{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:08:23Z","timestamp":1785888503488,"version":"3.56.0"},"reference-count":67,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2016,8,2]],"date-time":"2016-08-02T00:00:00Z","timestamp":1470096000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2016,8,30]],"date-time":"2016-08-30T00:00:00Z","timestamp":1472515200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen","award":["31003A_140514"],"award-info":[{"award-number":["31003A_140514"]}]},{"name":"Fonds De La Recherche Scientifique M\u00e9dicale - FRSM - Belgium","award":["3.4558.10"],"award-info":[{"award-number":["3.4558.10"]}]},{"name":"Executive Unit for Higher Education, Research, Development and Innovation Funding - UEFISCDI - Romania","award":["594\/2012"],"award-info":[{"award-number":["594\/2012"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2016,8,30]]},"abstract":"<jats:p>Dermatophytoses (ringworm, jock itch, athlete\u2019s foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing annotation for<jats:italic>A. benhamiae<\/jats:italic>. Comparing gene expression during infection on guinea pigs with keratin degradation<jats:italic>in vitro<\/jats:italic>, which is supposed to mimic the host environment, revealed the critical importance of using real<jats:italic>in vivo<\/jats:italic>conditions for investigating virulence mechanisms. The analysis of genes expressed<jats:italic>in vivo<\/jats:italic>, encoding cell surface and secreted proteins, particularly proteases, led to the identification of new allergen and virulence factor candidates.<\/jats:p>","DOI":"10.1128\/msystems.00036-16","type":"journal-article","created":{"date-parts":[[2016,8,3]],"date-time":"2016-08-03T02:19:10Z","timestamp":1470190750000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":35,"title":["RNA Sequencing-Based Genome Reannotation of the Dermatophyte<i>Arthroderma benhamiae<\/i>and Characterization of Its Secretome and Whole Gene Expression Profile during Infection"],"prefix":"10.1128","volume":"1","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2074-5029","authenticated-orcid":false,"given":"Van Du T.","family":"Tran","sequence":"first","affiliation":[{"name":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niccol\u00f2","family":"De Coi","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Feuermann","sequence":"additional","affiliation":[{"name":"Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuel","family":"Schmid-Siegert","sequence":"additional","affiliation":[{"name":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena-Tatiana","family":"B\u0103gu\u0163","sequence":"additional","affiliation":[{"name":"Fundamental and Applied Research for Animals &amp; Health (FARAH), Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e8ge, Li\u00e8ge, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Mignon","sequence":"additional","affiliation":[{"name":"Fundamental and Applied Research for Animals &amp; Health (FARAH), Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e8ge, Li\u00e8ge, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrice","family":"Waridel","sequence":"additional","affiliation":[{"name":"Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corinne","family":"Peter","sequence":"additional","affiliation":[{"name":"Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Pradervand","sequence":"additional","affiliation":[{"name":"Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Pagni","sequence":"additional","affiliation":[{"name":"Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel","family":"Monod","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.8.2.240"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11046-008-9101-8"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-1-r7"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00259-12"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.67.3.400-428.2003"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-arplant-043014-114623"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.033464-0"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.26690-0"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2004.06.024"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.27484-0"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2007.11.005"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.45.29489"},{"key":"e_1_3_2_14_2","volume-title":"Gene prediction with a hidden Markov model","author":"Stanke M","year":"2004","unstructured":"Stanke M Steinkamp R Waack S Morgenstern B . 2004. Gene prediction with a hidden Markov model. University of G\u00f6ttingen, G\u00f6ttingen, Germany."},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1220270"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00106a001"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.201100234"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/EC.00037-12"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku989"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki442"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.9.847"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.5b00009"},{"key":"e_1_3_2_23_2","first-page":"1","article-title":"FunSecKB2: a fungal protein subcellular location knowledgebase","volume":"4","author":"Meinken J","year":"2014","unstructured":"Meinken J Asch DK Neizer-Ashun KA Chang G-H Cooper CR Jr Min XJ . 2014. FunSecKB2: a fungal protein subcellular location knowledgebase. Comput Mol Biol4(6):1\u201317.","journal-title":"Comput Mol Biol"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.6.7.2490"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1080\/02681219780001131"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1853-1"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0135720"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2013.00013"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-695"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00942-15"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005493"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0044088"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2015.09.054"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2005.04654.x"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02747-10"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.17.4.804-839.2004"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00807-07"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2004.04199.x"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2013.12.005"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature08264"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/jid.2015.367"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr070153m"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1994.tb01327.x"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2008.09.007"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00425-09"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1080\/13693780500410909"},{"key":"e_1_3_2_47_2","doi-asserted-by":"crossref","first-page":"96","DOI":"10.4049\/jimmunol.147.1.96","article-title":"Trichophyton tonsurans allergen. I. Characterization of a protein that causes immediate but not delayed hypersensitivity","volume":"147","author":"Deuell B","year":"1991","unstructured":"Deuell B Arruda LK Hayden ML Chapman MD Platts-Mills TA . 1991. Trichophyton tonsurans allergen. I. Characterization of a protein that causes immediate but not delayed hypersensitivity. J Immunol147:96\u2013101.","journal-title":"J Immunol"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.18.1.30-43.2005"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/br.38.2.222-250.1974"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.3109\/1040841X.2011.645520"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1159\/000077311"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-4-r36"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2012.016"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-9525(00)02024-2"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/0888-7543(91)90071-L"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.03.016"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1701"},{"key":"e_1_3_2_58_2","first-page":"175","article-title":"A hidden Markov model for predicting transmembrane helices in protein sequences","volume":"6","author":"Sonnhammer EL","year":"1998","unstructured":"Sonnhammer EL von Heijne G Krogh A . 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol6:175\u2013182.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4315"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-392"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(84)90309-7"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00176a037"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-2-r29"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1007\/0-387-29362-0_23"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1214\/aos\/1013699998"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki107"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00036-16","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00036-16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T17:14:44Z","timestamp":1718730884000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00036-16"}},"subtitle":[],"editor":[{"given":"Barbara","family":"Methe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,8,30]]},"references-count":67,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,8,30]]}},"alternative-id":["10.1128\/mSystems.00036-16"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00036-16","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,30]]},"assertion":[{"value":"2016-03-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-06-27","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-08-02","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00036-16"}}