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Virus Res","volume":"130","author":"CL Washenberger","year":"2007"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1007\/s00535-008-2258-6","article-title":"The epidemiology of hepatocellular cancer: from the perspectives of public health problem to tumor biology","volume":"44","author":"S Caldwell","year":"2009","journal-title":"J Gastroenterol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.antiviral.2005.12.001","article-title":"A target on the move: innate and adaptive immune escape strategies of hepatitis C virus","volume":"69","author":"R Thimme","year":"2006","journal-title":"Antiviral Res"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1111\/j.1574-6976.2011.00319.x","article-title":"Failure of innate and adaptive immune responses in controlling hepatitis C virus infection","volume":"36","author":"R Thimme","year":"2012","journal-title":"FEMS Microbiol Rev"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1002\/jmv.21629","article-title":"Influence of amino-acid polymorphism in the core protein on progression of liver disease in patients infected with hepatitis C virus genotype 1b","volume":"82","author":"M Kobayashi","year":"2010","journal-title":"J Med Virol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"e24514","DOI":"10.1371\/journal.pone.0024514","article-title":"Analysis of the complete open reading frame of genotype 2b hepatitis C virus in association with the response to peginterferon and ribavirin therapy","volume":"6","author":"M Kadokura","year":"2011","journal-title":"PLoS ONE"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/1096-9071(20000201)63:2<128::AID-JMV1007>3.0.CO;2-S","article-title":"Comparative sequence analysis of the core- and NS5-region of hepatitis C virus from tumor and adjacent non-tumor tissue","volume":"63","author":"B Ruster","year":"2001","journal-title":"J Med Virol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1002\/hep.21898","article-title":"Distinct hepatitis C virus core and F protein quasispecies in tumoral and nontumoral hepatocytes isolated via microdissection","volume":"46","author":"R Sobesky","year":"2007","journal-title":"Hepatology"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0103748","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,4]],"date-time":"2025-05-04T01:19:33Z","timestamp":1746321573000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0103748"}},"subtitle":[],"editor":[{"given":"Naglaa H.","family":"Shoukry","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,7,31]]},"references-count":88,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2014,7,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0103748","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2014,7,31]]}}}