Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data
Tài liệu tham khảo
Ganem, 2004, Hepatitis B virus infection–natural history and clinical consequences, N. Engl. J. Med., 350, 1118, 10.1056/NEJMra031087
Lavanchy, 2004, Hepatitis B virus epidemiology, disease burden, treatment, and current and emerging prevention and control measures, J. Viral Hepat., 11, 97, 10.1046/j.1365-2893.2003.00487.x
A.S. Lok, B.J. McMahon, Chronic hepatitis B, Hepatology (Baltimore, Md.) 45(2) (2007) 507-539.
Sugauchi, 2002, Hepatitis B virus of genotype B with or without recombination with genotype C over the precore region plus the core gene, J. Virol., 76, 5985, 10.1128/JVI.76.12.5985-5992.2002
Seeger, 2015, Molecular biology of hepatitis B virus infection, Virology, 479–480, 672, 10.1016/j.virol.2015.02.031
Rodriguez-Frias, 2013, Quasispecies structure, cornerstone of hepatitis B virus infection: mass sequencing approach, World J. Gastroenterol., 19, 6995, 10.3748/wjg.v19.i41.6995
Lin, 1991, Application of hepatitis B virus (HBV) DNA sequence polymorphisms to the study of HBV transmission, J. Infect. Dis., 164, 284, 10.1093/infdis/164.2.284
Sterneck, 1997, Hepatitis B virus sequence changes evolving in liver transplant recipients with fulminant hepatitis, J. Hepatol., 26, 754, 10.1016/S0168-8278(97)80239-5
Bozkaya, 1997, High degree of conservation in the hepatitis B virus core gene during the immune tolerant phase in perinatally acquired chronic hepatitis B virus infection, J. Hepatol., 26, 508, 10.1016/S0168-8278(97)80415-1
Whalley, 2001, Kinetics of acute hepatitis B virus infection in humans, J. Exp. Med., 193, 847, 10.1084/jem.193.7.847
Okamoto, 1988, Typing hepatitis B virus by homology in nucleotide sequence: comparison of surface antigen subtypes, J. General Virol., 69, 2575, 10.1099/0022-1317-69-10-2575
Cassidy, 2011, Hepatitis B vaccine effectiveness in the face of global HBV genotype diversity, Expert Rev. Vac., 10, 1709, 10.1586/erv.11.151
Kramvis, 2008, Relationship of serological subtype, basic core promoter and precore mutations to genotypes/subgenotypes of hepatitis B virus, J. Med. Virol., 80, 27, 10.1002/jmv.21049
Liu, 2007, Five subgenotypes of hepatitis B virus genotype B with distinct geographic and virological characteristics, Virus Res., 129, 212, 10.1016/j.virusres.2007.07.016
Shendure, 2008, Next-generation DNA sequencing, Nat. Biotechnol., 26, 1135, 10.1038/nbt1486
Chen, 2009, BreakDancer: an algorithm for high-resolution mapping of genomic structural variation, Nat. Methods, 6, 677, 10.1038/nmeth.1363
Sindi, 2009, A geometric approach for classification and comparison of structural variants, Bioinformatics, 25, i222, 10.1093/bioinformatics/btp208
Korbel, 2009, PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data, Genome biology, 10, R23, 10.1186/gb-2009-10-2-r23
Sun, 2012, Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads, Bioinformatics, 28, 1024, 10.1093/bioinformatics/bts064
Jiang, 2012, PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants, Bioinformatics, 28, 2576, 10.1093/bioinformatics/bts484
Sindi, 2012, An integrative probabilistic model for identification of structural variation in sequencing data, Genome Biol., 13, R22, 10.1186/gb-2012-13-3-r22
Zhang, 2012, An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data, BMC Bioinform., 13, S6, 10.1186/1471-2105-13-S6-S6
Ye, 2009, Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads, Bioinformatics, 25, 2865, 10.1093/bioinformatics/btp394
Medvedev, 2009, Computational methods for discovering structural variation with next-generation sequencing, Nat. Methods, 6, S13, 10.1038/nmeth.1374
Guan, 2016, Structural variation detection using next-generation sequencing data: A comparative technical review, Methods, 102, 36, 10.1016/j.ymeth.2016.01.020
Liu, 2016, Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus, Hepatol. Int., 10, 147, 10.1007/s12072-015-9645-x
Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923
Li, 2009, Project data processing, the sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698
Cheng, 2016, DeF-GPU: Efficient and effective deletions finding in hepatitis B viral genomic DNA using a GPU architecture, Methods, 111, 56, 10.1016/j.ymeth.2016.07.020
B.-E. Shie, J.-H. Cheng, K.-T. Chuang, V.S. Tseng, A One-Phase Method for Mining High Utility Mobile Sequential Patterns in Mobile Commerce Environments, in: H. Jiang, W. Ding, M. Ali, X. Wu (Eds.), Advanced Research in Applied Artificial Intelligence: 25th International Conference on Industrial Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2012, Dalian, China, June 9-12, 2012. Proceedings, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 616-626.
Hsieh, 2007, Hepatitis B virus pre-S2 mutant surface antigen induces degradation of cyclin-dependent kinase inhibitor p27Kip1 through c-Jun activation domain-binding protein 1, Mol. Cancer Res.: MCR, 5, 1063, 10.1158/1541-7786.MCR-07-0098
Hung, 2004, Endoplasmic reticulum stress stimulates the expression of cyclooxygenase-2 through activation of NF-kappaB and pp38 mitogen-activated protein kinase, J. Biol. Chem., 279, 46384, 10.1074/jbc.M403568200
Wang, 2006, Hepatitis B virus pre-S mutants, endoplasmic reticulum stress and hepatocarcinogenesis, Cancer Sci., 97, 683, 10.1111/j.1349-7006.2006.00235.x
Liu, 2012, Hepatitis B virus X protein mutant upregulates CENP-A expression in hepatoma cells, Oncol. Rep., 27, 168
Zhang, 2014, Hepatitis B virus X protein accelerates the development of hepatoma, Cancer Biol. Med., 11, 182