{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:55:07Z","timestamp":1790747707793,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1009313","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T00:00:00Z","timestamp":1612396800000}}],"reference-count":211,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,25]],"date-time":"2021-01-25T00:00:00Z","timestamp":1611532800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI133654"],"award-info":[{"award-number":["R01 AI133654"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI133654"],"award-info":[{"award-number":["R01 AI133654"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of\n                    <jats:italic>Cryptococcus deneoformans<\/jats:italic>\n                    , which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent\n                    <jats:italic>C. deneoformans<\/jats:italic>\n                    strains. Using a \u201cfunction-valued\u201d QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes,\n                    <jats:italic>RIC8<\/jats:italic>\n                    , which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes\n                    <jats:italic>SSK1<\/jats:italic>\n                    and\n                    <jats:italic>SSK2<\/jats:italic>\n                    , which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of\n                    <jats:italic>Cryptococcus<\/jats:italic>\n                    , and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1009313","type":"journal-article","created":{"date-parts":[[2021,1,25]],"date-time":"2021-01-25T13:56:29Z","timestamp":1611582989000},"page":"e1009313","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":23,"title":["Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4934-6160","authenticated-orcid":true,"given":"Cullen","family":"Roth","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debra","family":"Murray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5568-7565","authenticated-orcid":true,"given":"Alexandria","family":"Scott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ci","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna F.","family":"Averette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2895-1153","authenticated-orcid":true,"given":"Sheng","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Heitman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7659-2589","authenticated-orcid":true,"given":"Paul M.","family":"Magwene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,1,25]]},"reference":[{"issue":"7","key":"pgen.1009313.ref001","doi-asserted-by":"crossref","first-page":"e1002136","DOI":"10.1371\/journal.ppat.1002136","article-title":"Microbial virulence as an emergent property: consequences and opportunities","volume":"7","author":"A Casadevall","year":"2011","journal-title":"PLoS Pathogens"},{"issue":"7393","key":"pgen.1009313.ref002","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature10947","article-title":"Emerging fungal threats to animal, plant and ecosystem health","volume":"484","author":"MC Fisher","year":"2012","journal-title":"Nature"},{"issue":"S5","key":"pgen.1009313.ref003","doi-asserted-by":"crossref","first-page":"S52","DOI":"10.1086\/424609","article-title":"The rise and fall of a six-year coral-fungal epizootic","volume":"164","author":"K Kim","year":"2004","journal-title":"the American Naturalist"},{"issue":"1","key":"pgen.1009313.ref004","doi-asserted-by":"crossref","first-page":"147","DOI":"10.5248\/108.147","article-title":"Geomyces destructans sp. nov. associated with bat white-nose syndrome","volume":"108","author":"A Gargas","year":"2009","journal-title":"Mycotaxon"},{"key":"pgen.1009313.ref005","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.micro.091208.073435","article-title":"Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host","volume":"63","author":"MC Fisher","year":"2009","journal-title":"Annual review of microbiology"},{"issue":"5992","key":"pgen.1009313.ref006","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1126\/science.1188594","article-title":"An emerging disease causes regional population collapse of a common North American bat species","volume":"329","author":"WF Frick","year":"2010","journal-title":"Science"},{"issue":"2","key":"pgen.1009313.ref007","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1073\/pnas.1014743108","article-title":"Patterns of widespread decline in North American bumble bees","volume":"108","author":"SA Cameron","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6","key":"pgen.1009313.ref008","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1111\/mpp.12618","article-title":"A review of wheat diseases\u2014a field perspective","volume":"19","author":"M Figueroa","year":"2018","journal-title":"Molecular plant pathology"},{"key":"pgen.1009313.ref009","doi-asserted-by":"crossref","first-page":"304","DOI":"10.3389\/fevo.2019.00304","article-title":"Geographical distribution of fungal plant pathogens in dust across the United States","volume":"7","author":"K Dietzel","year":"2019","journal-title":"Frontiers in Ecology and Evolution"},{"issue":"4","key":"pgen.1009313.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1000850","article-title":"Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the northwest United States","volume":"6","author":"EJ Byrnes","year":"2010","journal-title":"PLoS pathogens"},{"issue":"11","key":"pgen.1009313.ref011","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1016\/j.micinf.2011.05.009","article-title":"Cryptococcus gattii: an emerging fungal pathogen infecting humans and animals","volume":"13","author":"EJ Byrnes","year":"2011","journal-title":"Microbes and infection"},{"issue":"3","key":"pgen.1009313.ref012","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1007\/s11908-011-0181-0","article-title":"The outbreak of Cryptococcus gattii in western North America: epidemiology and clinical issues","volume":"13","author":"EJ Byrnes","year":"2011","journal-title":"Current infectious disease reports"},{"issue":"165","key":"pgen.1009313.ref013","doi-asserted-by":"crossref","first-page":"165rv13","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden killers: human fungal infections","volume":"4","author":"GD Brown","year":"2012","journal-title":"Science Translational Medicine"},{"issue":"7","key":"pgen.1009313.ref014","article-title":"Essential metals at the host\u2013pathogen interface: nutritional immunity and micronutrient assimilation by human fungal pathogens","volume":"15","author":"A Crawford","year":"2015","journal-title":"FEMS yeast research"},{"issue":"9","key":"pgen.1009313.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0137750","article-title":"Integrative model of oxidative stress adaptation in the fungal pathogen Candida albicans","volume":"10","author":"C Komalapriya","year":"2015","journal-title":"PLoS One"},{"issue":"11","key":"pgen.1009313.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003741","article-title":"Fungal immune evasion in a model host\u2013pathogen interaction: Candida albicans versus macrophages","volume":"9","author":"C Jimenez-Lopez","year":"2013","journal-title":"PLoS pathogens"},{"issue":"4","key":"pgen.1009313.ref017","doi-asserted-by":"crossref","first-page":"51","DOI":"10.3390\/jof3040051","article-title":"Fungal strategies to evade the host immune recognition","volume":"3","author":"MJ Hern\u00e1ndez-Ch\u00e1vez","year":"2017","journal-title":"Journal of Fungi"},{"issue":"2","key":"pgen.1009313.ref018","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1111\/j.1574-6976.2001.tb00577.x","article-title":"Virulence genes in the pathogenic yeast Candida albicans","volume":"25","author":"F Navarro-Garc\u00eda","year":"2001","journal-title":"FEMS microbiology reviews"},{"key":"pgen.1009313.ref019","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1146\/annurev.genet.36.052402.152652","article-title":"Genetics of Cryptococcus neoformans","volume":"36","author":"CM Hull","year":"2002","journal-title":"Annual Review of Genetics"},{"issue":"8","key":"pgen.1009313.ref020","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1128\/microbe.1.359.1","article-title":"Cards of virulence and the global virulome for humans","volume":"1","author":"A Casadevall","year":"2006","journal-title":"Microbe