{"id":"https://openalex.org/W3205003881","doi":"https://doi.org/10.1093/bioinformatics/btab725","title":"Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics","display_name":"Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics","publication_year":2021,"publication_date":"2021-10-19","ids":{"openalex":"https://openalex.org/W3205003881","doi":"https://doi.org/10.1093/bioinformatics/btab725","mag":"3205003881","pmid":"https://pubmed.ncbi.nlm.nih.gov/34672334"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab725","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab725","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756195","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004394877","display_name":"Simone Marini","orcid":"https://orcid.org/0000-0002-5704-3533"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simone Marini","raw_affiliation_strings":["Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA","Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008138111","display_name":"Carla Mavian","orcid":"https://orcid.org/0000-0003-3819-5520"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carla Mavian","raw_affiliation_strings":["Department of Pathology, University of Florida , Gainesville, FL 32611, USA","Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012026856","display_name":"Alberto Riva","orcid":"https://orcid.org/0000-0001-9150-8333"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alberto Riva","raw_affiliation_strings":["Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039419132","display_name":"Mattia Prosperi","orcid":"https://orcid.org/0000-0002-9021-5595"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mattia Prosperi","raw_affiliation_strings":["Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030387965","display_name":"Marco Salemi","orcid":"https://orcid.org/0000-0003-0136-2102"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marco Salemi","raw_affiliation_strings":["Department of Pathology, University of Florida , Gainesville, FL 32611, USA","Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003235834","display_name":"Brittany Rife Magalis","orcid":"https://orcid.org/0000-0001-6088-4651"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brittany Rife Magalis","raw_affiliation_strings":["Department of Pathology, University of Florida , Gainesville, FL 32611, USA","Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5003235834","https://openalex.org/A5030387965"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2171,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.79041431,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"856","last_page":"860"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958000183105469,"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":0.9958000183105469,"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/T10625","display_name":"Herpesvirus Infections and Treatments","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genetic-diversity","display_name":"Genetic diversity","score":0.7852767705917358},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6042258143424988},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5196877121925354},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5113058090209961},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.4998347759246826},{"id":"https://openalex.org/keywords/distribution","display_name":"Distribution (mathematics)","score":0.4669293761253357},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.464474081993103},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4416861832141876},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3639428913593292},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26402151584625244},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1316843330860138},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11030998826026917},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.06613731384277344}],"concepts":[{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.7852767705917358},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6042258143424988},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5196877121925354},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5113058090209961},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.4998347759246826},{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.4669293761253357},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.464474081993103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4416861832141876},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3639428913593292},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26402151584625244},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1316843330860138},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11030998826026917},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.06613731384277344},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"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/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"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":"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":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab725","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab725","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:34672334","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34672334","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:8756195","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756195","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8756195","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756195","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G944052996","display_name":null,"funder_award_id":"R21 AI138815","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1605984840","https://openalex.org/W2038978937","https://openalex.org/W2111728961","https://openalex.org/W2140689424","https://openalex.org/W2142773663","https://openalex.org/W2157322272","https://openalex.org/W2322358787","https://openalex.org/W2336948744","https://openalex.org/W2568426016","https://openalex.org/W2604907813","https://openalex.org/W2605343262","https://openalex.org/W2915293297","https://openalex.org/W2952045272","https://openalex.org/W3005151311","https://openalex.org/W3011855308","https://openalex.org/W3013925160","https://openalex.org/W3021396888","https://openalex.org/W3025717907","https://openalex.org/W3031121540","https://openalex.org/W3048320454","https://openalex.org/W3097776377","https://openalex.org/W3113090047"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2375383082","https://openalex.org/W2604174992","https://openalex.org/W1974895455","https://openalex.org/W3023641210"],"abstract_inverted_index":{"TARDiS,":[0],"along":[1],"with":[2],"example":[3],"datasets":[4],"and":[5],"a":[6],"user":[7],"manual,":[8],"is":[9],"available":[10],"at":[11],"https://github.com/smarini/tardis-phylogenetics.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2025-10-10T00:00:00"}
