{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T02:06:20Z","timestamp":1789697180830,"version":"4.0.1"},"reference-count":62,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2012,7,20]],"date-time":"2012-07-20T00:00:00Z","timestamp":1342742400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0041034","type":"journal-article","created":{"date-parts":[[2012,7,21]],"date-time":"2012-07-21T08:39:16Z","timestamp":1342859956000},"page":"e41034","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":75,"title":["Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in Coccidioides spp"],"prefix":"10.1371","volume":"7","author":[{"given":"Emily","family":"Whiston","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hua","family":"Zhang Wise","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Sharpton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ginger","family":"Jui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garry T.","family":"Cole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John W.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,7,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1111\/j.1574-6968.2011.02276.x","article-title":"Genetic advances in dermatophytes.","volume":"320","author":"M Grumbt","year":"2011","journal-title":"Fems Microbiology Letters"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.ijmm.2011.04.009","article-title":"Host-pathogen interactions and virulence-associated genes during Candida albicans oral infections.","volume":"301","author":"R Martin","year":"2011","journal-title":"International Journal of Medical Microbiology"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1111\/j.1364-3703.2009.00565.x","article-title":"Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology.","volume":"10","author":"KC Tan","year":"2009","journal-title":"Molecular Plant Pathology"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.mib.2007.04.002","article-title":"Dimorphism and virulence in fungi.","volume":"10","author":"BS Klein","year":"2007","journal-title":"Current Opinion in Microbiology"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.3390\/ijerph8041150","article-title":"The public health impact of coccidioidomycosis in Arizona and California.","volume":"8","author":"RF Hector","year":"2011","journal-title":"International Journal of Environmental Research and Public Health"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"73","DOI":"10.2307\/3761847","article-title":"Molecular and phenotypic description of Coccidioides posadasii sp nov., previously recognized as the non-California population of Coccidioides immitis.","volume":"94","author":"MC Fisher","year":"2002","journal-title":"Mycologia"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/S1369-5274(03)00088-2","article-title":"Fungal multilocus sequence typing - it\u2019s not just for bacteria.","volume":"6","author":"JW Taylor","year":"2003","journal-title":"Current Opinion in Microbiology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1101\/gr.103911.109","article-title":"Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.","volume":"20","author":"DE Neafsey","year":"2010","journal-title":"Genome Research"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1007\/s11046-010-9285-6","article-title":"Measuring Cellular Immunity in Coccidioidomycosis: The Time is Now.","volume":"169","author":"NM Ampel","year":"2010","journal-title":"Mycopathologia"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3443","DOI":"10.1128\/IAI.70.7.3443-3456.2002","article-title":"A parasitic phase-specific adhesin of Coccidioides immitis contributes to the virulence of this respiratory fungal pathogen.","volume":"70","author":"CY Hung","year":"2002","journal-title":"Infection and Immunity"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"3010","DOI":"10.1128\/IAI.71.6.3010-3019.2003","article-title":"A recombinant beta-1,3-glucanosyltransferase homolog of Coccidioides posadasii protects mice against coccidioidomycosis.","volume":"71","author":"N Delgado","year":"2003","journal-title":"Infection and Immunity"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.autrev.2010.08.010","article-title":"The immune response in Coccidioidomycosis.","volume":"10","author":"AT Borchers","year":"2010","journal-title":"Autoimmunity Reviews"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1371\/annotation\/0675044c-d80f-456f-bb63-4f85fb1d0c33","article-title":"Fungal cell gigantism during mammalian infection.","volume":"6","author":"O Zaragoza","year":"2010","journal-title":"Plos Pathogens"},{"key":"ref14","article-title":"CDC - Coccidioidomycosis: General Information - NCZVED.","year":"2010"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1097\/INF.0b013e3181bcfd7f","article-title":"Hospitalizations for coccidioidomycosis at forty-one Children\u2019s Hospitals in the United States.","volume":"29","author":"BT Fisher","year":"2010","journal-title":"Pediatric Infectious Disease Journal"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1128\/JCM.38.2.807-813.2000","article-title":"Pathogenic clones versus environmentally driven population increase: Analysis of an epidemic of the human fungal pathogen Coccidioides immitis.","volume":"38","author":"MC Fisher","year":"2000","journal-title":"Journal of Clinical Microbiology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1046\/j.1365-2672.2001.01496.x","article-title":"Coccidioides immitis as a Select Agent of bioterrorism.","volume":"91","author":"DM Dixon","year":"2001","journal-title":"Journal of Applied