Magazine"},{"issue":"1","key":"pgen.1009313.ref021","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.cell.2008.07.046","article-title":"Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans","volume":"135","author":"OW Liu","year":"2008","journal-title":"Cell"},{"issue":"4","key":"pgen.1009313.ref022","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1128\/EC.00352-08","article-title":"Isolation and characterization of Cryptococcus neoformans spores reveal a critical role for capsule biosynthesis genes in spore biogenesis","volume":"8","author":"MR Botts","year":"2009","journal-title":"Eukaryotic Cell"},{"issue":"6","key":"pgen.1009313.ref023","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1128\/EC.00044-12","article-title":"The RAM network in pathogenic fungi","volume":"11","author":"S Saputo","year":"2012","journal-title":"Eukaryotic cell"},{"issue":"12","key":"pgen.1009313.ref024","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1128\/EC.00218-13","article-title":"Stress signaling pathways for the pathogenicity of Cryptococcus","volume":"12","author":"YS Bahn","year":"2013","journal-title":"Eukaryotic Cell"},{"issue":"4","key":"pgen.1009313.ref025","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1128\/MCB.01359-13","article-title":"The Cryptococcus neoformans Rim101 transcription factor directly regulates genes required for adaptation to the host","volume":"34","author":"TR O\u2019Meara","year":"2014","journal-title":"Molecular and Cellular Biology"},{"issue":"1","key":"pgen.1009313.ref026","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1242\/jeb.088930","article-title":"Stress adaptation in a pathogenic fungus","volume":"217","author":"AJ Brown","year":"2014","journal-title":"Journal of Experimental Biology"},{"key":"pgen.1009313.ref027","article-title":"Aspergillus fumigatus virulence through the lens of transcription factors","author":"KM Bultman","year":"2016","journal-title":"Medical mycology"},{"issue":"1","key":"pgen.1009313.ref028","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1080\/21505594.2019.1614383","article-title":"Basic principles of the virulence of Cryptococcus","volume":"10","author":"O Zaragoza","year":"2019","journal-title":"Virulence"},{"issue":"12","key":"pgen.1009313.ref029","article-title":"Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance","volume":"15","author":"Castro PA de","year":"2019","journal-title":"PLoS Genetics"},{"issue":"2","key":"pgen.1009313.ref030","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2008-9-2-r41","article-title":"Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans","volume":"9","author":"G Hu","year":"2008","journal-title":"Genome biology"},{"issue":"4","key":"pgen.1009313.ref031","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000046","article-title":"Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus","volume":"4","author":"ND Fedorova","year":"2008","journal-title":"PLoS genetics"},{"issue":"7247","key":"pgen.1009313.ref032","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/nature08064","article-title":"Evolution of pathogenicity and sexual reproduction in eight Candida genomes","volume":"459","author":"G Butler","year":"2009","journal-title":"Nature"},{"issue":"6","key":"pgen.1009313.ref033","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0005862","article-title":"Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties","volume":"4","author":"P Ngamskulrungroj","year":"2009","journal-title":"PloS one"},{"issue":"1","key":"pgen.1009313.ref034","doi-asserted-by":"crossref","first-page":"e00342","DOI":"10.1128\/mBio.00342-10","article-title":"Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts","volume":"2","author":"C D\u2019Souza","year":"2011","journal-title":"mBio"},{"issue":"3","key":"pgen.1009313.ref035","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1101\/gr.174623.114","article-title":"Genetic and phenotypic intra-species variation in Candida albicans","volume":"25","author":"MP Hirakawa","year":"2015","journal-title":"Genome research"},{"key":"pgen.1009313.ref036","doi-asserted-by":"crossref","first-page":"383","DOI":"10.3389\/fgene.2019.00383","article-title":"Whole-genome sequencing of the opportunistic yeast pathogen Candida inconspicua uncovers its hybrid origin","volume":"10","author":"V Mix\u00e3o","year":"2019","journal-title":"Frontiers in genetics"},{"issue":"4","key":"pgen.1009313.ref037","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1534\/g3.113.005660","article-title":"Comparative genomics of serial isolates of Cryptococcus neoformans reveals gene associated with carbon utilization and virulence","volume":"3","author":"KL Ormerod","year":"2013","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"4","key":"pgen.1009313.ref038","doi-asserted-by":"crossref","first-page":"e1004261","DOI":"10.1371\/journal.pgen.1004261","article-title":"Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation","volume":"10","author":"G Janbon","year":"2014","journal-title":"PLoS Genetics"},{"issue":"8","key":"pgen.1009313.ref039","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/S1473-3099(17)30243-8","article-title":"Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis","volume":"17","author":"R Rajasingham","year":"2017","journal-title":"The Lancet Infectious Diseases"},{"key":"pgen.1009313.ref040","unstructured":"Singh N, Alexander B, Gupta K. Characteristics and outcome of Cryptococcus neoformans infection of the central nervous system in organ transplant recipients: a prospective, multicenter study. 42nd ICAAC, 392. San Diego, CA. 2002;."},{"issue":"5","key":"pgen.1009313.ref041","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1086\/432486","article-title":"Prevalence of clinical isolates of Cryptococcus gattii serotype C among patients with AIDS in Sub-Saharan Africa","volume":"192","author":"AP Litvintseva","year":"2005","journal-title":"The Journal of infectious diseases"},{"issue":"3","key":"pgen.1009313.ref042","doi-asserted-by":"crossref","first-page":"622","DOI":"10.2214\/ajr.185.3.01850622","article-title":"Pulmonary cryptococcosis in immunocompetent patients: CT findings in 12 patients","volume":"185","author":"DL Fox","year":"2005","journal-title":"American Journal of Roentgenology"},{"issue":"4","key":"pgen.1009313.ref043","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1097\/QAD.0b013e328322ffac","article-title":"Estimation of the current global burden of cryptococcal meningitis among persons living with HIV\/AIDS","volume":"23","author":"BJ Park","year":"2009","journal-title":"AIDS"},{"issue":"3","key":"pgen.1009313.ref044","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofw167","article-title":"Pulmonary cryptococcosis in the immunocompetent patient\u2014many questions, some answers","volume":"3","author":"JF Fisher","year":"2016","journal-title":"Open Forum Infectious Diseases"},{"issue":"1","key":"pgen.1009313.ref045","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrneurol.2016.167","article-title":"Cryptococcal meningitis: epidemiology, immunology, diagnosis and therapy","volume":"13","author":"PR Williamson","year":"2017","journal-title":"Nature Reviews Neurology"},{"issue":"7","key":"pgen.1009313.ref046","doi-asserted-by":"crossref","DOI":"10.1590\/0074-02760170391","article-title":"The war on cryptococcosis: a review of the antifungal arsenal","volume":"113","author":"A Mourad","year":"2018","journal-title":"Mem\u00f3rias do Instituto Oswaldo Cruz"},{"issue":"10","key":"pgen.1009313.ref047","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1046\/j.1365-294x.2000.01021.x","article-title":"Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans","volume":"9","author":"J Xu","year":"2000","journal-title":"Molecular Ecology"},{"issue":"1","key":"pgen.1009313.ref048","doi-asserted-by":"crossref","first-page":"e00091","DOI":"10.1128\/mBio.00091-10","article-title":"Mixed infections and In Vivo evolution in the human fungal pathogen Cryptococcus neoformans","volume":"1","author":"M Desnos-Ollivier","year":"2010","journal-title":"mBio"},{"issue":"6","key":"pgen.1009313.ref049","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1128\/JCM.06750-11","article-title":"Extensive genetic diversity within the Dutch clinical Cryptococcus neoformans population","volume":"50","author":"F Hagen","year":"2012","journal-title":"Journal of