/W2042774332","https://openalex.org/W2051986117","https://openalex.org/W2057280377","https://openalex.org/W2114369768","https://openalex.org/W2115638597","https://openalex.org/W2127964182","https://openalex.org/W2130138677","https://openalex.org/W2144462058","https://openalex.org/W2266356354","https://openalex.org/W2295797791","https://openalex.org/W2312890204","https://openalex.org/W2344026690","https://openalex.org/W2345610960","https://openalex.org/W2605394804","https://openalex.org/W2741899203","https://openalex.org/W2746012438","https://openalex.org/W2774734636","https://openalex.org/W2775777653","https://openalex.org/W2789052566","https://openalex.org/W2840568513","https://openalex.org/W2888343454","https://openalex.org/W2910230320","https://openalex.org/W2912205626","https://openalex.org/W2951570719","https://openalex.org/W2952712909","https://openalex.org/W2962725223","https://openalex.org/W2962883559","https://openalex.org/W2966923908","https://openalex.org/W2969621323","https://openalex.org/W3009362918","https://openalex.org/W3011947420","https://openalex.org/W3027311537","https://openalex.org/W3040650981","https://openalex.org/W3081157667","https://openalex.org/W3119774682","https://openalex.org/W3120473550","https://openalex.org/W3154495432","https://openalex.org/W4236590756","https://openalex.org/W4254268221"],"related_works":[],"abstract_inverted_index":{"Phylogenetic":[0],"networks":[1,25,44,107],"represent":[2],"evolutionary":[3,12,31,49],"history":[4,32],"of":[5,30,80,95,104,111],"species":[6],"and":[7,19,113],"can":[8,57],"record":[9],"natural":[10],"reticulate":[11],"processes":[13,38],"such":[14],"as":[15,64,70],"horizontal":[16],"gene":[17,20],"transfer":[18],"recombination.":[21],"This":[22],"makes":[23],"phylogenetic":[24,35,96],"a":[26,78,93],"more":[27,71],"comprehensive":[28],"representation":[29],"compared":[33],"to":[34],"trees.":[36],"Stochastic":[37],"for":[39,60,66,84],"generating":[40],"random":[41],"trees":[42],"or":[43,62,82],"are":[45,74],"important":[46],"tools":[47],"in":[48,52],"analysis,":[50],"especially":[51],"phylogeny":[53],"reconstruction":[54],"where":[55],"they":[56],"be":[58],"utilized":[59],"validation":[61],"serve":[63],"priors":[65],"Bayesian":[67],"methods.":[68],"However,":[69],"network":[72,97],"generators":[73,98],"developed,":[75],"there":[76],"is":[77],"lack":[79],"discussion":[81],"comparison":[83],"different":[85],"generators.":[86],"To":[87],"bridge":[88],"this":[89],"gap,":[90],"we":[91],"compare":[92],"set":[94],"by":[99],"profiling":[100],"topological":[101,116],"summary":[102],"statistics":[103],"the":[105,109,115],"generated":[106],"over":[108],"number":[110],"reticulations":[112],"comparing":[114],"profiles.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2021-06-22T00:00:00"}
