Hopp TP: Retrospective: 12 years of antigenic determinant predictions, and more. Peptide Research. 1993, 6: 183-190.
CAS
PubMed
Google Scholar
Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B: Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proceedings of the National Academy of Sciences of the United States of America. 2009, 106: 20365-20370. 10.1073/pnas.0911580106.
PubMed Central
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S: NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PloS One. 2007, 2: e796-10.1371/journal.pone.0000796.
PubMed Central
PubMed
Google Scholar
Flower DR: Bioinformatics for Vaccinology. 2008, Wiley, 1
Google Scholar
Van Regenmortel MHV: The rational design of biological complexity: a deceptive metaphor. Proteomics. 2007, 7: 965-975. 10.1002/pmic.200600407.
CAS
PubMed
Google Scholar
Yang X, Yu X: An introduction to epitope prediction methods and software. Reviews in Medical Virology. 2009, 19: 77-96. 10.1002/rmv.602.
CAS
PubMed
Google Scholar
Gershburg E, Pagano JS: Epstein-Barr virus infections: prospects for treatment. The Journal of Antimicrobial Chemotherapy. 2005, 56: 277-281. 10.1093/jac/dki240.
CAS
PubMed
Google Scholar
Cohen JI, Bollard CM, Khanna R, Pittaluga S: Current understanding of the role of Epstein-Barr virus in lymphomagenesis and therapeutic approaches to EBV-associated lymphomas. Leukemia & Lymphoma. 2008, 49 (Suppl 1): 27-34. 10.1080/10428190802311417.
CAS
Google Scholar
Lahiri A, Das P, Chakravortty D: Engagement of TLR signaling as adjuvant: towards smarter vaccine and beyond. Vaccine. 2008, 26: 6777-6783. 10.1016/j.vaccine.2008.09.045.
CAS
PubMed
Google Scholar
De Gregorio E, D'Oro U, Wack A: Immunology of TLR-independent vaccine adjuvants. Current Opinion in Immunology. 2009, 21: 339-345. 10.1016/j.coi.2009.05.003.
CAS
PubMed
Google Scholar
Mutwiri G, Gerdts V, Lopez M, Babiuk LA: Innate immunity and new adjuvants. Revue Scientifique Et Technique (International Office of Epizootics). 2007, 26: 147-156.
CAS
Google Scholar
Nickle DC, Rolland M, Jensen MA, Pond SLK, Deng W, Seligman M, Heckerman D, Mullins JI, Jojic N: Coping with viral diversity in HIV vaccine design. PLoS Computational Biology. 2007, 3: e75-10.1371/journal.pcbi.0030075.
PubMed Central
PubMed
Google Scholar
Azizi A, Diaz-Mitoma F: Viral peptide immunogens: current challenges and opportunities. Journal of Peptide Science: An Official Publication of the European Peptide Society. 2007, 13: 776-786.
CAS
Google Scholar
Bijker MS, Melief CJM, Offringa R, van der Burg SH: Design and development of synthetic peptide vaccines: past, present and future. Expert Review of Vaccines. 2007, 6: 591-603. 10.1586/14760584.6.4.591.
CAS
PubMed
Google Scholar
Purcell AW, McCluskey J, Rossjohn J: More than one reason to rethink the use of peptides in vaccine design. Nature Reviews. Drug Discovery. 2007, 6: 404-414. 10.1038/nrd2224.
CAS
PubMed
Google Scholar
Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: a tool for building and running workflows of services. Nucleic Acids Research. 2006, 34: W729-732. 10.1093/nar/gkl320.
PubMed Central
CAS
PubMed
Google Scholar
Niller HH, Wolf H, Minarovits J: Regulation and dysregulation of Epstein-Barr virus latency: implications for the development of autoimmune diseases. Autoimmunity. 2008, 41: 298-328. 10.1080/08916930802024772.
CAS
PubMed
Google Scholar
Pohl D: Epstein-Barr virus and multiple sclerosis. Journal of the Neurological Sciences. 2009, 286: 62-64. 10.1016/j.jns.2009.03.028.
CAS
PubMed
Google Scholar
De Roure D, Goble C: Software Design for Empowering Scientists. IEEE Software. 2009, 26: 88-95. 10.1109/MS.2009.22.