Clinical Microbiology"},{"key":"pgen.1009313.ref050","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.fgb.2015.02.009","article-title":"Recognition of seven species in the Cryptococcus gattii\/Cryptococcus neoformans species complex","volume":"78","author":"F Hagen","year":"2015","journal-title":"Fungal Genetics & Biology"},{"issue":"4","key":"pgen.1009313.ref051","first-page":"943","article-title":"A new species of Filobasidiella, the sexual state of Cryptococcus neoformans B and C serotypes","volume":"68","author":"KJ Kwon-Chung","year":"1976","journal-title":"Mycologia"},{"issue":"2","key":"pgen.1009313.ref052","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1534\/genetics.103.023408","article-title":"A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D (Filobasidiella neoformans)","volume":"167","author":"RE Marra","year":"2004","journal-title":"Genetics"},{"issue":"5","key":"pgen.1009313.ref053","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1128\/JB.175.5.1405-1411.1993","article-title":"Gene transfer in Cryptococcus neoformans by use of biolistic delivery of DNA","volume":"175","author":"DL Toffaletti","year":"1993","journal-title":"Journal of bacteriology"},{"issue":"8","key":"pgen.1009313.ref054","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1016\/j.fgb.2006.02.007","article-title":"Improvements to gene deletion in the fungal pathogen Cryptococcus neoformans: absence of Ku proteins increases homologous recombination, and co-transformation of independent DNA molecules allows rapid complementation of deletion phenotypes","volume":"43","author":"CL Goins","year":"2006","journal-title":"Fungal genetics & Biology"},{"key":"pgen.1009313.ref055","doi-asserted-by":"crossref","first-page":"31145","DOI":"10.1038\/srep31145","article-title":"A \u2018suicide\u2019 CRISPR-Cas9 system to promote gene deletion and restoration by electroporation in Cryptococcus neoformans","volume":"6","author":"Y Wang","year":"2016","journal-title":"Scientific Reports"},{"issue":"4","key":"pgen.1009313.ref056","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1534\/genetics.117.300656","article-title":"Multiple applications of a transient CRISPR-Cas9 coupled with electroporation (TRACE) system in the Cryptococcus neoformans species complex","volume":"208","author":"Y Fan","year":"2018","journal-title":"Genetics"},{"issue":"1","key":"pgen.1009313.ref057","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1128\/IAI.51.1.218-223.1986","article-title":"Encapsulation and melanin formation as indicators of virulence in Cryptococcus neoformans","volume":"51","author":"K Kwon-Chung","year":"1986","journal-title":"Infection & Immunity"},{"issue":"4","key":"pgen.1009313.ref058","doi-asserted-by":"crossref","first-page":"2012","DOI":"10.1128\/IAI.73.4.2012-2019.2005","article-title":"Melanization of Cryptococcus neoformans affects lung inflammatory responses during cryptococcal infection","volume":"73","author":"AJ Mednick","year":"2005","journal-title":"Infection & Immunity"},{"issue":"1","key":"pgen.1009313.ref059","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1128\/EC.00370-07","article-title":"Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence","volume":"7","author":"ML Rodrigues","year":"2008","journal-title":"Eukaryotic Cell"},{"key":"pgen.1009313.ref060","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0065-2164(08)01005-8","article-title":"Virulence in Cryptococcus species","volume":"67","author":"H Ma","year":"2009","journal-title":"Advances in Applied Microbiology"},{"issue":"3","key":"pgen.1009313.ref061","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1128\/CMR.00001-12","article-title":"The Cryptococcus neoformans capsule: a sword and a shield","volume":"25","author":"TR O\u2019Meara","year":"2012","journal-title":"Clinical microbiology reviews"},{"key":"pgen.1009313.ref062","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/B978-0-12-800261-2.00001-3","article-title":"The tools for virulence of Cryptococcus neoformans","volume":"87","author":"C Coelho","year":"2014","journal-title":"Advances in Applied Microbiology"},{"key":"pgen.1009313.ref063","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.fgb.2014.09.004","article-title":"Virulence mechanisms and Cryptococcus neoformans pathogenesis","volume":"78","author":"JA Alspaugh","year":"2015","journal-title":"Fungal Genetics & Biology"},{"issue":"3","key":"pgen.1009313.ref064","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1128\/EC.00373-08","article-title":"Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales","volume":"8","author":"K Findley","year":"2009","journal-title":"Eukaryotic Cell"},{"key":"pgen.1009313.ref065","doi-asserted-by":"crossref","unstructured":"Casadevall A, Perfect JR. Cryptococcus neoformans. vol. 595. Citeseer; 1998.","DOI":"10.1128\/9781555818241"},{"issue":"4","key":"pgen.1009313.ref066","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/S1369-5274(00)00103-X","article-title":"Melanin and virulence in Cryptococcus neoformans","volume":"3","author":"A Casadevall","year":"2000","journal-title":"Current Opinion in Microbiology"},{"issue":"12","key":"pgen.1009313.ref067","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1128\/EC.00308-07","article-title":"Accidental virulence, cryptic pathogenesis, martians, lost hosts, and the pathogenicity of environmental microbes","volume":"6","author":"A Casadevall","year":"2007","journal-title":"Eukaryotic cell"},{"issue":"2","key":"pgen.1009313.ref068","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/S0378-1097(97)00239-5","article-title":"Melanization affects susceptibility of Cryptococcus neoformans to heat and cold","volume":"153","author":"AL Rosas","year":"1997","journal-title":"FEMS Microbiology Letters"},{"issue":"5","key":"pgen.1009313.ref069","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0000457","article-title":"Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi","volume":"2","author":"E Dadachova","year":"2007","journal-title":"PloS one"},{"issue":"21","key":"pgen.1009313.ref070","doi-asserted-by":"crossref","first-page":"7102","DOI":"10.1128\/JB.175.21.7102-7104.1993","article-title":"Antioxidant function of fungal melanin","volume":"175","author":"ES Jacobson","year":"1993","journal-title":"Journal of bacteriology"},{"issue":"21","key":"pgen.1009313.ref071","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1016\/j.cub.2006.09.061","article-title":"Phagosome extrusion and host-cell survival after Cryptococcus neoformans phagocytosis by macrophages","volume":"16","author":"M Alvarez","year":"2006","journal-title":"Current Biology"},{"issue":"26","key":"pgen.1009313.ref072","doi-asserted-by":"crossref","first-page":"15245","DOI":"10.1073\/pnas.261418798","article-title":"Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages","volume":"98","author":"J Steenbergen","year":"2001","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"pgen.1009313.ref073","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1111\/j.1462-5822.2008.01186.x","article-title":"Capsule enlargement in Cryptococcus neoformans confers resistance to oxidative stress suggesting a mechanism for intracellular survival","volume":"10","author":"O Zaragoza","year":"2008","journal-title":"Cellular microbiology"},{"issue":"7","key":"pgen.1009313.ref074","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/S0141-0229(99)00086-1","article-title":"Emergence of Saccharomyces cerevisiae as a human pathogen: implications for biotechnology","volume":"25","author":"A Murphy","year":"1999","journal-title":"Enzyme and Microbial Technology"},{"issue":"8","key":"pgen.1009313.ref075","doi-asserted-by":"crossref","first-page":"4731","DOI":"10.1128\/IAI.72.8.4731-4740.2004","article-title":"Disruption of the Aspergillus fumigatus gene encoding nucleolar protein CgrA impairs thermotolerant growth and reduces virulence","volume":"72","author":"R Bhabhra","year":"2004","journal-title":"Infection & Immunity"},{"issue":"4","key":"pgen.1009313.ref076","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1111\/j.1567-1364.2006.00051.x","article-title":"Cryptococcus neoformans: the yeast that likes it hot","volume":"6","author":"JR Perfect","year":"2006","journal-title":"FEMS Yeast