{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T03:30:37Z","timestamp":1772767837709,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,1]]},"DOI":"10.1093\/mmy\/myv003","type":"journal-article","created":{"date-parts":[[2015,4,7]],"date-time":"2015-04-07T05:46:08Z","timestamp":1428385568000},"page":"353-360","source":"Crossref","is-referenced-by-count":40,"title":["Genome sequence comparison of Aspergillus fumigatus strains isolated from patients with pulmonary aspergilloma and chronic necrotizing pulmonary aspergillosis"],"prefix":"10.1093","volume":"53","author":[{"given":"Azusa","family":"Takahashi-Nakaguchi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasunori","family":"Muraosa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Hagiwara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kanae","family":"Sakai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takahito","family":"Toyotome","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akira","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susumu","family":"Kawamoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katsuhiko","family":"Kamei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tohru","family":"Gonoi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroki","family":"Takahashi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,4,2]]},"reference":[{"key":"key\n\t\t\t\t20171012023118_bib1","doi-asserted-by":"crossref","DOI":"10.1097\/00010694-194510000-00008","volume-title":"A Manual of the Aspergilli","author":"Thom","year":"1945"},{"issue":"5","key":"key\n\t\t\t\t20171012023118_bib2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1007\/BF01964057","article-title":"Aspergillosis","volume":"8","author":"Bodey","year":"1989","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"121","key":"key\n\t\t\t\t20171012023118_bib3","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1183\/09059180.00001011","article-title":"Pulmonary aspergillosis: a clinical review","volume":"20","author":"Kousha","year":"2011","journal-title":"Eur Respir Rev"},{"issue":"2","key":"key\n\t\t\t\t20171012023118_bib4","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1148\/radiology.140.2.7255737","article-title":"The pulmonary aspergilloses: three distinct entities or a spectrum of disease","volume":"140","author":"Greene","year":"1981","journal-title":"Radiology"},{"issue":"2","key":"key\n\t\t\t\t20171012023118_bib5","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1148\/radiology.140.2.7255704","article-title":"\u201cSemi-invasive\u201d pulmonary aspergillosis: a new look at the spectrum of Aspergillus infections of the lung","volume":"140","author":"Gefter","year":"1981","journal-title":"Radiology"},{"issue":"Suppl 2","key":"key\n\t\t\t\t20171012023118_bib6","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1111\/j.1469-0691.2001.tb00006.x","article-title":"Chronic forms of pulmonary aspergillosis","volume":"7","author":"Denning","year":"2001","journal-title":"Clin Microbiol Infect"},{"issue":"3","key":"key\n\t\t\t\t20171012023118_bib7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2174\/1875036201307010001","article-title":"Comparison of sequencing utility programs","volume":"7","author":"Aronesty","year":"2013","journal-title":"Open Bioinformat J"},{"issue":"Database issue","key":"key\n\t\t\t\t20171012023118_bib8","doi-asserted-by":"crossref","first-page":"D653","DOI":"10.1093\/nar\/gkr875","article-title":"The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources","volume":"40","author":"Arnaud","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"7071","key":"key\n\t\t\t\t20171012023118_bib9","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nature04332","article-title":"Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus","volume":"438","author":"Nierman","year":"2005","journal-title":"Nature"},{"issue":"4","key":"key\n\t\t\t\t20171012023118_bib10","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"issue":"16","key":"key\n\t\t\t\t20171012023118_bib11","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"12","key":"key\n\t\t\t\t20171012023118_bib12","doi-asserted-by":"crossref","first-page":"e28550","DOI":"10.1371\/journal.pone.0028550","article-title":"Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity","volume":"6","author":"Gillece","year":"2011","journal-title":"PLoS One."},{"issue":"16","key":"key\n\t\t\t\t20171012023118_bib13","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1093\/bioinformatics\/btp344","article-title":"Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA","volume":"25","author":"Holt","year":"2009","journal-title":"Bioinformatics"},{"issue":"2","key":"key\n\t\t\t\t20171012023118_bib14","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief Bioinform"},{"issue":"1","key":"key\n\t\t\t\t20171012023118_bib15","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20171012023118_bib16","volume-title":"PHYLIP (Phylogeny Inference Package), version 3.6","author":"Felsenstein","year":"2005"},{"issue":"5","key":"key\n\t\t\t\t20171012023118_bib17","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/0300-9084(96)84768-7","article-title":"WWW-query: an on-line retrieval system for biological sequence banks","volume":"78","author":"Perri\u00e8re","year":"1996","journal-title":"Biochimie"},{"issue":"9","key":"key\n\t\t\t\t20171012023118_bib18","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"issue":"5","key":"key\n\t\t\t\t20171012023118_bib19","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20171012023118_bib20","volume-title":"CummeRbund: analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data","author":"Goff","year":"2012"},{"key":"key\n\t\t\t\t20171012023118_bib21","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2014"},{"issue":"6","key":"key\n\t\t\t\t20171012023118_bib22","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1128\/JCM.36.6.1494-1500.1998","article-title":"Molecular typing of environmental and patient isolates of Aspergillus fumigatus from various hospital settings","volume":"36","author":"Chazalet","year":"1998","journal-title":"J Clin Microbiol"},{"issue":"6","key":"key\n\t\t\t\t20171012023118_bib23","doi-asserted-by":"crossref","first-page":"586","DOI":"10.3109\/13693786.2012.761359","article-title":"Microsatellite typing of Aspergillus flavus in patients with various clinical presentations of aspergillosis","volume":"51","author":"Hadrich","year":"2013","journal-title":"Med Mycol"},{"issue":"1","key":"key\n\t\t\t\t20171012023118_bib24","doi-asserted-by":"crossref","first-page":"e16016","DOI":"10.1371\/journal.pone.0016016","article-title":"The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro","volume":"6","author":"Morton","year":"2011","journal-title":"PLoS One"},{"issue":"1","key":"key\n\t\t\t\t20171012023118_bib25","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1007\/s00294-006-0073-2","article-title":"Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole","volume":"50","author":"da Silva Ferreira","year":"2006","journal-title":"Curr Genet"},{"issue":"Database issue","key":"key\n\t\t\t\t20171012023118_bib26","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gkr1202","article-title":"GenBank","volume":"40","author":"Benson","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"key\n\t\t\t\t20171012023118_bib27","doi-asserted-by":"crossref","first-page":"e1000046","DOI":"10.1371\/journal.pgen.1000046","article-title":"Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus","volume":"4","author":"Fedorova","year":"2008","journal-title":"PLoS Genet"}],"container-title":["Medical Mycology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/mmy\/article-pdf\/53\/4\/353\/17488200\/myv003.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T14:49:19Z","timestamp":1598885359000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/mmy\/article\/53\/4\/353\/973015\/Genome-sequence-comparison-of-Aspergillus"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,4,2]]},"references-count":27,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2015,4,2]]},"published-print":{"date-parts":[[2015,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/mmy\/myv003","relation":{},"ISSN":["1460-2709","1369-3786"],"issn-type":[{"value":"1460-2709","type":"electronic"},{"value":"1369-3786","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,5]]},"published":{"date-parts":[[2015,4,2]]}}}