Microbiology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.fgb.2006.02.003","article-title":"Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii.","volume":"43","author":"H Johannesson","year":"2006","journal-title":"Fungal Genetics and Biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1101\/gr.087551.108","article-title":"Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.","volume":"19","author":"TJ Sharpton","year":"2009","journal-title":"Genome Research"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"14573","DOI":"10.1073\/pnas.0806221105","article-title":"Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.","volume":"105","author":"RH Webster","year":"2008","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4880","DOI":"10.1073\/pnas.0710448105","article-title":"Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator.","volume":"105","author":"VQ Nguyen","year":"2008","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"12813","DOI":"10.1073\/pnas.0605270103","article-title":"Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans.","volume":"103","author":"GH Huang","year":"2006","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/S0378-1119(99)00496-5","article-title":"Sequence, expression and functional analysis of the Coccidioides immitis ODC (ornithine decarboxylase) gene.","volume":"242","author":"L Guevara-Olvera","year":"2000","journal-title":"Gene"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1128\/EC.4.12.2115-2128.2005","article-title":"Transcriptome analysis of Paracoccidioides brasiliensis cells undergoing mycelium-to-yeast transition.","volume":"4","author":"LR Nunes","year":"2005","journal-title":"Eukaryotic Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1146\/annurev.micro.59.030804.121055","article-title":"Defining virulence genes in the dimorphic fungi.","volume":"60","author":"CA Rappleye","year":"2006","journal-title":"Annual Review of Microbiology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"3543","DOI":"10.1128\/IAI.62.8.3543-3546.1994","article-title":"Altered expression of surface alpha-1,3-glucan in genetically related strains of Blastomyces dermatitidis that differ in virulence.","volume":"62","author":"LH Hogan","year":"1994","journal-title":"Infection and Immunity"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2997","DOI":"10.1128\/IAI.56.11.2997-3000.1988","article-title":"Cell-walls from avirulent variants of Histoplasma capsulatum lack alpha-(1,3)-glucan.","volume":"56","author":"KR Klimpel","year":"1988","journal-title":"Infection and Immunity"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1111\/j.1365-2958.2004.04131.x","article-title":"RNA interference in Histoplasma capsulatum demonstrates a role for alpha-(1,3)-glucan in virulence.","volume":"53","author":"CA Rappleye","year":"2004","journal-title":"Molecular Microbiology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1128\/IAI.15.2.343-346.1977","article-title":"Host-parasite relationships in yeastlike form of Paracoccidioides brasiliensis strain IVIC PB9.","volume":"15","author":"G Sanblas","year":"1977","journal-title":"Infection and Immunity"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.fgb.2006.01.006","article-title":"AGS3, an alpha(1\u20133)glucan synthase gene family member of Aspergillus fumigatus, modulates mycelium growth in the lung of experimentally infected mice.","volume":"43","author":"D Maubon","year":"2006","journal-title":"Fungal Genetics and Biology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1128\/IAI.68.2.584-593.2000","article-title":"A major cell surface antigen of Coccidioides immitis which elicits both humoral and cellular immune responses.","volume":"68","author":"CY Hung","year":"2000","journal-title":"Infection and Immunity"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"6689","DOI":"10.1128\/IAI.73.10.6689-6703.2005","article-title":"A metalloproteinase of Coccidioides posadasii contributes to evasion of host detection.","volume":"73","author":"CY Hung","year":"2005","journal-title":"Infection and Immunity"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1091\/mbc.E09-02-0172","article-title":"Yeast Sec1p Functions before and after Vesicle Docking.","volume":"20","author":"K Hashizume","year":"2009","journal-title":"Molecular Biology of the Cell"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.1126\/science.1161748","article-title":"Membrane fusion: Grappling with SNARE and SM proteins [Review].","author":"TC Sudhof","year":"2009"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1534\/genetics.105.040923","article-title":"Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii.","volume":"171","author":"H Johannesson","year":"2005","journal-title":"Genetics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"77","DOI":"10.2174\/1568005033342064","article-title":"Chitin synthesis as a target for antifungal drugs.","volume":"3","author":"J Ruiz-Herrera","year":"2003","journal-title":"Current Drug Targets - Infectious Disorders"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1128\/IAI.74.1.504-515.2006","article-title":"Urease produced by Coccidioides posadasii contributes to the virulence of this respiratory pathogen.","volume":"74","author":"F Mirbod-Donovan","year":"2006","journal-title":"Infection and Immunity"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1073\/pnas.0609848104","article-title":"Histoplasma capsulatum alpha-(1,3)-glucan blocks innate immune recognition by the beta-glucan receptor.","volume":"104","author":"CA Rappleye","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"5777","DOI":"10.1128\/IAI.00807-07","article-title":"Evaluation of two homologous proline-rich proteins