Res"},{"issue":"5","key":"pgen.1009313.ref077","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1101\/gr.185538.114","article-title":"The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen","volume":"25","author":"PK Strope","year":"2015","journal-title":"Genome Research"},{"issue":"6","key":"pgen.1009313.ref078","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1128\/JCM.03392-13","article-title":"Antifungal drug susceptibility and phylogenetic diversity among Cryptococcus isolates from dogs and cats in North America","volume":"52","author":"L Singer","year":"2014","journal-title":"Journal of Clinical Microbiology"},{"issue":"9","key":"pgen.1009313.ref079","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1534\/g3.116.029595","article-title":"Identification of QTLs Associated with Virulence Related Traits and Drug Resistance in Cryptococcus neoformans","volume":"6","author":"AA Vogan","year":"2016","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"3","key":"pgen.1009313.ref080","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1128\/AAC.48.3.985-991.2004","article-title":"Amphotericin B and fluconazole, a potent combination therapy for cryptococcal meningitis","volume":"48","author":"RA Larsen","year":"2004","journal-title":"Antimicrobial Agents and Chemotherapy"},{"issue":"4","key":"pgen.1009313.ref081","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1054\/drup.1999.0090","article-title":"Drug resistance in Cryptococcus neoformans","volume":"2","author":"JR Perfect","year":"1999","journal-title":"Drug Resistance Updates"},{"issue":"7","key":"pgen.1009313.ref082","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1073\/pnas.1117280109","article-title":"Amphotericin primarily kills yeast by simply binding ergosterol","volume":"109","author":"KC Gray","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5","key":"pgen.1009313.ref083","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nchembio.1496","article-title":"Amphotericin forms an extramembranous and fungicidal sterol sponge","volume":"10","author":"TM Anderson","year":"2014","journal-title":"Nature Chemical Biology"},{"issue":"1-2","key":"pgen.1009313.ref084","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/j.1574-6968.1994.tb07140.x","article-title":"Resistance to amphotericin B associated with defective sterol \u0394\u2192 isomerase in a Cryptococcus neoformans strain from an AIDS patient","volume":"122","author":"SL Kelly","year":"1994","journal-title":"FEMS microbiology letters"},{"issue":"12","key":"pgen.1009313.ref085","doi-asserted-by":"crossref","first-page":"7197","DOI":"10.1128\/AAC.01299-15","article-title":"Increased antifungal drug resistance in clinical isolates of Cryptococcus neoformans in Uganda","volume":"59","author":"KD Smith","year":"2015","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"pgen.1009313.ref086","first-page":"369","volume-title":"Open forum infectious diseases","author":"S Chesdachai","year":"2019"},{"issue":"3","key":"pgen.1009313.ref087","doi-asserted-by":"crossref","first-page":"e0008137","DOI":"10.1371\/journal.pntd.0008137","article-title":"Decreasing fluconazole susceptibility of clinical South African Cryptococcus neoformans isolates over a decade","volume":"14","author":"SD Naicker","year":"2020","journal-title":"PLoS neglected tropical diseases"},{"issue":"1","key":"pgen.1009313.ref088","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jinf.2004.07.013","article-title":"Comparative analysis of pathogenicity of Cryptococcus neoformans serotypes A, D and AD in murine cryptococcosis","volume":"51","author":"F Barchiesi","year":"2005","journal-title":"Journal of Infection"},{"issue":"8","key":"pgen.1009313.ref089","doi-asserted-by":"crossref","first-page":"3188","DOI":"10.1128\/IAI.00296-09","article-title":"Most environmental isolates of Cryptococcus neoformans var. grubii (serotype A) are not lethal for mice","volume":"77","author":"AP Litvintseva","year":"2009","journal-title":"Infection & Immunity"},{"issue":"5","key":"pgen.1009313.ref090","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00046-19","article-title":"The mouse inhalation model of Cryptococcus neoformans infection recapitulates strain virulence in humans and shows that closely related strains can possess differential virulence","volume":"87","author":"L Mukaremera","year":"2019","journal-title":"Infection and immunity"},{"issue":"9","key":"pgen.1009313.ref091","doi-asserted-by":"crossref","first-page":"3365","DOI":"10.1128\/JCM.39.9.3365-3367.2001","article-title":"Cryptococcus neoformans var. neoformans (Serotype D) Strains Are More Susceptible to Heat than C. neoformans var. grubii (Serotype A) Strains","volume":"39","author":"LR Martinez","year":"2001","journal-title":"Journal of Clinical Microbiology"},{"issue":"12","key":"pgen.1009313.ref092","doi-asserted-by":"crossref","first-page":"e1004849","DOI":"10.1371\/journal.pgen.1004849","article-title":"Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans","volume":"10","author":"S Sun","year":"2014","journal-title":"PLoS Genetics"},{"issue":"12","key":"pgen.1009313.ref093","doi-asserted-by":"crossref","first-page":"3751","DOI":"10.1128\/IAI.57.12.3751-3756.1989","article-title":"Strain variation in antiphagocytic activity of capsular polysaccharides from Cryptococcus neoformans serotype A","volume":"57","author":"JM Small","year":"1989","journal-title":"Infection and immunity"},{"key":"pgen.1009313.ref094","doi-asserted-by":"crossref","first-page":"132","DOI":"10.3389\/fmicb.2018.00132","article-title":"Genotypic and phenotypic diversity of Cryptococcus gattii VGII clinical isolates and its impact on virulence","volume":"9","author":"VA Barcellos","year":"2018","journal-title":"Frontiers in microbiology"},{"issue":"1","key":"pgen.1009313.ref095","doi-asserted-by":"crossref","first-page":"9824","DOI":"10.1038\/s41598-018-27813-3","article-title":"Genetic factors and genotype-Environment interactions contribute to variation in melanin production in the fungal pathogen Cryptococcus neoformans","volume":"8","author":"H Samarasinghe","year":"2018","journal-title":"Scientific Reports"},{"issue":"9","key":"pgen.1009313.ref096","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1111\/myc.12507","article-title":"Molecular epidemiology and in vitro antifungal susceptibility testing of 108 clinical Cryptococcus neoformans sensu lato and Cryptococcus gattii sensu lato isolates from Denmark","volume":"59","author":"F Hagen","year":"2016","journal-title":"Mycoses"},{"issue":"2","key":"pgen.1009313.ref097","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1007\/s11046-017-0214-9","article-title":"Molecular characterization and antifungal susceptibility testing of sequentially obtained clinical Cryptococcus deneoformans and Cryptococcus neoformans isolates from Ljubljana, Slovenia","volume":"183","author":"T Matos","year":"2018","journal-title":"Mycopathologia"},{"issue":"1","key":"pgen.1009313.ref098","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/genetics\/121.1.185","article-title":"Mapping mendelian factors underlying quantitative traits using RFLP linkage maps","volume":"121","author":"ES Lander","year":"1989","journal-title":"Genetics"},{"key":"pgen.1009313.ref099","volume-title":"Genetics and Analysis of Quantitative Traits","author":"M Lynch","year":"1998"},{"issue":"11","key":"pgen.1009313.ref100","doi-asserted-by":"crossref","first-page":"e1002255","DOI":"10.1371\/journal.pcbi.1002255","article-title":"The statistics of bulk segregant analysis using next generation sequencing","volume":"7","author":"PM Magwene","year":"2011","journal-title":"PLoS computational biology"},{"issue":"3","key":"pgen.1009313.ref101","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1534\/genetics.112.143107","article-title":"Small-and large-effect quantitative trait locus interactions underlie variation in yeast sporulation efficiency","volume":"192","author":"K Lorenz","year":"2012","journal-title":"Genetics"},{"issue":"3","key":"pgen.1009313.ref102","doi-asserted-by":"crossref","first-page":"e1002570","DOI":"10.1371\/journal.pgen.1002570","article-title":"Genetic architecture of highly complex chemical resistance traits across four yeast strains","volume":"8","author":"IM Ehrenreich","year":"2012","journal-title":"PLoS genetics"},{"issue":"2","key":"pgen.1009313.ref103","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1534\/genetics.112.142067","article-title":"The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae","volume":"193","author":"JA