{"id":"https://openalex.org/W2113923028","doi":"https://doi.org/10.1109/tcbb.2013.2297913","title":"Effect of Incomplete Lineage Sorting On Tree-Reconciliation-Based Inference of Gene Duplication","display_name":"Effect of Incomplete Lineage Sorting On Tree-Reconciliation-Based Inference of Gene Duplication","publication_year":2014,"publication_date":"2014-01-31","ids":{"openalex":"https://openalex.org/W2113923028","doi":"https://doi.org/10.1109/tcbb.2013.2297913","mag":"2113923028","pmid":"https://pubmed.ncbi.nlm.nih.gov/26356016"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2013.2297913","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2013.2297913","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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":"https://openalex.org/A5103176848","display_name":"Y. Zheng","orcid":"https://orcid.org/0000-0002-4617-3252"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Yu Zheng","raw_affiliation_strings":["Department of Mathematics, Singapore","Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Singapore","institution_ids":[]},{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012300835","display_name":"Louxin Zhang","orcid":"https://orcid.org/0000-0003-0260-824X"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Louxin Zhang","raw_affiliation_strings":["Department of Mathematics, Singapore","Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Singapore","institution_ids":[]},{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5103176848"],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":null,"apc_paid":null,"fwci":0.4278,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.64543235,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"3","first_page":"477","last_page":"485"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9803000092506409,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9765999913215637,"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/coalescent-theory","display_name":"Coalescent theory","score":0.9085922241210938},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.9056925773620605},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6726614832878113},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.538532018661499},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.4285874366760254},{"id":"https://openalex.org/keywords/sorting","display_name":"Sorting","score":0.4153899550437927},{"id":"https://openalex.org/keywords/gene-family","display_name":"Gene family","score":0.4148377478122711},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3684212267398834},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.36621978878974915},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.36260169744491577},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35808688402175903},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34231340885162354},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3231349587440491},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2637423276901245},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.2608029246330261},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.20925986766815186},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1920810341835022},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1908949613571167},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14597401022911072}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.9085922241210938},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.9056925773620605},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6726614832878113},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.538532018661499},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.4285874366760254},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.4153899550437927},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.4148377478122711},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3684212267398834},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36621978878974915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36260169744491577},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35808688402175903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34231340885162354},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3231349587440491},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2637423276901245},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.2608029246330261},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.20925986766815186},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1920810341835022},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1908949613571167},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14597401022911072}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049750","descriptor_name":"Genome, Insect","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049750","descriptor_name":"Genome, Insect","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D049750","descriptor_name":"Genome, Insect","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2013.2297913","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2013.2297913","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26356016","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26356016","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.638.7606","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.638.7606","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.math.nus.edu.sg/~matzlx/papers/TCBB_ZhengZhang.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320313889","display_name":"Lanzhou University","ror":"https://ror.org/01mkqqe32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W650383694","https://openalex.org/W1523611852","https://openalex.org/W1576387209","https://openalex.org/W1872045777","https://openalex.org/W1892960895","https://openalex.org/W1929783548","https://openalex.org/W1972204941","https://openalex.org/W1988471037","https://openalex.org/W2004096961","https://openalex.org/W2007270568","https://openalex.org/W2017051353","https://openalex.org/W2020089203","https://openalex.org/W2032299129","https://openalex.org/W2037654474","https://openalex.org/W2046039468","https://openalex.org/W2055758623","https://openalex.org/W2061646232","https://openalex.org/W2067547496","https://openalex.org/W2084761838","https://openalex.org/W2095829109","https://openalex.org/W2101896427","https://openalex.org/W2102665886","https://openalex.org/W2112621018","https://openalex.org/W2112755610","https://openalex.org/W2115688047","https://openalex.org/W2127688908","https://openalex.org/W2128252278","https://openalex.org/W2132318428","https://openalex.org/W2134824589","https://openalex.org/W2135281627","https://openalex.org/W2142718629","https://openalex.org/W2144345157","https://openalex.org/W2145608399","https://openalex.org/W2157360426","https://openalex.org/W2159447863","https://openalex.org/W2166145142","https://openalex.org/W2170753094","https://openalex.org/W2172696783","https://openalex.org/W2177816505","https://openalex.org/W2178682494","https://openalex.org/W2331613197","https://openalex.org/W4230073781","https://openalex.org/W4230603454","https://openalex.org/W4239151680"],"related_works":["https://openalex.org/W2952954362","https://openalex.org/W1914610732","https://openalex.org/W3126460685","https://openalex.org/W3025364102","https://openalex.org/W2999254484","https://openalex.org/W2002623332","https://openalex.org/W1970221653","https://openalex.org/W2810780526","https://openalex.org/W3040603050","https://openalex.org/W4236246458"],"abstract_inverted_index":{"In":[0],"the":[1,7,14,21,35,57,72,96,102,105,158],"tree":[2,17,40,50,68,115,145,154],"reconciliation":[3,51,146],"approach":[4,150],"to":[5,20,31],"infer":[6],"duplication":[8,46,63,77,110,130,141],"history":[9],"of":[10,37,59,71,75,107],"a":[11,38,49,66,82,89,113],"gene":[12,15,39,62,84,140,153],"family,":[13],"(family)":[16],"is":[18,53,142],"compared":[19],"corresponding":[22],"species":[23,67,97,114,136],"tree.":[24,98,137],"Incomplete":[25],"lineage":[26],"sorting":[27],"(ILS)":[28],"gives":[29],"rise":[30],"stochastic":[32],"variation":[33],"in":[34,65,69,92,112],"topology":[36,155],"and":[41,95,116],"hence":[42],"likely":[43],"introduces":[44],"false":[45,76],"events":[47,78],"when":[48,139],"method":[52],"used.":[54],"We":[55,99],"quantify":[56],"effect":[58,106],"ILS":[60,108,124],"on":[61,109,129,133],"inference":[64,111],"terms":[70],"expected":[73],"number":[74],"inferred":[79,143],"from":[80],"reconciling":[81],"random":[83],"tree,":[85],"which":[86],"occurs":[87],"with":[88],"probability":[90],"predicted":[91],"coalescent":[93],"theory,":[94],"computationally":[100],"examine":[101],"relationship":[103],"between":[104],"its":[117],"topological":[118],"parameters.":[119],"Our":[120],"findings":[121],"suggest":[122],"that":[123,151],"may":[125],"cause":[126],"non-negligible":[127],"bias":[128,160],"inference,":[131],"particularly":[132],"an":[134],"asymmetric":[135],"Hence,":[138],"via":[144],"or":[147],"any":[148],"other":[149],"takes":[152],"into":[156],"account,":[157],"ILS-induced":[159],"should":[161],"be":[162],"examined":[163],"cautiously.":[164]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