of Coccidioides posadasii as candidate vaccines against coccidioidomycosis.","volume":"75","author":"RA Herr","year":"2007","journal-title":"Infection and Immunity"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/35008652","article-title":"A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane.","volume":"2","author":"G Jedd","year":"2000","journal-title":"Nature Cell Biology"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/fgbi.2000.1230","article-title":"hex-1, a gene unique to filamentous fungi, encodes the major protein of the Woronin body and functions as a plug for septal pores.","volume":"31","author":"K Tenney","year":"2000","journal-title":"Fungal Genetics and Biology"},{"key":"ref42","first-page":"281","article-title":"Arthroconidium-spherule-endospore transformation in <italic>Coccidioides immitis<\/italic>.","author":"GT Cole","year":"1985"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1007\/s004380100455","article-title":"Characterization of Gac1p, a regulatory subunit of protein phosphatase type I involved in glycogen accumulation in Saccharomyces cerevisiae.","volume":"265","author":"X Wu","year":"2001","journal-title":"Molecular Genetics and Genomics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"19533","DOI":"10.1073\/pnas.0907416106","article-title":"A key role for vesicles in fungal secondary metabolism.","volume":"106","author":"A Chanda","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref45","article-title":"LaeA Control of velvet family regulatory proteins for light-dependent development and fungal cell-type specificity.","author":"OS Bayram","year":"2010"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"3952","DOI":"10.1128\/IAI.59.11.3952-3961.1991","article-title":"Coccidioides immitis fractions which are antigenic for immune lymphocytes-T.","volume":"59","author":"TN Kirkland","year":"1991","journal-title":"Infection and Immunity"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/0378-1119(95)00250-A","article-title":"Cloning and expression of a gene encoding a t-cell reactive protein from Coccidioides immitis - Homology to 4-hydroxyphenylpyruvate dioxygenase and the mammalian F-antigen.","volume":"161","author":"EE Wyckoff","year":"1995","journal-title":"Gene"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1007\/s00438-003-0965-5","article-title":"The transcription factor HACA mediates the unfolded protein response in Aspergillus niger, and up-regulates its own transcription.","volume":"271","author":"HJ Mulder","year":"2004","journal-title":"Molecular Genetics and Genomics"},{"key":"ref49","doi-asserted-by":"crossref","DOI":"10.4049\/jimmunol.87.2.218","article-title":"Immunogenicity of spherule-endospore vaccines of Coccidioides immitis for mice.","author":"HB Levine","year":"1961"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1128\/IAI.73.3.1553-1560.2005","article-title":"Innate immunity to the pathogenic fungus Coccidioides posadasii is dependent on toll-like receptor 2 and dectin-1.","volume":"73","author":"S Viriyakosol","year":"2005","journal-title":"Infection and Immunity"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1101\/gr.076091.108","article-title":"Identification of ancient remains through genomic sequencing.","volume":"18","author":"MJ Blow","year":"2008","journal-title":"Genome Research"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1101\/gr.789803","article-title":"AVID: A global alignment program.","volume":"13","author":"N Bray","year":"2003","journal-title":"Genome Research"},{"key":"ref53","article-title":"Whole-genome alignments and polytopes for comparative genomics: University of California, Berkeley.","author":"CN Dewey","year":"2006"},{"key":"ref54","first-page":"221","article-title":"Aligning multiple whole genomes with Mercator and MAVID.","author":"CN Dewey","year":"2007"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nature Genetics"},{"key":"ref56","article-title":"Smit AF, Hubley R, Green P (1996\u20132010) <italic>RepeatMasker Open-3.0<\/italic>."},{"key":"ref57","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","article-title":"Improved prediction of signal peptides: SignalP 3.0.","volume":"340","author":"JD Bendtsen","year":"2004","journal-title":"Journal of Molecular Biology"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq.","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"ref59","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data.","author":"S Anders","year":"2010"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/bioinformatics\/btg114","article-title":"GeneMerge - post-genomic analysis, data mining, and hypothesis testing.","volume":"19","author":"CI Castillo-Davis","year":"2003","journal-title":"Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate - A practical and powerful approach to multiple testing.","author":"Y Benjamini","year":"1995"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1126\/science.1124105","article-title":"Global control of dimorphism and virulence in fungi.","volume":"312","author":"JC Nemecek","year":"2006","journal-title":"Science"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0041034","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T15:25:43Z","timestamp":1687620343000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0041034"}},"subtitle":[],"editor":[{"given":"Yong-Sun","family":"Bahn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,7,20]]},"references-count":62,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2012,7,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0041034","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,7,20]]}}}