Các vùng bảo tồn cao trong RNA polymerase phụ thuộc RNA của virus Ebola có thể hoạt động như một mục tiêu vaccine peptide mới toàn cầu: một tiếp cận tính toán

Apweiler R, Bairoch A, Wu CH et al (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32(1):115–119

Arnold K, Bordoli L, Kopp J et al (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2):195–201

Bacchetta R, Gregori S, Roncarolo M-G (2005) CD4+ regulatory T cells: mechanisms of induction and effector function. Autoimmun Rev 4(8):491–496

Baize S, Pannetier D, Oestereich L et al (2014) Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med 371(15):1418–1425

Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27(3):343–350

Bhasin M, Raghava G (2004) Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine 22(23):3195–3204

Bourdette DN, Edmonds E, Smith C et al (2005) A highly immunogenic trivalent T cell receptor peptide vaccine for multiple sclerosis. Mult Scler 11(5):552–561

Bui HH, Sidney J, Dinh K et al (2006) Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 17(7):153

Bui HH, Sidney J, Li W et al (2007) Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 8(1):361

Choi JH, Croyle MA (2013) Emerging targets and novel approaches to Ebola virus prophylaxis and treatment. BioDrugs 27(6):565–583

Chou PY, Fasman GD (1979) Empirical predictions of protein conformation. Annu Rev Biochem 47:251–276

Chowell G, Hengartner NW, Castillo-Chavez C et al (2004) The basic reproductive number of Ebola and the effects of public health measures: the cases of Congo and Uganda. J Theor Biol 229(1):119–126

Crary S, Towner J, Honig J et al (2003) Analysis of the role of predicted RNA secondary structures in Ebola virus replication. Virology 306:210–218

Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8(1):4

Elisha A, Adegboro B (2014) Ebola virus diseases. Afr J Clin Exp Microbiol 15(3):117–121

Emini EA, Hughes JV, Perlow DS et al (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55(3):836–839

Evans DK, Popova A (2015) West African Ebola crisis and orphans. Lancet 385(9972):945–946

Feldmann H, Volchkov VE, Volchkova VA et al (1999) The glycoproteins of Marburg and Ebola virus and their potential roles in pathogenesis. Arch Virol 15:159–169

Feldmann H, Volchkov V, Ströher U et al (2001) Biosynthesis and role of filovirus glycoprotein. J Gen Virol 82:2839–2848

Feldmann H, Jones S, Klenk HD et al (2003) Ebola virus: from discovery to vaccine. Nat Rev Immunol 3(8):677–685

Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753–1773

Frieden TR, Damon I, Bell BP et al (2014) Ebola 2014—new challenges, new global response and responsibility. N Engl J Med 371(13):1177–1180

Garcia KC, Teyton L, Wilson IA (1999) Structural basis of T cell recognition. Annu Rev Immunol 17:369–397

Garcia-Boronat M, Diez-Rivero CM, Reinherz EL et al (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res 36(2):35–41

Gatherer D (2014) The 2014 Ebola virus disease outbreak in West Africa. J Gen Virol 95(8):1619–1624

Geisbert TW, Geisbert JB, Leung A et al (2009) Single-injection vaccine protects nonhuman primates against infection with marburg virus and three species of ebola virus. J Virol 83(14):7296–7304

Germain RN (1994) MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation. Cell 76(2):287–299

Goeijenbier M, van Kampen JJ, Reusken CB (2014) Ebola virus disease: a review on epidemiology, symptoms, treatment and pathogenesis. Neth J Med 72(9):442–448

Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

Hasan MA, Hossain M, Alam MJ (2013) A computational assay to design an epitope-based Peptide vaccine against Saint Louis encephalitis virus. Bioinform Biol Insights 7:347–355

Hasan MA, Khan MA, Datta A et al (2015) A comprehensive immunoinformatics and target site study revealedthe corner-stone toward Chikungunya virus treatment. Mol Immunol 65:189–204

Hewlett BL, Hewlett BS (2005) Providing care and facing death: nursing during Ebola outbreaks in central Africa. J Transcult Nurs 16(4):289–297

Hoenen T, Groseth A, Feldmann H (2012) Current Ebola vaccines. Expert Opin Biol Ther 12(7):859–872

Holland J, Domingo E (1998) Origin and evolution of viruses. Virus Genes 16(1):13–21

Hoof I, Peters B, Sidney J et al (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61:1–13

Igietseme JU, Eko FO, He Q, Black CM (2004) Antibody regulation of T-cell immunity: implications for vaccine strategies against intracellular pathogens. Expert Rev Vaccines 3(1):23–34

Keiser J, Utzinger J, Tanner M, Singer BH (2004) Representation of authors and editors from countries with different human development indexes in the leading literature on tropical medicine: survey of current evidence. BMJ 328(7450):1229–1232

Khan MK, Zaman S, Chakraborty S et al (2014) In silico predicted mycobacterial epitope elicits in vitro T-cell responses. Mol Immunol 61(1):16–22

Klein RS, Lin E, Zhang B et al (2005) Neuronal CXCL10 directs CD8+ T-cell recruitment and control of West Nile virus encephalitis. J Virol 79(17):11457–11466

