{"id":"https://openalex.org/W4307032578","doi":"https://doi.org/10.1093/bioinformatics/btac695","title":"SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes","display_name":"SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes","publication_year":2022,"publication_date":"2022-10-21","ids":{"openalex":"https://openalex.org/W4307032578","doi":"https://doi.org/10.1093/bioinformatics/btac695","pmid":"https://pubmed.ncbi.nlm.nih.gov/36269177"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac695","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5434/47887007/btac695.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/38/24/5434/47887007/btac695.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018972286","display_name":"Nicolas Robert","orcid":"https://orcid.org/0000-0002-7367-2241"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Nicolas Serge Matthieu Robert","raw_affiliation_strings":["Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052805561","display_name":"Fatih Sarigol","orcid":"https://orcid.org/0000-0002-5842-6114"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Fatih Sarigol","raw_affiliation_strings":["Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046884720","display_name":"Elisabeth Zieger","orcid":"https://orcid.org/0000-0003-3266-834X"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Elisabeth Zieger","raw_affiliation_strings":["Department of Evolutionary Biology, University of Vienna , Vienna A-1030, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Evolutionary Biology, University of Vienna , Vienna A-1030, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041816560","display_name":"Oleg Simakov","orcid":"https://orcid.org/0000-0002-3585-4511"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Oleg Simakov","raw_affiliation_strings":["Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5018972286","https://openalex.org/A5041816560"],"corresponding_institution_ids":["https://openalex.org/I129774422"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6932,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67341662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"38","issue":"24","first_page":"5434","last_page":"5436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.998199999332428,"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/synteny","display_name":"Synteny","score":0.9708505868911743},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7508608102798462},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6037111878395081},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5420641899108887},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5311347842216492},{"id":"https://openalex.org/keywords/collinearity","display_name":"Collinearity","score":0.48089078068733215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4507661759853363},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4107398986816406},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3996361494064331},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3437994420528412},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3280390501022339},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20406559109687805},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16348403692245483},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1603376269340515},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1602843701839447},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11975648999214172}],"concepts":[{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.9708505868911743},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7508608102798462},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6037111878395081},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5420641899108887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5311347842216492},{"id":"https://openalex.org/C106192678","wikidata":"https://www.wikidata.org/wiki/Q1419761","display_name":"Collinearity","level":2,"score":0.48089078068733215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4507661759853363},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4107398986816406},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3996361494064331},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3437994420528412},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3280390501022339},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20406559109687805},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16348403692245483},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1603376269340515},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1602843701839447},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11975648999214172}],"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":"D000818","descriptor_name":"Animals","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":"D010802","descriptor_name":"Phylogeny","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":"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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac695","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5434/47887007/btac695.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:36269177","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36269177","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:9750109","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9750109","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/btac695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac695","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5434/47887007/btac695.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":[{"score":0.7200000286102295,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G4437207346","display_name":null,"funder_award_id":"P32190","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4307032578.pdf","grobid_xml":"https://content.openalex.org/works/W4307032578.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1986009232","https://openalex.org/W1995958191","https://openalex.org/W2002833133","https://openalex.org/W2019829411","https://openalex.org/W2020134788","https://openalex.org/W2033203401","https://openalex.org/W2054345649","https://openalex.org/W2073523429","https://openalex.org/W2113102609","https://openalex.org/W2118910836","https://openalex.org/W2527473185","https://openalex.org/W2654359665","https://openalex.org/W2965948555","https://openalex.org/W2973945229","https://openalex.org/W2977230705","https://openalex.org/W3083715203","https://openalex.org/W3213085595","https://openalex.org/W4210701812","https://openalex.org/W4212873598","https://openalex.org/W4213188328"],"related_works":["https://openalex.org/W1969010119","https://openalex.org/W2571897395","https://openalex.org/W2626545547","https://openalex.org/W2159670039","https://openalex.org/W2167155214","https://openalex.org/W4226120311","https://openalex.org/W2124599625","https://openalex.org/W2952105401","https://openalex.org/W2347154653","https://openalex.org/W2058928070"],"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},{"year":2024,"cited_by_count":6}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