Google Scholar
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ: Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England). 2009, 25: 1189-1191. 10.1093/bioinformatics/btp033.
CAS
Google Scholar
The MD5 Message-Digest Algorithm. [http://tools.ietf.org/html/rfc1321]
Fieldhouse RJ, Merrill AR: Needle in the haystack: structure-based toxin discovery. Trends in Biochemical Sciences. 2008, 33: 546-556. 10.1016/j.tibs.2008.08.003.
CAS
PubMed
Google Scholar
Sachdeva G, Kumar K, Jain P, Ramachandran S: SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks. Bioinformatics (Oxford, England). 2005, 21: 483-491. 10.1093/bioinformatics/bti028.
CAS
Google Scholar
Ansari HR, Flower DR, Raghava GPS: AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Research. 2009
Google Scholar
Doytchinova IA, Flower DR: VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007, 8: 4-10.1186/1471-2105-8-4.
PubMed Central
PubMed
Google Scholar
Reitmaier R, Reitmaier R: Review of Immunoinformatic approaches to in-silico B-cell epitope prediction. Nature Precedings. 2007
Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.
PubMed Central
CAS
PubMed
Google Scholar
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (Oxford, England). 2007, 23: 1282-1288. 10.1093/bioinformatics/btm098.
CAS
Google Scholar
Buzan T: The Mind Map Book. 2006, BBC Active, 1
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003, 13: 2498-2504. 10.1101/gr.1239303.
PubMed Central
CAS
PubMed
Google Scholar
Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong Y, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J: Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathogens. 2009, 5: e1000570-10.1371/journal.ppat.1000570.
PubMed Central
PubMed
Google Scholar
Calderwood MA, Venkatesan K, Xing L, Chase MR, Vazquez A, Holthaus AM, Ewence AE, Li N, Hirozane-Kishikawa T, Hill DE, Vidal M, Kieff E, Johannsen E: Epstein-Barr virus and virus human protein interaction maps. Proceedings of the National Academy of Sciences of the United States of America. 2007, 104: 7606-7611. 10.1073/pnas.0702332104.
PubMed Central
CAS
PubMed
Google Scholar
Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, Sacco F, Tinti M, Smolyar A, Castagnoli L, Vidal M, Cusick ME, Cesareni G: VirusMINT: a viral protein interaction database. Nucleic Acids Research. 2009, 37: D669-673. 10.1093/nar/gkn739.
PubMed Central
CAS
PubMed
Google Scholar
Chen X, Liang S, Zheng W, Liao Z, Shang T, Ma W: Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation. BMC Genomics. 2008, 9: 322-10.1186/1471-2164-9-322.
PubMed Central
PubMed
Google Scholar
Bernthaler A, Mühlberger I, Fechete R, Perco P, Lukas A, Mayer B: A dependency graph approach for the analysis of differential gene expression profiles. Molecular BioSystems. 2009
Google Scholar
Brown KR, Jurisica I: Online predicted human interaction database. Bioinformatics (Oxford, England). 2005, 21: 2076-2082. 10.1093/bioinformatics/bti273.
CAS
Google Scholar
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H: The IntAct molecular interaction database in 2010. Nucleic Acids Research. 2010, 38: D525-531. 10.1093/nar/gkp878.
PubMed Central
CAS
PubMed
Google Scholar
Stark C, Breitkreutz B, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Research. 2006, 34: D535-539. 10.1093/nar/gkj109.
PubMed Central
CAS
PubMed
Google Scholar
Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L: Reactome: a knowledge base of biologic pathways and processes. Genome Biology. 2007, 8: R39-10.1186/gb-2007-8-3-r39.
PubMed Central
PubMed
Google Scholar
D'Addario M, Ahmad A, Morgan A, Menezes J: Binding of the Epstein-Barr virus major envelope glycoprotein gp350 results in the upregulation of the TNF-alpha gene expression in monocytic cells via NF-kappaB involving PKC, PI3-K and tyrosine kinases. Journal of Molecular Biology. 2000, 298: 765-778. 10.1006/jmbi.2000.3717.
