{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T16:41:16Z","timestamp":1774629676743,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T00:00:00Z","timestamp":1634774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01 AI145552"],"award-info":[{"award-number":["R01 AI145552"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21 AI138815"],"award-info":[{"award-number":["R21 AI138815"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation","award":["RAPID DEB2028221"],"award-info":[{"award-number":["RAPID DEB2028221"]}]},{"name":"National Science Foundation","award":["NSF RAPID DMS2028728"],"award-info":[{"award-number":["NSF RAPID DMS2028728"]}]},{"name":"Stephany W. Holloway University Chair in AIDS Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both genetic diversity and temporal distribution through a genetic algorithm.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>TARDiS, along with example datasets and a user manual, is available at https:\/\/github.com\/smarini\/tardis-phylogenetics<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab725","type":"journal-article","created":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T07:52:20Z","timestamp":1634629940000},"page":"856-860","source":"Crossref","is-referenced-by-count":17,"title":["Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics"],"prefix":"10.1093","volume":"38","author":[{"given":"Simone","family":"Marini","sequence":"first","affiliation":[{"name":"Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA"},{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carla","family":"Mavian","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"},{"name":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9150-8333","authenticated-orcid":false,"given":"Alberto","family":"Riva","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mattia","family":"Prosperi","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Salemi","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"},{"name":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6088-4651","authenticated-orcid":false,"given":"Brittany","family":"Rife Magalis","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, FL 32611, USA"},{"name":"Department of Pathology, University of Florida , Gainesville, FL 32611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,10,21]]},"reference":[{"key":"2023020108482459500_btab725-B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1111\/2041-210X.12299","article-title":"Split diversity in constrained conservation prioritization using integer linear programming","volume":"6","author":"Chernomor","year":"2015","journal-title":"Methods Ecol. Evol"},{"key":"2023020108482459500_btab725-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3376916","article-title":"Indicator-based multi-objective evolutionary algorithms: a comprehensive survey","volume":"53","author":"Falc\u00f3n-Cardona","year":"2020","journal-title":"ACM Comput. Surv"},{"key":"2023020108482459500_btab725-B3","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.epidem.2014.09.001","article-title":"Eight challenges in phylodynamic inference","volume":"10","author":"Frost","year":"2015","journal-title":"Epidemics"},{"key":"2023020108482459500_btab725-B4","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1126\/science.1090727","article-title":"Unifying the epidemiological and evolutionary dynamics of pathogens","volume":"303","author":"Grenfell","year":"2004","journal-title":"Science"},{"key":"2023020108482459500_btab725-B5","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2023020108482459500_btab725-B6","doi-asserted-by":"crossref","first-page":"vew003","DOI":"10.1093\/ve\/vew003","article-title":"The effects of sampling strategy on the quality of reconstruction of viral population dynamics using bayesian skyline family coalescent methods: a simulation study","volume":"2","author":"Hall","year":"2016","journal-title":"Virus Evol"},{"key":"2023020108482459500_btab725-B7","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3390\/v12020182","article-title":"In search of covariates of HIV-1 subtype b spread in the united states\u2014a cautionary tale of large-scale bayesian phylogeography","volume":"12","author":"Hong","year":"2020","journal-title":"Viruses"},{"key":"2023020108482459500_btab725-B8","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-52156-5","volume-title":"Genetic Algorithm Essentials","author":"Kramer","year":"2017"},{"key":"2023020108482459500_btab725-B9","doi-asserted-by":"crossref","first-page":"e0245352","DOI":"10.1371\/journal.pone.0245352","article-title":"Earliest detection to date of SARS-CoV-2 in Florida: identification together with influenza virus on the main entry door of a university building, february 2020","volume":"16","author":"Lednicky","year":"2021","journal-title":"PLoS One"},{"key":"2023020108482459500_btab725-B10","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1111\/2041-210X.13422","article-title":"nosoi: a stochastic agent-based transmission chain simulation framework in R","volume":"11","author":"Lequime","year":"2020","journal-title":"Methods Ecol. Evol"},{"key":"2023020108482459500_btab725-B12","doi-asserted-by":"crossref","first-page":"12522","DOI":"10.1073\/pnas.2007295117","article-title":"Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-CoV-2 infections unreliable","volume":"117","author":"Mavian","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108482459500_btab725-B13","doi-asserted-by":"crossref","first-page":"e19170","DOI":"10.2196\/19170","article-title":"A snapshot of SARS-CoV-2 genome availability up to April 2020 and its implications: data analysis","volume":"6","author":"Mavian","year":"2020","journal-title":"JMIR Public Health Surveill"},{"key":"2023020108482459500_btab725-B14","doi-asserted-by":"crossref","first-page":"7897","DOI":"10.1073\/pnas.1918763117","article-title":"Toxigenic vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems","volume":"117","author":"Mavian","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108482459500_btab725-B15","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.bbrc.2020.10.092","article-title":"Host-directed editing of the SARS-CoV-2 genome","volume":"538","author":"Mourier","year":"2021","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023020108482459500_btab725-B16","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s41232-020-00126-7","article-title":"Genome evolution of SARS-CoV-2 and its virological characteristics","volume":"40","author":"Nakagawa","year":"2020","journal-title":"Inflamm. Regen"},{"key":"2023020108482459500_btab725-B17","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1093\/oxfordjournals.molbev.a026369","article-title":"A fast algorithm for joint reconstruction of ancestral amino acid sequences","volume":"17","author":"Pupko","year":"2000","journal-title":"Mol. Biol. Evol"},{"key":"2023020108482459500_btab725-B18","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using tempest (formerly path-o-gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"2023020108482459500_btab725-B19","volume-title":"R: A Language and Environment for Statistical Computing","year":"2020"},{"key":"2023020108482459500_btab725-B20","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things)","volume":"3","author":"Revell","year":"2012","journal-title":"Methods Ecol. Evol"},{"key":"2023020108482459500_btab725-B21","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s41256-017-0034-y","article-title":"Phylodynamic applications in 21 st century global infectious disease research","volume":"2","author":"Rife","year":"2017","journal-title":"Global Health Res. Policy"},{"key":"2023020108482459500_btab725-B22","doi-asserted-by":"crossref","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"Gisaid: global initiative on sharing all influenza data\u2014from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Eurosurveillance"},{"key":"2023020108482459500_btab725-B23","doi-asserted-by":"crossref","first-page":"6815","DOI":"10.1073\/pnas.94.13.6815","article-title":"Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment","volume":"94","author":"Strimmer","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108482459500_btab725-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-37749-3","article-title":"The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis","volume":"9","author":"Wilkinson","year":"2019","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab725\/40795015\/btab725.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/856\/49007895\/btab725.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/856\/49007895\/btab725.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:06:41Z","timestamp":1675264001000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/3\/856\/6407117"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,10,21]]},"references-count":23,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,1,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab725","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.01.15.426832","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,1]]},"published":{"date-parts":[[2021,10,21]]}}}