{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T12:06:54Z","timestamp":1753877214410,"version":"3.41.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,1]],"date-time":"2023-03-01T00:00:00Z","timestamp":1677628800000},"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\/501100009543","name":"Pontificia Universidad Javeriana","doi-asserted-by":"publisher","award":["7170"],"award-info":[{"award-number":["7170"]}],"id":[{"id":"10.13039\/501100009543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008793","name":"Universidad del Rosario","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008793","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Clinical isolates of a fungal pathogen from a single region or country often exhibit structural clonality or phylogenetic clustering at the sequence or MLST level; such population structure can persist also in larger samples. In efforts to improve causal understanding of pathogenesis at the molecular level, genome-wide association screening methods initially designed for other kingdoms have been applied to fungi. The example of a Colombian dataset of 28 clinical Cryptococcus neoformans VNI isolates indicates where the output from standard pipelines may need to be analyzed in new ways in order to efficiently extract hypotheses for experiments from fungal genotype\u2013phenotype data.<\/jats:p>","DOI":"10.1093\/mmy\/myad024","type":"journal-article","created":{"date-parts":[[2023,3,8]],"date-time":"2023-03-08T01:45:47Z","timestamp":1678239947000},"source":"Crossref","is-referenced-by-count":0,"title":["The structure of associations: Method insights from analyzing 28 clinical isolates of<i>Cryptococcus neoformans<\/i>"],"prefix":"10.1093","volume":"61","author":[{"given":"N\u00f3rida","family":"V\u00e9lez","sequence":"first","affiliation":[{"name":"Unidad de Prote\u00f3mica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiolog\u00eda, Facultad de Ciencias, Pontificia Universidad Javeriana , Bogot\u00e1 , Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nelson","family":"Vega-Vela","sequence":"additional","affiliation":[{"name":"Unidad de Prote\u00f3mica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiolog\u00eda, Facultad de Ciencias, Pontificia Universidad Javeriana , Bogot\u00e1 , Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2881-3815","authenticated-orcid":false,"given":"Oliver Keatinge","family":"Clay","sequence":"additional","affiliation":[{"name":"Studies in Translational Microbiology and Emerging Diseases (MICROS), ITM, School of Medicine and Health Sciences, Universidad del Rosario , Bogot\u00e1 , Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia-Marcela","family":"Parra-Giraldo","sequence":"additional","affiliation":[{"name":"Unidad de Prote\u00f3mica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiolog\u00eda, Facultad de Ciencias, Pontificia Universidad Javeriana , Bogot\u00e1 , Colombia"},{"name":"Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Farmacia, Universidad Complutense de Madrid , Madrid , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,3,7]]},"reference":[{"journal-title":"On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life","year":"1859","author":"Darwin","key":"2023032922201797500_"},{"key":"2023032922201797500_","first-page":"245","article-title":"Deciphering the association among pathogenicity, production and polymorphisms of capsule\/melanin in clinical isolates of Cryptococcus neoformans var. grubii VNI","volume":"8","author":"V\u00e9lez","year":"2022","journal-title":"J Fungi(Basel)"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198546412.001.0001","volume-title":"The Comparative Method in Evolutionary Biology","author":"Harvey","year":"1991"},{"volume-title":"The Evolution of Life Histories","year":"1992","author":"Stearns","key":"2023032922201797500_"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1080\/13693780902953886","article-title":"Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii","volume":"47","author":"Meyer","year":"2009","journal-title":"Med Mycol"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","first-page":"e1003669","DOI":"10.1371\/journal.pgen.1003669","article-title":"Genome wide association identifies novel loci involved in fungal communication","volume":"9","author":"Palma-Guerrero","year":"2013","journal-title":"PLoS Genet"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3390\/jof8010057","article-title":"The combination of iron and copper increases pathogenicity and induces proteins related to the main virulence factors in clinical isolates of Cryptococcus neoformans var. grubii","volume":"8","author":"V\u00e9lez","year":"2022","journal-title":"J Fungi (Basel)"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-2763-0","volume-title":"Fractals and Scaling in Finance: Discontinuity, Concentration, Risk","author":"Mandelbrot","year":"1997"},{"key":"2023032922201797500_","first-page":"4912","article-title":"Complementation of a capsule-deficient mutation of Cryptococcus neoformans restores its virulence","volume":"14","author":"Chang","year":"1994","journal-title":"Mol Cell Biol"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/S0378-1119(98)00590-3","article-title":"The yeast Cryptococcus neoformans uses \u2018mammalian\u2019 enhancer sites in the regulation of the virulence gene, CNLAC1","volume":"227","author":"Zhang","year":"1999","journal-title":"Gene"},{"key":"2023032922201797500_","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1093\/nar\/gkaa060","article-title":"Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom","volume":"48","author":"Wallace","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023032922201797500_","first-page":"103265","article-title":"Genomic perspective of triazole resistance in clinical and environmental Aspergillus fumigatus isolates without cyp51A mutations","volume-title":"Fungal Genet Biol","author":"Sharma","year":"2019"}],"container-title":["Medical Mycology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mmy\/advance-article-pdf\/doi\/10.1093\/mmy\/myad024\/49448004\/myad024.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mmy\/article-pdf\/61\/3\/myad024\/49689619\/myad024.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mmy\/article-pdf\/61\/3\/myad024\/49689619\/myad024.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,8]],"date-time":"2023-12-08T10:59:43Z","timestamp":1702033183000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mmy\/article\/doi\/10.1093\/mmy\/myad024\/7071900"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3]]},"references-count":12,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,3,2]]}},"URL":"https:\/\/doi.org\/10.1093\/mmy\/myad024","relation":{},"ISSN":["1369-3786","1460-2709"],"issn-type":[{"type":"print","value":"1369-3786"},{"type":"electronic","value":"1460-2709"}],"subject":[],"published-other":{"date-parts":[[2023,3]]},"published":{"date-parts":[[2023,3]]},"article-number":"myad024"}}