Granek","year":"2013","journal-title":"Genetics"},{"issue":"5","key":"pgen.1009313.ref104","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1534\/g3.113.009142","article-title":"Yeast growth plasticity is regulated by environment-specific multi-QTL interactions","volume":"4","author":"A Bhatia","year":"2014","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"3","key":"pgen.1009313.ref105","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1534\/genetics.113.160291","article-title":"An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae","volume":"196","author":"S Wilkening","year":"2014","journal-title":"Genetics"},{"issue":"1","key":"pgen.1009313.ref106","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1534\/g3.117.300392","article-title":"Natural variation in SER1 and ENA6 underlie condition-specific growth defects in Saccharomyces cerevisiae","volume":"8","author":"A Sirr","year":"2018","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"12","key":"pgen.1009313.ref107","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.1534\/g3.114.015289","article-title":"Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici","volume":"4","author":"MH Lendenmann","year":"2014","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"pgen.1009313.ref108","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.fgb.2015.05.001","article-title":"QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici","volume":"80","author":"MH Lendenmann","year":"2015","journal-title":"Fungal Genetics and Biology"},{"issue":"4","key":"pgen.1009313.ref109","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/hdy.2015.111","article-title":"QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici","volume":"116","author":"MH Lendenmann","year":"2016","journal-title":"Heredity"},{"issue":"4","key":"pgen.1009313.ref110","doi-asserted-by":"crossref","first-page":"e19325","DOI":"10.1371\/journal.pone.0019325","article-title":"Quantitative trait locus (QTL) mapping reveals a role for unstudied genes in Aspergillus virulence","volume":"6","author":"JK Christians","year":"2011","journal-title":"PLoS One"},{"issue":"11","key":"pgen.1009313.ref111","doi-asserted-by":"crossref","first-page":"e187","DOI":"10.1371\/journal.pgen.0020187","article-title":"Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MAT allele enhances filamentation","volume":"2","author":"X Lin","year":"2006","journal-title":"PLoS Genetics"},{"issue":"5","key":"pgen.1009313.ref112","doi-asserted-by":"crossref","first-page":"e62790","DOI":"10.1371\/journal.pone.0062790","article-title":"Evidence for mitotic recombination within the basidia of a hybrid cross of Cryptococcus neoformans","volume":"8","author":"AA Vogan","year":"2013","journal-title":"PLoS One"},{"issue":"6","key":"pgen.1009313.ref113","doi-asserted-by":"crossref","first-page":"e0178691","DOI":"10.1371\/journal.pone.0178691","article-title":"The use of Gompertz models in growth analyses, and new Gompertz-model approach: An addition to the Unified-Richards family","volume":"12","author":"KM Tj\u00f8rve","year":"2017","journal-title":"PloS one"},{"issue":"2","key":"pgen.1009313.ref114","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1101\/gr.210286.116","article-title":"Detecting differential growth of microbial populations with Gaussian process regression","volume":"27","author":"PD Tonner","year":"2017","journal-title":"Genome research"},{"issue":"4","key":"pgen.1009313.ref115","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/BF00290638","article-title":"A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters","volume":"27","author":"M Kirkpatrick","year":"1989","journal-title":"Journal of mathematical biology"},{"issue":"4","key":"pgen.1009313.ref116","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1093\/genetics\/124.4.979","article-title":"Analysis of the inheritance, selection and evolution of growth trajectories","volume":"124","author":"M Kirkpatrick","year":"1990","journal-title":"Genetics"},{"key":"pgen.1009313.ref117","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/978-94-010-0585-2_7","volume-title":"Microevolution rate, pattern, process","author":"JG Kingsolver","year":"2001"},{"issue":"6","key":"pgen.1009313.ref118","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/sj.hdy.6800462","article-title":"Genetic covariance structure of growth in the salamander Ambystoma macrodactylum","volume":"92","author":"G Ragland","year":"2004","journal-title":"Heredity"},{"issue":"5","key":"pgen.1009313.ref119","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1111\/j.1558-5646.2008.00340.x","article-title":"Hypothesis testing in comparative and experimental studies of function-valued traits","volume":"62","author":"CK Griswold","year":"2008","journal-title":"Evolution"},{"issue":"11","key":"pgen.1009313.ref120","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.tree.2012.07.002","article-title":"Genetics and evolution of function-valued traits: understanding environmentally responsive phenotypes","volume":"27","author":"JR Stinchcombe","year":"2012","journal-title":"Trends in Ecology & Evolution"},{"key":"pgen.1009313.ref121","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1146\/annurev-ecolsys-110316-022830","article-title":"Variation and evolution of function-valued traits","volume":"49","author":"R Gomulkiewicz","year":"2018","journal-title":"Annual Review of Ecology, Evolution, and Systematics"},{"issue":"4","key":"pgen.1009313.ref122","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1093\/genetics\/161.4.1751","article-title":"Functional mapping of quantitative trait loci underlying the character process: a theoretical framework","volume":"161","author":"CX Ma","year":"2002","journal-title":"Genetics"},{"issue":"3","key":"pgen.1009313.ref123","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1152\/physiolgenomics.00013.2003","article-title":"Functional mapping for quantitative trait loci governing growth rates: a parametric model","volume":"14","author":"R Wu","year":"2003","journal-title":"Physiological Genomics"},{"issue":"4","key":"pgen.1009313.ref124","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1534\/genetics.105.054775","article-title":"Mapping quantitative trait loci for longitudinal traits in line crosses","volume":"173","author":"R Yang","year":"2006","journal-title":"Genetics"},{"issue":"6","key":"pgen.1009313.ref125","article-title":"A computational approach for functional mapping of quantitative trait loci that regulate thermal performance curves","volume":"2","author":"JS Yap","year":"2007","journal-title":"PLoS One"},{"issue":"12","key":"pgen.1009313.ref126","doi-asserted-by":"crossref","first-page":"2365","DOI":"10.1534\/g3.114.014068","article-title":"Functional multi-locus QTL mapping of temporal trends in scots pine wood traits","volume":"4","author":"Z Li","year":"2014","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"pgen.1009313.ref127","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.3389\/fpls.2018.01632","article-title":"Integrated QTL and eQTL mapping provides insights and candidate genes for fatty acid composition, flowering time, and growth traits in a F2 population of a novel synthetic allopolyploid Brassica napus","volume":"9","author":"R Li","year":"2018","journal-title":"Frontiers in plant science"},{"key":"pgen.1009313.ref128","doi-asserted-by":"crossref","first-page":"887","DOI":"10.3389\/fpls.2018.00887","article-title":"Functional mapping of quantitative trait loci (QTLs) associated with plant performance in a wheat magic mapping population","volume":"9","author":"AV Camargo","year":"2018","journal-title":"Frontiers in plant science"},{"key":"pgen.1009313.ref129","first-page":"619148","article-title":"Geographic variation in the genetic basis of resistance to leaf rust in locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)","author":"A VanWallendael","year":"2019","journal-title":"bioRxiv"},{"issue":"1","key":"pgen.1009313.ref130","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1111\/j.1541-0420.2008.01063.x","article-title":"Nonparametric functional mapping of quantitative trait loci","volume":"65","author":"J