{"id":"https://openalex.org/W4283716880","doi":"https://doi.org/10.1093/bioinformatics/btac433","title":"Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families","display_name":"Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families","publication_year":2022,"publication_date":"2022-06-30","ids":{"openalex":"https://openalex.org/W4283716880","doi":"https://doi.org/10.1093/bioinformatics/btac433","pmid":"https://pubmed.ncbi.nlm.nih.gov/35771653"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac433","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac433","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4039/45301000/btac433.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4039/45301000/btac433.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085566781","display_name":"Tsukasa Fukunaga","orcid":"https://orcid.org/0000-0003-4442-6049"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tsukasa Fukunaga","raw_affiliation_strings":["Waseda Institute for Advanced Study, Waseda University , Tokyo 1690051, Japan"],"affiliations":[{"raw_affiliation_string":"Waseda Institute for Advanced Study, Waseda University , Tokyo 1690051, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088277364","display_name":"Wataru Iwasaki","orcid":"https://orcid.org/0000-0002-9169-9245"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Wataru Iwasaki","raw_affiliation_strings":["Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo , Chiba 2770882, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo , Chiba 2770882, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085566781"],"corresponding_institution_ids":["https://openalex.org/I150744194"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1733,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47388727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"38","issue":"16","first_page":"4039","last_page":"4041"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9969000220298767,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9948999881744385,"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/computer-science","display_name":"Computer science","score":0.6704847812652588},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6230510473251343},{"id":"https://openalex.org/keywords/content","display_name":"Content (measure theory)","score":0.5333831906318665},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5124347805976868},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4701136648654938},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4338107109069824},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3788753151893616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2503197491168976},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18299415707588196},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1202608048915863},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08311411738395691},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.06304916739463806}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6704847812652588},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6230510473251343},{"id":"https://openalex.org/C2778152352","wikidata":"https://www.wikidata.org/wiki/Q5165061","display_name":"Content (measure theory)","level":2,"score":0.5333831906318665},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5124347805976868},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4701136648654938},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4338107109069824},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3788753151893616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2503197491168976},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18299415707588196},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1202608048915863},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08311411738395691},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.06304916739463806},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003776","descriptor_name":"Dental Porcelain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003776","descriptor_name":"Dental Porcelain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003776","descriptor_name":"Dental Porcelain","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":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac433","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac433","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4039/45301000/btac433.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35771653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35771653","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9364385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9364385","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac433","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac433","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4039/45301000/btac433.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1132990285","display_name":null,"funder_award_id":"JPMJCR19S2","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G1449818552","display_name":null,"funder_award_id":"JP20H05582","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4709092590","display_name":null,"funder_award_id":"JP22H04925","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4727676461","display_name":null,"funder_award_id":"JP22H04891","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7099850900","display_name":null,"funder_award_id":"JP19K20395","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283716880.pdf","grobid_xml":"https://content.openalex.org/works/W4283716880.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2041624900","https://openalex.org/W2059279601","https://openalex.org/W2139493455","https://openalex.org/W2186184898","https://openalex.org/W2563535234","https://openalex.org/W3107527779","https://openalex.org/W3113087152","https://openalex.org/W3189875465","https://openalex.org/W3200103613","https://openalex.org/W4205933632","https://openalex.org/W6686512395","https://openalex.org/W6730974599"],"related_works":["https://openalex.org/W4250539519","https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W4294018197","https://openalex.org/W193851735","https://openalex.org/W2773861473","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