Kolaskar AS, Tongaonkar PC (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276(1–2):172–174

Kuhn JH, Becker S, Ebihara H et al (2010) Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch Virol 155(12):2083–2103

Larsen MV, Lundegaard C, Lamberth K et al (2007) Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 8(1):424

Laskowski RA, Rullmann JAC, MacArthur MW et al (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4):477–486

Leroy EM, Rouquet P, Formenty P et al (2004) Multiple Ebola virus transmission events and rapid decline of central African wildlife. Science 303(5656):387–390

Li YH, Chen SP (2014) Evolutionary history of Ebola virus. Epidemiol Infect 142(06):1138–1145

Liao L, Noble WS (2003) Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol 10(6):857–868

López JA, Weilenman C, Audran R et al (2001) A synthetic malaria vaccine elicits a potent CD8+ and CD4+ T lymphocyte immune response in humans. Implications for vaccination strategies. Eur J Immunol 31(7):1989–1998

McKeever TM, Lewis SA, Smith C et al (2004) Vaccination and allergic disease: a birth cohort study. Am J Public Health 94(6):985

Muh HC, Tong JC, Tammi MT (2009) AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins. PLoS One 4(6):5861

Mühlberger E, Lotfering B, Klenk H-D et al (1998) Three of the four nucleocapsid proteins of Marburg virus, NP, VP35, and L, are sufficient to mediate replication and transcription of Marburg virus-specific monocistronic minigenomes. J Virol 72:8756–8764

Mühlberger E, Weik M, Volchkov V et al (1999) Comparison of the transcription and replication strategies of Marburg virus and Ebola virus by using artificial replication systems. J Virol 73:2333–2342

Nair DT, Singh K, Siddiqui Z et al (2002) Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. J Immunol 168(5):2371–2382

Nielsen M, Lundegaard C, Blicher T et al (2007) NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One 2:796

Oany AR, Emran AA, Jyoti TP (2008) Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach. Drug Des Devel Ther 8:1139–1149

Oany AR, Ahmad SAI, Hossain MU, Jyoti TP (2015) Identification of highly conserved regions in L-segment of Crimean–Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine. Adv Appl Bioinformatics Chem 8:1–10

Parker JM, Guo D, Hodges RS (1986) New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25:5425–5432

Peters CJ, Peters JW (1999) An introduction to Ebola: the virus and the disease. J Infect Dis 179(1):ix–xvi

Peters B, Sette A (2005) Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6(1):132

Petrovsky N, Brusic V (2002) Computational immunology: the coming of age. Immunol Cell Biol 80(3):248–254

Poch O, Blumberg BM, Bougueleret L et al (1990) Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains. J Gen Virol 71:1153–1162

Poland GA, Ovsyannikova IG, Jacobson RM (2009) Application of pharmacogenomics to vaccines. Pharmacogenomics 10(5):837–852

Rini JM, Schulze-Gahmen U, Wilson IA (1992) Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 255(5047):959–965

Robinson HL, Amara RR (2005) T cell vaccines for microbial infections. Nat Med 11:25–32

Rouquet P, Froment JM, Bermejo M (2005) Wild animal mortality monitoring and human Ebola outbreaks, Gabon and Republic of Congo, 2001–2003. Emerg Infect Dis 11(2):283–290

Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815

Šali A, Potterton L, Yuan F et al (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23(3):318–326

Sette A, Fikes J (2003) Epitope-based vaccines: an update on epitope identification, vaccine design and delivery. Curr Opin Immunol 15(4):461–470

Sette A, Newman M, Livingston B et al (2002) Optimizing vaccine design for cellular processing, MHC binding and TCR recognition. Tissue Antigens 59(6):443–451

Shrestha B, Diamond MS (2004) Role of CD8+ T cells in control of West Nile virus infection. J Virol 78(15):8312–8321

Sullivan NJ, Sanchez A, Rollin PE, Yang ZY, Nabel GJ (2000) Development of a preventive vaccine for Ebola virus infection in primates. Nature 408:605–609

Takada A, Robison C, Goto H et al (1997) A system for functional analysis of Ebola virus glycoprotein. Proc Natl Acad Sci 94(26):14764–14769

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680

Trainor NB, Crill WD, Roberson JA et al (2007) Mutation analysis of the fusion domain region of St. Louis encephalitis virus envelope protein. Virology 360(2):398–406

Twiddy SS, Holmes EC, Rambaut A (2003) Inferring the rate and time-scale of dengue virus evolution. Mol Biol Evol 20(1):122–129

Volchkov VE et al (1999) Characterization of the L gene and 5′trailer region of Ebola virus. J Gen Virol 80(2):355–362

Wang P, Sidney J, Dow C et al (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 4(4):e1000048

Wang P, Sidney J, Kim Y et al (2010) Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics 11(1):568

Ward JJ, McGuffin LJ, Bryson K et al (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20(13):2138–2139

Waterhouse AM, Procter JB, Martin DM et al (2009) Jalview version 2 – a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191

Wilson CC, McKinney D, Anders M et al (2003) Development of a DNA vaccine designed to induce cytotoxic T lymphocyte responses to multiple conserved epitopes in HIV-1. J Immunol 171(10):5611–5623