Hepatitis C databases, principles and utility to researchers

Hepatology

Volumn 43, Issue 5, 2006, Pages 1157-1165

  Kuiken, Carla ^a   Mizokami, Masashi ^b   Deleage, Gilbert ^c   Yusim, Karina ^a   Penin, Francois ^c   Shin I, Tadasu ^b   Charavay, Céline ^c   Tao, Ning ^a   Crisan, Daniel ^c   Grande, Delphine ^c   Dalwani, Anita ^a   Geourjon, Christophe ^c   Agrawal, Ashish ^a   Combet, Christophe ^c  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b NAGOYA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCES   (Japan)

^c INSTITUT DE BIOLOGIE ET CHIMIE DES PROTÉINES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; HEPATITIS C VACCINE;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; GENE MAPPING; GENE SEQUENCE; GENETIC VARIABILITY; HEPATITIS C; IMMUNOLOGY; MOLECULAR MODEL; PHYLOGENY; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 33646572892     PISSN: 02709139     EISSN: None     Source Type: Journal    
DOI: 10.1002/hep.21162     Document Type: Article

References (31)

1. Alter MJ, Margolis HS, Krawczynski K, Judson FN, Mares A, Alexander WJ, et al. The natural history of community-acquired hepatitis C in the United States. The Sentinel Counties Chronic non-A, non-B Hepatitis Study Team. N Engl J Med 1992;327:1899-1905.
2. Hoofnagle JH. Hepatitis C: the clinical spectrum of disease. HEPATOLOGY1997;26(Suppl):15S-20S.
3. Krahn M, Wong JB, Heathcote J, Scully L, Seeff L. Estimating the prognosis of hepatitis C patients infected by transfusion in Canada between 1986 and 1990. Med Decis Making 2004;24:20-29.
4. Simmonds P. Viral heterogeneity of the hepatitis C virus. J Hepatol 1999;31(Suppl 1):54-60.
5. Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S, et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. HEPATOLOGY 2005;42:962-973.
6. Weiner AJ, Christopherson C, Hall JE, Bonino F, Saracco G, Brunetto MR, et al. Sequence variation in hepatitis C viral isolates. J Hepatol 1991;13(Suppl 4):S6-1S4.
7. Farci P, Purcell RH. Clinical significance of hepatitis C virus genotypes and quasispecies. Semin Liver Dis 2000;20:103-126.
8. Combet C, Penin F, Geourjon C, Deleage G. HCVDB : hepatitis C virus sequences database. Appl Bioinformatics 2004;3:237-240.
9. Penin F, Brass V, Appel N, Ramboarina S, Montserret R, Ficheux D, et al. Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A. J Biol Chem 2004;279:40835-40843.
10. Kuiken C, Yusim K, Boykin L, Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics 2005;21:379-384.
11. Yusim K, Richardson R, Tao N, Szinger JJ, Funkhouser R, Korber B, Kuiken CL. The Los Alamos Hepatitis C Immunology Database. Appl Bioinformatics 2005;4:217-225.
12. Combet C, Blanchet C, Geourjon C, Deléage G. NPS@: network protein sequence analysis. Trends Biochem Sci 2000;25:147-150.
13. Combet C, Jambon M, Deléage G, Geourjon C. Geno3D: automatic comparative molecular modelling of protein. Bioinformatics 2002;18:213-214.
14. Jambon M, Imberty A, Deléage G, Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003;52:137-145.
15. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, et al. Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes, and influenza hemagglutinin. Glycobiology 2004;14:1229-1246.
16. Korber BT, MacInnes K, Smith RF, Myers G. Mutational trends in V3 loop protein sequences observed in different genetic lineages of human immunodeficiency virus type 1. J Virol 1994;68:6730-6744.
17. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998;14:817-818.
18. Higgins DG. Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. Comput Appl Biosci 1992;8:15-22.
19. Mukaide M, Tanaka Y, Kakuda H, Fujiwara K, Kurbanov F, Orito E, et al. New combination test for hepatitis C virus genotype and viral load determination using Amplicor GT HCV MONITOR test v2.0. World J Gastroenterol 2005;11:469-475.
20. Kato T, Miyamoto M, Date T, Furusaka A, Hiramoto J, Nagayama K, et al. Differences in hepatitis C virus core protein processing among genotypes 1 and 2. Hepatol Res 2004;30:204-209.
21. Ndjomou J, Pybus OG, Matz B. Phylogenetic analysis of hepatitis C virus isolates indicates a unique pattern of endemic infection in Cameroon. J Gen Virol 2003;84:2333-2341.
22. Nakano T, Lu L, He Y, Fu Y, Robertson BH, Pybus OG. Population genetic history of hepatitis C virus 1b infection in China. J Gen Virol 2006;87:73-82.
23. Penin F, Combet C, Germanidis G, Frainais PO, Deléage G, Pawlotsky JM, et al. Conservation of the conformation and positive charges of hepatitis C virus E2 envelope glycoprotein hypervariable region 1 points to a role in cell attachment. J Virol 2001;75:5703-5710.
24. Carrère-Kremer S, Montpellier-Pala C, Cocquerel L, Wychowski C, Penin F, Dubuisson J. Subcellular localization and topology of the p7 polypeptide of hepatitis C virus. J Virol 2002;76:3720-3730.
25. Timm J, Lauer GM, Kavanagh DG, Sheridan I, Kim AY, Lucas M, Pillay T, et al. CD8 epitope escape and reversion in acute HCV infection. J Exp Med 2004;200:1593-1604.
26. Pond SLK, Frost SDW. A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol 2005;22:223-234.
27. Tuplin A, Evans DJ, Simmonds P. Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. J Gen Virol 2004;85:3037-3047.
28. Simmonds P. Genetic diversity and evolution of hepatitis C virus - 15 years on. J Gen Virol 2004;85:3173-3188.
29. McKeating JA, Zhang LQ, Logvinoff C, Flint M, Zhang J, Yu J, et al. Diverse hepatitis C virus glycoproteins mediate viral infection in a CD81-dependent manner. J Virol 2004;78:8496-8505.
30. Sumpter R, Wang C, Foy E, Loo Y-M, Gale M. Viral evolution and interferon resistance of hepatitis C virus RNA replication in a cell culture model. J Virol 2004;78:11591-11604.
31. Nicot F, Legrand-Abravanel F, Sandres-Saune K, Boulestin A, Dubois M, Alric L, et al. Heterogeneity of hepatitis C virus genotype 4 strains circulating in south-western France. J Gen Virol 2005;86:107-114.