{"id":"https://openalex.org/W3002103667","doi":"https://doi.org/10.1093/bioinformatics/btaa043","title":"Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks","display_name":"Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks","publication_year":2020,"publication_date":"2020-01-17","ids":{"openalex":"https://openalex.org/W3002103667","doi":"https://doi.org/10.1093/bioinformatics/btaa043","mag":"3002103667","pmid":"https://pubmed.ncbi.nlm.nih.gov/31971565"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa043","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076510089","display_name":"Henry Xing","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Henry Xing","raw_affiliation_strings":["Department of Computer Sciences"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001473679","display_name":"Steven W. Kembel","orcid":"https://orcid.org/0000-0001-5224-0952"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Steven W Kembel","raw_affiliation_strings":["Department of Biology , Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology , Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, Canada","institution_ids":["https://openalex.org/I159129438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004592090","display_name":"Vladimir Makarenkov","orcid":"https://orcid.org/0000-0003-3753-5925"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Vladimir Makarenkov","raw_affiliation_strings":["Department of Computer Sciences"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004592090"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1657,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47816382,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"36","issue":"9","first_page":"2740","last_page":"2749"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965999722480774,"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":0.9965999722480774,"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/T10066","display_name":"Gut microbiota and health","score":0.9887999892234802,"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":0.9711999893188477,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.879848837852478},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.6966764330863953},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6431393027305603},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"Horizontal gene transfer","score":0.639473557472229},{"id":"https://openalex.org/keywords/unifrac","display_name":"UniFrac","score":0.5846524238586426},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5821347236633301},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5387903451919556},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5034610629081726},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.49231278896331787},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4794546365737915},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3602107763290405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2889598608016968},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27539530396461487},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27318263053894043},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2686660885810852},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14910772442817688}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.879848837852478},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.6966764330863953},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6431393027305603},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.639473557472229},{"id":"https://openalex.org/C151437367","wikidata":"https://www.wikidata.org/wiki/Q7884646","display_name":"UniFrac","level":4,"score":0.5846524238586426},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5821347236633301},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5387903451919556},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5034610629081726},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.49231278896331787},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4794546365737915},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3602107763290405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2889598608016968},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27539530396461487},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27318263053894043},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2686660885810852},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14910772442817688},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"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":"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":"D019143","descriptor_name":"Evolution, Molecular","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":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa043","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31971565","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31971565","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1987157480","display_name":null,"funder_award_id":"173878","funder_id":"https://openalex.org/F4320321747","funder_display_name":"Fonds Qu\u00e9b\u00e9cois de la Recherche sur la Nature et les Technologies"},{"id":"https://openalex.org/G4926246454","display_name":null,"funder_award_id":"249644","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320321747","display_name":"Fonds Qu\u00e9b\u00e9cois de la Recherche sur la Nature et les Technologies","ror":"https://ror.org/00b9f9778"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1600022668","https://openalex.org/W1971421925","https://openalex.org/W1977358834","https://openalex.org/W2017519756","https://openalex.org/W2025410674","https://openalex.org/W2033193852","https://openalex.org/W2055298722","https://openalex.org/W2055615060","https://openalex.org/W2056246809","https://openalex.org/W2082397064","https://openalex.org/W2097706568","https://openalex.org/W2107387420","https://openalex.org/W2108718991","https://openalex.org/W2110141882","https://openalex.org/W2113561798","https://openalex.org/W2120976598","https://openalex.org/W2121166240","https://openalex.org/W2124547924","https://openalex.org/W2132926880","https://openalex.org/W2765676440","https://openalex.org/W2766807003","https://openalex.org/W2952113249","https://openalex.org/W2963517728","https://openalex.org/W4233815609","https://openalex.org/W6654563908","https://openalex.org/W6674647444"],"related_works":["https://openalex.org/W2086569686","https://openalex.org/W2955985798","https://openalex.org/W3012252241","https://openalex.org/W147961746","https://openalex.org/W2739728095","https://openalex.org/W2065083790","https://openalex.org/W2409815428","https://openalex.org/W2604174992","https://openalex.org/W2057191541","https://openalex.org/W2105489997"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}