PubMed
Google Scholar
Szakonyi G, Klein MG, Hannan JP, Young KA, Ma RZ, Asokan R, Holers VM, Chen XS: Structure of the Epstein-Barr virus major envelope glycoprotein. Nature Structural & Molecular Biology. 2006, 13: 996-1001. 10.1038/nsmb1161.
CAS
Google Scholar
Urquiza M, Lopez R, Patiño H, Rosas JE, Patarroyo ME: Identification of three gp350/220 regions involved in Epstein-Barr virus invasion of host cells. The Journal of Biological Chemistry. 2005, 280: 35598-35605. 10.1074/jbc.M504544200.
CAS
PubMed
Google Scholar
Backovic M, Longnecker R, Jardetzky TS: Structure of a trimeric variant of the Epstein-Barr virus glycoprotein B. Proceedings of the National Academy of Sciences of the United States of America. 2009, 106: 2880-2885. 10.1073/pnas.0810530106.
PubMed Central
CAS
PubMed
Google Scholar
Beisel C, Tanner J, Matsuo T, Thorley-Lawson D, Kezdy F, Kieff E: Two major outer envelope glycoproteins of Epstein-Barr virus are encoded by the same gene. Journal of Virology. 1985, 54: 665-674.
PubMed Central
CAS
PubMed
Google Scholar
Park SJ, Seo M, Lee SK, Lee BJ: Membrane binding properties of EBV gp110 C-terminal domain; evidences for structural transition in the membrane environment. Virology. 2008, 379: 181-190. 10.1016/j.virol.2008.06.031.
CAS
PubMed
Google Scholar
Henrick K, Thornton JM: PQS: a protein quaternary structure file server. Trends in Biochemical Sciences. 1998, 23: 358-361. 10.1016/S0968-0004(98)01253-5.
CAS
PubMed
Google Scholar
Sorem J, Longnecker R: Cleavage of Epstein-Barr virus glycoprotein B is required for full function in cell-cell fusion with both epithelial and B cells. The Journal of General Virology. 2009, 90: 591-595. 10.1099/vir.0.007237-0.
PubMed Central
CAS
PubMed
Google Scholar
Herold BC, Gerber SI, Belval BJ, Siston AM, Shulman N: Differences in the susceptibility of herpes simplex virus types 1 and 2 to modified heparin compounds suggest serotype differences in viral entry. Journal of Virology. 1996, 70: 3461-3469.
PubMed Central
CAS
PubMed
Google Scholar
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LL: UniProt: the Universal Protein knowledgebase. Nucleic Acids Research. 2004, 32: D115-119. 10.1093/nar/gkh131.
PubMed Central
CAS
PubMed
Google Scholar
Heger A, Holm L: Rapid automatic detection and alignment of repeats in protein sequences. Proteins. 2000, 41: 224-237. 10.1002/1097-0134(20001101)41:2<224::AID-PROT70>3.0.CO;2-Z.
CAS
PubMed
Google Scholar
Biegert A, Söding J: De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics (Oxford, England). 2008, 24: 807-814. 10.1093/bioinformatics/btn039.
CAS
Google Scholar
Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Séguin C: DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature. 1984, 310: 207-211. 10.1038/310207a0.
CAS
PubMed
Google Scholar
Chene A, Donati D, Orem J, Mbidde ER, Kironde F, Wahlgren M, Bejarano MT: Endemic Burkitt's lymphoma as a polymicrobial disease: new insights on the interaction between Plasmodium falciparum and Epstein-Barr virus. Seminars in Cancer Biology. 2009, 19: 411-420. 10.1016/j.semcancer.2009.10.002.
CAS
PubMed
Google Scholar
Tsurui H, Takahashi T: Prediction of T-cell epitope. Journal of Pharmacological Sciences. 2007, 105: 299-316. 10.1254/jphs.CR0070056.
CAS
PubMed
Google Scholar
Middleton D, Menchaca L, Rood H, Komerofsky R: New allele frequency database: http://www.allelefrequencies.net. Tissue Antigens. 2003, 61: 403-407. 10.1034/j.1399-0039.2003.00062.x.