Yang","year":"2009","journal-title":"Biometrics"},{"issue":"1","key":"pgen.1009313.ref131","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/hdy.2010.20","article-title":"Bayesian analysis for genetic architecture of dynamic traits","volume":"106","author":"L Min","year":"2011","journal-title":"Heredity"},{"issue":"1","key":"pgen.1009313.ref132","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1534\/genetics.111.129221","article-title":"A flexible estimating equations approach for mapping function-valued traits","volume":"189","author":"H Xiong","year":"2011","journal-title":"Genetics"},{"issue":"4","key":"pgen.1009313.ref133","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1534\/genetics.113.152736","article-title":"A Bayesian nonparametric approach for mapping dynamic quantitative traits","volume":"194","author":"Z Li","year":"2013","journal-title":"Genetics"},{"issue":"4","key":"pgen.1009313.ref134","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1534\/genetics.114.166306","article-title":"A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes","volume":"197","author":"IY Kwak","year":"2014","journal-title":"Genetics"},{"issue":"1","key":"pgen.1009313.ref135","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1534\/g3.115.024133","article-title":"Mapping quantitative trait loci underlying function-valued traits using functional principal component analysis and multi-trait mapping","volume":"6","author":"IY Kwak","year":"2016","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"19","key":"pgen.1009313.ref136","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1093\/bioinformatics\/btz164","article-title":"A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data","volume":"35","author":"J Vanhatalo","year":"2019","journal-title":"Bioinformatics"},{"issue":"7","key":"pgen.1009313.ref137","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1128\/IAI.00259-13","article-title":"Congenic strains of the filamentous form of Cryptococcus neoformans for studies of fungal morphogenesis and virulence","volume":"81","author":"B Zhai","year":"2013","journal-title":"Infection & Immunity"},{"issue":"7","key":"pgen.1009313.ref138","doi-asserted-by":"crossref","first-page":"e1002810","DOI":"10.1371\/journal.pgen.1002810","article-title":"Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction","volume":"8","author":"S Sun","year":"2012","journal-title":"PLoS Genetics"},{"issue":"6","key":"pgen.1009313.ref139","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1093\/oxfordjournals.aje.a112423","article-title":"Epidemiologic differences among serotypes of Cryptococcus neoformans","volume":"105","author":"JE Bennett","year":"1977","journal-title":"American Journal of Epidemiology"},{"issue":"10","key":"pgen.1009313.ref140","first-page":"1975","article-title":"\u03b1AD\u03b1 hybrids of Cryptococcus neoformans: evidence of same-sex mating in nature and hybrid fitness","volume":"3","author":"X Lin","year":"2007","journal-title":"PLoS Genetics"},{"issue":"2","key":"pgen.1009313.ref141","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1534\/genetics.118.300996","article-title":"A high-resolution map of meiotic recombination in Cryptococcus deneoformans demonstrates decreased recombination in unisexual reproduction","volume":"209","author":"C Roth","year":"2018","journal-title":"Genetics"},{"issue":"3","key":"pgen.1009313.ref142","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/genetics\/138.3.963","article-title":"Empirical threshold values for quantitative trait mapping","volume":"138","author":"GA Churchill","year":"1994","journal-title":"Genetics"},{"issue":"12","key":"pgen.1009313.ref143","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1128\/EC.00349-07","article-title":"Ssk2 mitogen-activated protein kinase kinase kinase governs divergent patterns of the stress-activated Hog1 signaling pathway in Cryptococcus neoformans","volume":"6","author":"YS Bahn","year":"2007","journal-title":"Eukaryotic Cell"},{"issue":"10","key":"pgen.1009313.ref144","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1128\/EC.00109-14","article-title":"A Ric8\/synembryn homolog promotes Gpa1 and Gpa2 activation to respectively regulate cyclic AMP and pheromone signaling in Cryptococcus neoformans","volume":"13","author":"J Gong","year":"2014","journal-title":"Eukaryotic Cell"},{"key":"pgen.1009313.ref145","doi-asserted-by":"crossref","first-page":"2014","DOI":"10.3389\/fmicb.2016.02014","article-title":"Phenylpyrroles: 30 years, two molecules and (nearly) no resistance","volume":"7","author":"J Kilani","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"4","key":"pgen.1009313.ref146","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1136\/amiajnl-2012-001525","article-title":"An information-gain approach to detecting three-way epistatic interactions in genetic association studies","volume":"20","author":"T Hu","year":"2013","journal-title":"Journal of the American Medical Informatics Association"},{"key":"pgen.1009313.ref147","volume-title":"Elements of Information Theory","author":"T Cover","year":"2006"},{"issue":"7","key":"pgen.1009313.ref148","doi-asserted-by":"crossref","first-page":"3122","DOI":"10.1091\/mbc.e06-02-0113","article-title":"A unique fungal two-component system regulates stress responses, drug sensitivity, sexual development, and virulence of Cryptococcus neoformans","volume":"17","author":"YS Bahn","year":"2006","journal-title":"Molecular Biology of the Cell"},{"issue":"12","key":"pgen.1009313.ref149","doi-asserted-by":"crossref","first-page":"5694","DOI":"10.1128\/IAI.62.12.5694-5697.1994","article-title":"Genetic study of oxygen resistance and melanization in Cryptococcus neoformans","volume":"62","author":"HS Emery","year":"1994","journal-title":"Infection and immunity"},{"issue":"4","key":"pgen.1009313.ref150","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1099\/00221287-142-4-937","article-title":"Stress tolerance and pathogenic potential of a mannitol mutant of Cryptococcus neoformans","volume":"142","author":"V Chaturvedi","year":"1996","journal-title":"Microbiology"},{"key":"pgen.1009313.ref151","doi-asserted-by":"crossref","first-page":"755","DOI":"10.3389\/fmicb.2017.00755","article-title":"Novel antifungal activity for the lectin scytovirin: inhibition of Cryptococcus neoformans and Cryptococcus gattii","volume":"8","author":"TH Jones","year":"2017","journal-title":"Frontiers in microbiology"},{"key":"pgen.1009313.ref152","first-page":"29","volume-title":"Methods in Enzymology","author":"S Hohmann","year":"2007"},{"issue":"343","key":"pgen.1009313.ref153","doi-asserted-by":"crossref","first-page":"re7","DOI":"10.1126\/scisignal.2005458","article-title":"Hog1: 20 years of discovery and impact","volume":"7","author":"JL Brewster","year":"2014","journal-title":"Sci Signal"},{"key":"pgen.1009313.ref154","doi-asserted-by":"crossref","first-page":"212","DOI":"10.3389\/fcimb.2019.00212","article-title":"The cAMP\/protein kinase A pathway regulates virulence and adaptation to host conditions in Cryptococcus neoformans","volume":"9","author":"M Caza","year":"2019","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"issue":"6","key":"pgen.1009313.ref155","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1016\/j.mib.2011.09.004","article-title":"Pleiotropic signaling pathways orchestrate yeast development","volume":"14","author":"JA Granek","year":"2011","journal-title":"Current Opinion in Microbiology"},{"issue":"2","key":"pgen.1009313.ref156","doi-asserted-by":"crossref","first-page":"68","DOI":"10.3390\/jof4020068","article-title":"Conserved and divergent functions of the cAMP\/PKA signaling pathway in Candida albicans and Candida tropicalis","volume":"4","author":"CJ Lin","year":"2018","journal-title":"Journal of Fungi"},{"issue":"5","key":"pgen.1009313.ref157","first-page":"e00506","article-title":"Hog1 regulates stress tolerance and virulence in the emerging fungal pathogen Candida auris","volume":"3","author":"AM Day","year":"2018","journal-title":"mSphere"},{"issue":"1","key":"pgen.1009313.ref158","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1534\/genetics.111.129270","article-title":"RIC8 is a guanine-nucleotide exchange factor for G\u03b1 subunits that regulates growth and development in Neurospora crassa","volume":"189","author":"SJ Wright","year":"2011","journal-title":"Genetics"},{"issue":"11","key":"pgen.1009313.ref159","doi-asserted-by":"crossref","first-page":"e1007744","DOI":"10.1371\/journal.pgen.1007744","article-title":"Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors","volume":"14","author":"S Li","year":"2018","journal-title":"PLoS genetics"},{"issue":"7","key":"pgen.1009313.ref160","doi-asserted-by":"crossref","first-page":"3004","DOI":"10.1128\/IAI.62.7.3004-3007.1994","article-title":"Susceptibility of melanized and nonmelanized Cryptococcus neoformans to nitrogen-and oxygen-derived oxidants","volume":"62","author":"Y Wang","year":"1994","journal-title":"Infection and Immunity"},{"issue":"1","key":"pgen.1009313.ref161","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1128\/EC.3.1.14-26.2004","article-title":"Cyclic AMP-dependent protein kinase catalytic subunits have divergent roles in virulence factor production in two varieties of the fungal pathogen Cryptococcus neoformans","volume":"3","author":"JK Hicks","year":"2004","journal-title":"Eukaryot Cell"},{"issue":"3","key":"pgen.1009313.ref162","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1128\/EC.00213-06","article-title":"Divergence of protein kinase A catalytic subunits in Cryptococcus neoformans and Cryptococcus gattii illustrates evolutionary reconfiguration of a signaling cascade","volume":"6","author":"JK Hicks","year":"2007","journal-title":"Eukaryot Cell"},{"issue":"3","key":"pgen.1009313.ref163","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/S0092-8674(04)00118-7","article-title":"Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast","volume":"116","author":"A Halme","year":"2004","journal-title":"Cell"},{"issue":"2","key":"pgen.1009313.ref164","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1534\/genetics.113.155341","article-title":"Rare variants in hypermutable genes underlie common morphology and growth traits in wild Saccharomyces paradoxus","volume":"195","author":"JI Roop","year":"2013","journal-title":"Genetics"},{"issue":"5","key":"pgen.1009313.ref165","doi-asserted-by":"crossref","first-page":"e1004324","DOI":"10.1371\/journal.pgen.1004324","article-title":"Genetic interactions involving five or more genes contribute to a complex trait in yeast","volume":"10","author":"MB Taylor","year":"2014","journal-title":"PLoS genetics"},{"issue":"9","key":"pgen.1009313.ref166","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1128\/EC.00122-14","article-title":"The underlying structure of adaptation under strong selection in 12 experimental yeast populations","volume":"13","author":"LM Kohn","year":"2014","journal-title":"Eukaryotic cell"},{"issue":"11","key":"pgen.1009313.ref167","doi-asserted-by":"crossref","first-page":"3529","DOI":"10.1534\/g3.118.200413","article-title":"Divergent roles for cAMP-PKA signaling in the regulation of filamentous growth in Saccharomyces cerevisiae and Saccharomyces bayanus","volume":"8","author":"O Kayikci","year":"2018","journal-title":"G3: Genes, Genomes, Genetics"},{"issue":"8","key":"pgen.1009313.ref168","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1128\/EC.00120-09","article-title":"Remodeling of global transcription patterns of Cryptococcus neoformans genes mediated by the stress-activated HOG signaling pathways","volume":"8","author":"YJ Ko","year":"2009","journal-title":"Eukaryotic Cell"},{"issue":"5","key":"pgen.1009313.ref169","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1091\/mbc.e04-11-0987","article-title":"Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans","volume":"16","author":"YS Bahn","year":"2005","journal-title":"Molecular Biology of the Cell"},{"issue":"24","key":"pgen.1009313.ref170","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1016\/j.febslet.2009.10.069","article-title":"Control of high osmolarity signalling in the yeast Saccharomyces cerevisiae","volume":"583","author":"S Hohmann","year":"2009","journal-title":"FEBS letters"},{"issue":"7","key":"pgen.1009313.ref171","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1128\/EC.00145-06","article-title":"Transcription factor Nrg1 mediates capsule formation, stress response, and pathogenesis in Cryptococcus neoformans","volume":"5","author":"KL Cramer","year":"2006","journal-title":"Eukaryotic Cell"},{"issue":"12","key":"pgen.1009313.ref172","doi-asserted-by":"crossref","first-page":"e1002411","DOI":"10.1371\/journal.ppat.1002411","article-title":"Toward an integrated model of capsule regulation in Cryptococcus neoformans","volume":"7","author":"BC Haynes","year":"2011","journal-title":"PLoS Pathog"},{"issue":"10","key":"pgen.1009313.ref173","doi-asserted-by":"crossref","first-page":"829","DOI":"10.15252\/msb.20156451","article-title":"Condition-specific genetic interaction maps reveal crosstalk between the cAMP\/PKA and the HOG MAPK pathways in the activation of the general stress response","volume":"11","author":"J Gutin","year":"2015","journal-title":"Molecular systems biology"},{"issue":"2","key":"pgen.1009313.ref174","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1111\/mmi.13461","article-title":"Opposing PKA and Hog1 signals control the post-transcriptional response to glucose availability in Cryptococcus neoformans","volume":"102","author":"D Banerjee","year":"2016","journal-title":"Molecular microbiology"},{"issue":"8","key":"pgen.1009313.ref175","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.fgb.2010.05.007","article-title":"Turgor and net ion flux responses to activation of the osmotic MAP kinase cascade by fludioxonil in the filamentous fungus Neurospora crassa","volume":"47","author":"RR Lew","year":"2010","journal-title":"Fungal Genetics and Biology"},{"issue":"5","key":"pgen.1009313.ref176","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/ps.302","article-title":"Characterization of mutations in the two-component histidine kinase gene that confer fludioxonil resistance and osmotic sensitivity in the os-1 mutants of Neurospora crassa","volume":"57","author":"N Ochiai","year":"2001","journal-title":"Pest Management Science: formerly Pesticide Science"},{"issue":"3","key":"pgen.1009313.ref177","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1128\/EC.00309-09","article-title":"Comparative transcriptome analysis reveals novel roles of the Ras and cyclic AMP signaling pathways in environmental stress response and antifungal drug sensitivity in Cryptococcus neoformans","volume":"9","author":"S Maeng","year":"2010","journal-title":"Eukaryotic cell"},{"issue":"23","key":"pgen.1009313.ref178","doi-asserted-by":"crossref","first-page":"3206","DOI":"10.1101\/gad.11.23.3206","article-title":"Cryptococcus neoformans mating and virulence are regulated by the G-protein \u03b1 subunit GPA1 and cAMP","volume":"11","author":"JA Alspaugh","year":"1997","journal-title":"Genes Dev"},{"issue":"1","key":"pgen.1009313.ref179","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1128\/EC.1.1.75-84.2002","article-title":"Adenylyl cyclase functions downstream of the G\u03b1 protein Gpa1 and controls mating and pathogenicity of Cryptococcus neoformans","volume":"1","author":"JA Alspaugh","year":"2002","journal-title":"Eukaryotic cell"},{"issue":"2","key":"pgen.1009313.ref180","doi-asserted-by":"crossref","first-page":"e1000776","DOI":"10.1371\/journal.ppat.1000776","article-title":"Interaction of Cryptococcus neoformans Rim101 and protein kinase A regulates capsule","volume":"6","author":"TR O\u2019Meara","year":"2010","journal-title":"PLoS Pathog"},{"issue":"9","key":"pgen.1009313.ref181","doi-asserted-by":"crossref","first-page":"3003","DOI":"10.1534\/g3.116.032342","article-title":"Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale","volume":"6","author":"M Zackrisson","year":"2016","journal-title":"G3 (Bethesda)"},{"issue":"3","key":"pgen.1009313.ref182","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1111\/j.1365-2958.2010.07121.x","article-title":"Pleiotropic function of intersectin homologue Cin1 in Cryptococcus neoformans","volume":"76","author":"G Shen","year":"2010","journal-title":"Molecular microbiology"},{"issue":"6","key":"pgen.1009313.ref183","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0038326","article-title":"Pleiotropic effects of deubiquitinating enzyme Ubp5 on growth and pathogenesis of Cryptococcus neoformans","volume":"7","author":"W Fang","year":"2012","journal-title":"PLoS