{"id":"https://openalex.org/W2882992890","doi":"https://doi.org/10.1093/bioinformatics/bty631","title":"SonicParanoid: fast, accurate and easy orthology inference","display_name":"SonicParanoid: fast, accurate and easy orthology inference","publication_year":2018,"publication_date":"2018-07-14","ids":{"openalex":"https://openalex.org/W2882992890","doi":"https://doi.org/10.1093/bioinformatics/bty631","mag":"2882992890","pmid":"https://pubmed.ncbi.nlm.nih.gov/30032301"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty631","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/149/27183029/bty631.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/35/1/149/27183029/bty631.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100723453","display_name":"Salvatore Cosentino","orcid":"https://orcid.org/0000-0002-1066-8659"},"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":true,"raw_author_name":"Salvatore Cosentino","raw_affiliation_strings":["Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"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":true,"raw_author_name":"Wataru Iwasaki","raw_affiliation_strings":["Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan","Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan","Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan"],"affiliations":[{"raw_affiliation_string":"Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5088277364","https://openalex.org/A5100723453"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.7495,"has_fulltext":false,"cited_by_count":165,"citation_normalized_percentile":{"value":0.96081575,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"1","first_page":"149","last_page":"151"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983999729156494,"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/inference","display_name":"Inference","score":0.8029177188873291},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7714512348175049},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7410288453102112},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.592434287071228},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.573307991027832},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5304676294326782},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.45697319507598877},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.454353004693985},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.415335088968277},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40609973669052124},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33789896965026855},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.31825006008148193},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.31013381481170654},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.288437157869339},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18090838193893433},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11501845717430115}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.8029177188873291},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7714512348175049},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7410288453102112},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.592434287071228},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.573307991027832},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5304676294326782},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.45697319507598877},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.454353004693985},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.415335088968277},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40609973669052124},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33789896965026855},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31825006008148193},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.31013381481170654},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.288437157869339},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18090838193893433},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11501845717430115},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty631","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/149/27183029/bty631.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30032301","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30032301","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:europepmc.org:5272913","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6298048","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty631","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/149/27183029/bty631.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2882992890.pdf","grobid_xml":"https://content.openalex.org/works/W2882992890.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1552559843","https://openalex.org/W1900937478","https://openalex.org/W1979835060","https://openalex.org/W2008856488","https://openalex.org/W2030530458","https://openalex.org/W2045204781","https://openalex.org/W2112884978","https://openalex.org/W2120141270","https://openalex.org/W2142678478","https://openalex.org/W2143335572","https://openalex.org/W2146709375","https://openalex.org/W2158714788","https://openalex.org/W2167188257","https://openalex.org/W2316262244","https://openalex.org/W2559466477","https://openalex.org/W2579640851","https://openalex.org/W2734735318","https://openalex.org/W2950954328","https://openalex.org/W3210308821","https://openalex.org/W4252553099"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W2546377002","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W4285209474","https://openalex.org/W3097598351","https://openalex.org/W3170192653"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}