CAS
PubMed
Google Scholar
Bui H, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A: Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics. 2006, 7: 153-10.1186/1471-2105-7-153.
PubMed Central
PubMed
Google Scholar
Sidney J, Peters B, Frahm N, Brander C, Sette A: HLA class I supertypes: a revised and updated classification. BMC Immunology. 2008, 9: 1-10.1186/1471-2172-9-1.
PubMed Central
PubMed
Google Scholar
Swanson-Mungerson M, Longnecker R: Epstein-Barr virus latent membrane protein 2A and autoimmunity. Trends in Immunology. 2007, 28: 213-218. 10.1016/j.it.2007.03.002.
CAS
PubMed
Google Scholar
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America. 1992, 89: 10915-10919. 10.1073/pnas.89.22.10915.
PubMed Central
CAS
PubMed
Google Scholar
Henikoff S, Henikoff JG: Performance evaluation of amino acid substitution matrices. Proteins. 1993, 17: 49-61. 10.1002/prot.340170108.
CAS
PubMed
Google Scholar
Herbeck JT, Wall DP, Wernegreen JJ: Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology. 2003, 149: 2585-2596. 10.1099/mic.0.26381-0.
CAS
PubMed
Google Scholar
Roymondal U, Das S, Sahoo S: Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes. 2009, 16: 13-30.
CAS
Google Scholar
Willenbrock H, Ussery D: Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Molecular Biology. 2007, 8: 11-10.1186/1471-2199-8-11.
PubMed Central
PubMed
Google Scholar
Oseroff C, Kos F, Bui H, Peters B, Pasquetto V, Glenn J, Palmore T, Sidney J, Tscharke DC, Bennink JR, Southwood S, Grey HM, Yewdell JW, Sette A: HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102: 13980-13985. 10.1073/pnas.0506768102.
PubMed Central
CAS
PubMed
Google Scholar
Pasquetto V, Bui H, Giannino R, Banh C, Mirza F, Sidney J, Oseroff C, Tscharke DC, Irvine K, Bennink JR, Peters B, Southwood S, Cerundolo V, Grey H, Yewdell JW, Sette A: HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products. Journal of Immunology (Baltimore, Md.: 1950). 2005, 175: 5504-5515.
CAS
Google Scholar
Bhadra R, Sandhya S, Abhinandan KR, Chakrabarti S, Sowdhamini R, Srinivasan N: Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Research. 2006, 34: W143-146. 10.1093/nar/gkl157.
PubMed Central
CAS
PubMed
Google Scholar
Melvin I, Weston J, Leslie C, Noble WS: RANKPROP: a web server for protein remote homology detection. Bioinformatics (Oxford, England). 2009, 25: 121-122. 10.1093/bioinformatics/btn567.
CAS
Google Scholar
Biegert A, Söding J: Sequence context-specific profiles for homology searching. Proceedings of the National Academy of Sciences of the United States of America. 2009, 106: 3770-3775. 10.1073/pnas.0810767106.
PubMed Central
CAS
PubMed
Google Scholar
Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, Kennedy K, Wu H, Bennouna S, Oluoch H, Miller J, Vencio RZ, Mulligan M, Aderem A, Ahmed R, Pulendran B: Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nature Immunology. 2009, 10: 116-125. 10.1038/ni.1688.
PubMed Central
CAS
PubMed
Google Scholar
Ressing ME, Horst D, Griffin BD, Tellam J, Zuo J, Khanna R, Rowe M, Wiertz EJHJ: Epstein-Barr virus evasion of CD8(+) and CD4(+) T cell immunity via concerted actions of multiple gene products. Seminars in Cancer Biology. 2008, 18: 397-408. 10.1016/j.semcancer.2008.10.008.
CAS
PubMed
Google Scholar
Caldwell RG, Wilson JB, Anderson SJ, Longnecker R: Epstein-Barr virus LMP2A drives B cell development and survival in the absence of normal B cell receptor signals. Immunity. 1998, 9: 405-411. 10.1016/S1074-7613(00)80623-8.