One"},{"issue":"6","key":"pgen.1009313.ref184","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.resmic.2014.04.001","article-title":"Deletion of the CAP10 gene of Cryptococcus neoformans results in a pleiotropic phenotype with changes in expression of virulence factors","volume":"165","author":"B Tefsen","year":"2014","journal-title":"Research in microbiology"},{"issue":"7","key":"pgen.1009313.ref185","doi-asserted-by":"crossref","first-page":"332","DOI":"10.3390\/genes9070332","article-title":"Host-pathogen interactions mediated by MDR transporters in fungi: as pleiotropic as it gets!","volume":"9","author":"M Cavalheiro","year":"2018","journal-title":"Genes"},{"issue":"4","key":"pgen.1009313.ref186","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1534\/genetics.119.302191","article-title":"The TOR Pathway Plays Pleiotropic Roles in Growth and Stress Responses of the Fungal Pathogen Cryptococcus neoformans","volume":"212","author":"YS So","year":"2019","journal-title":"Genetics"},{"key":"pgen.1009313.ref187","doi-asserted-by":"crossref","first-page":"248","DOI":"10.3389\/fcimb.2019.00248","article-title":"Fungal kinases with a sweet tooth: Pleiotropic roles of their phosphorylated inositol sugar products in the pathogenicity of Cryptococcus neoformans present novel drug targeting opportunities","volume":"9","author":"S Lev","year":"2019","journal-title":"Frontiers in cellular and infection microbiology"},{"issue":"5","key":"pgen.1009313.ref188","doi-asserted-by":"crossref","first-page":"e135","DOI":"10.1371\/journal.pbio.0030135","article-title":"Regulatory Variation at Glypican-3 Underlies a Major Growth QTL in Mice","volume":"3","author":"F Oliver","year":"2005","journal-title":"PLOS Biology"},{"issue":"4","key":"pgen.1009313.ref189","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1534\/genetics.119.301907","article-title":"Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait","volume":"211","author":"JT Lee","year":"2019","journal-title":"Genetics"},{"issue":"5","key":"pgen.1009313.ref190","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.cels.2019.04.002","article-title":"Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships","volume":"8","author":"CM Jakobson","year":"2019","journal-title":"Cell Syst"},{"issue":"3","key":"pgen.1009313.ref191","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1007\/s00122-012-1892-9","article-title":"Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection","volume":"125","author":"Z Li","year":"2012","journal-title":"Theoretical and applied genetics"},{"key":"pgen.1009313.ref192","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.49212","article-title":"Rare variants contribute disproportionately to quantitative trait variation in yeast","volume":"8","author":"JS Bloom","year":"2019","journal-title":"Elife"},{"issue":"8","key":"pgen.1009313.ref193","doi-asserted-by":"crossref","first-page":"e104432","DOI":"10.1371\/journal.pone.0104432","article-title":"Cryptococcus neoformans hyperfilamentous strain is hypervirulent in a murine model of cryptococcal meningoencephalitis","volume":"9","author":"M Feretzaki","year":"2014","journal-title":"PloS one"},{"key":"pgen.1009313.ref194","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.ijid.2016.02.459","article-title":"Rare case of amphotericin B resistant cryptococcal meningitis in HIV non reactive patient","volume":"45","author":"S Singhal","year":"2016","journal-title":"International Journal of Infectious Diseases"},{"issue":"6","key":"pgen.1009313.ref195","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1128\/AAC.00048-11","article-title":"Trends in antifungal drug susceptibility of Cryptococcus neoformans isolates obtained through population-based surveillance in South Africa in 2002-2003 and 2007-2008","volume":"55","author":"NP Govender","year":"2011","journal-title":"Antimicrobial Agents and Chemotherapy"},{"issue":"6","key":"pgen.1009313.ref196","doi-asserted-by":"crossref","first-page":"3107","DOI":"10.1128\/AAC.06252-11","article-title":"Cryptococcus neoformans-Cryptococcus gattii species complex: an international study of wild-type susceptibility endpoint distributions and epidemiological cutoff values for amphotericin B and flucytosine","volume":"56","author":"A Espinel-Ingroff","year":"2012","journal-title":"Antimicrobial Agents and Chemotherapy"},{"issue":"6390","key":"pgen.1009313.ref197","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1126\/science.aap7999","article-title":"Worldwide emergence of resistance to antifungal drugs challenges human health and food security","volume":"360","author":"MC Fisher","year":"2018","journal-title":"Science"},{"issue":"14","key":"pgen.1009313.ref198","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"21","key":"pgen.1009313.ref199","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"H Li","year":"2011","journal-title":"Bioinformatics"},{"key":"pgen.1009313.ref200","unstructured":"Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv Preprint. 2012; p. arXiv:1207.3907."},{"issue":"3","key":"pgen.1009313.ref201","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1534\/genetics.113.155309","article-title":"Genetic mapping and genomic selection using recombination breakpoint data","volume":"195","author":"S Xu","year":"2013","journal-title":"Genetics"},{"issue":"4","key":"pgen.1009313.ref202","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1016\/S0891-5520(02)00036-3","article-title":"Cryptococcosis","volume":"16","author":"JR Perfect","year":"2002","journal-title":"Infectious disease clinics of North America"},{"issue":"6","key":"pgen.1009313.ref203","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1109\/TASSP.1981.1163708","article-title":"A theoretical analysis of the properties of median filters","volume":"29","author":"N Gallagher","year":"1981","journal-title":"IEEE Transactions on Acoustics, Speech, and Signal Processing"},{"key":"pgen.1009313.ref204","volume-title":"Springer Series in Statistics","author":"J Friedman","year":"2001"},{"issue":"2","key":"pgen.1009313.ref205","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1093\/genetics\/143.2.1013","article-title":"Confidence intervals in QTL mapping by bootstrapping","volume":"143","author":"PM Visscher","year":"1996","journal-title":"Genetics"},{"key":"pgen.1009313.ref206","doi-asserted-by":"crossref","DOI":"10.1007\/b98888","volume-title":"Functional Data Analysis","author":"JO Ramsay","year":"2005"},{"key":"pgen.1009313.ref207","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"},{"issue":"5713","key":"pgen.1009313.ref208","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1103773","article-title":"The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans","volume":"307","author":"BJ Loftus","year":"2005","journal-title":"Science"},{"issue":"4","key":"pgen.1009313.ref209","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome research"},{"issue":"11","key":"pgen.1009313.ref210","doi-asserted-by":"crossref","first-page":"e1007113","DOI":"10.1371\/journal.pgen.1007113","article-title":"PRM1 and KAR5 function in cell-cell fusion and karyogamy to drive distinct bisexual and unisexual cycles in the Cryptococcus pathogenic species complex","volume":"13","author":"C Fu","year":"2017","journal-title":"PLoS Genetics"},{"issue":"2","key":"pgen.1009313.ref211","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1128\/IAI.60.2.602-605.1992","article-title":"Genetic association of mating types and virulence in Cryptococcus neoformans","volume":"60","author":"KJ Kwon-Chung","year":"1992","journal-title":"Infection and immunity"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1009313","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T00:00:00Z","timestamp":1612396800000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009313","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T03:53:32Z","timestamp":1670903612000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009313"}},"subtitle":[],"editor":[{"given":"Richard J","family":"Bennett","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,1,25]]},"references-count":211,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,1,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1009313","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.08.21.259861","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,25]]}}}