CAS
PubMed
Google Scholar
Miller CL, Burkhardt AL, Lee JH, Stealey B, Longnecker R, Bolen JB, Kieff E: Integral membrane protein 2 of Epstein-Barr virus regulates reactivation from latency through dominant negative effects on protein-tyrosine kinases. Immunity. 1995, 2: 155-166. 10.1016/S1074-7613(95)80040-9.
CAS
PubMed
Google Scholar
Graham JP, Moore CR, Bishop GA: Roles of the TRAF2/3 binding site in differential B cell signaling by CD40 and its viral oncogenic mimic, LMP1. Journal of Immunology (Baltimore, Md.: 1950). 2009, 183: 2966-2973.
CAS
Google Scholar
Lee DY, Sugden B: The latent membrane protein 1 oncogene modifies B-cell physiology by regulating autophagy. Oncogene. 2008, 27: 2833-2842. 10.1038/sj.onc.1210946.
CAS
PubMed
Google Scholar
Halary F, Amara A, Lortat-Jacob H, Messerle M, Delaunay T, Houlès C, Fieschi F, Arenzana-Seisdedos F, Moreau JF, Déchanet-Merville J: Human cytomegalovirus binding to DC-SIGN is required for dendritic cell infection and target cell trans-infection. Immunity. 2002, 17: 653-664. 10.1016/S1074-7613(02)00447-8.
CAS
PubMed
Google Scholar
Naniche D, Varior-Krishnan G, Cervoni F, Wild TF, Rossi B, Rabourdin-Combe C, Gerlier D: Human membrane cofactor protein (CD46) acts as a cellular receptor for measles virus. Journal of Virology. 1993, 67: 6025-6032.
PubMed Central
CAS
PubMed
Google Scholar
Santoro F, Kennedy PE, Locatelli G, Malnati MS, Berger EA, Lusso P: CD46 is a cellular receptor for human herpesvirus 6. Cell. 1999, 99: 817-827. 10.1016/S0092-8674(00)81678-5.
CAS
PubMed
Google Scholar
Kemper C, Chan AC, Green JM, Brett KA, Murphy KM, Atkinson JP: Activation of human CD4+ cells with CD3 and CD46 induces a T-regulatory cell 1 phenotype. Nature. 2003, 421: 388-392. 10.1038/nature01315.
CAS
PubMed
Google Scholar
He Y, Mou Z, Li W, Liu B, Fu T, Zhao S, Xiang D, Wu Y: Identification of IMPDH2 as a tumor-associated antigen in colorectal cancer using immunoproteomics analysis. International Journal of Colorectal Disease. 2009, 24: 1271-1279. 10.1007/s00384-009-0759-2.
PubMed
Google Scholar
Tobiume K, Saitoh M, Ichijo H: Activation of apoptosis signal-regulating kinase 1 by the stress-induced activating phosphorylation of pre-formed oligomer. Journal of Cellular Physiology. 2002, 191: 95-104. 10.1002/jcp.10080.
CAS
PubMed
Google Scholar
Chen Y, McPhie DL, Hirschberg J, Neve RL: The amyloid precursor protein-binding protein APP-BP1 drives the cell cycle through the S-M checkpoint and causes apoptosis in neurons. The Journal of Biological Chemistry. 2000, 275: 8929-8935. 10.1074/jbc.275.12.8929.
CAS
PubMed
Google Scholar
Subramanian RP, Geraghty RJ: Herpes simplex virus type 1 mediates fusion through a hemifusion intermediate by sequential activity of glycoproteins D, H, L, and B. Proceedings of the National Academy of Sciences of the United States of America. 2007, 104: 2903-2908. 10.1073/pnas.0608374104.
PubMed Central
CAS
PubMed
Google Scholar
Reimer JJ, Backovic M, Deshpande CG, Jardetzky T, Longnecker R: Analysis of Epstein-Barr virus glycoprotein B functional domains via linker insertion mutagenesis. Journal of Virology. 2009, 83: 734-747. 10.1128/JVI.01817-08.
PubMed Central
CAS
PubMed
Google Scholar
Backovic M, Leser GP, Lamb RA, Longnecker R, Jardetzky TS: Characterization of EBV gB indicates properties of both class I and class II viral fusion proteins. Virology. 2007, 368: 102-113. 10.1016/j.virol.2007.06.031.
PubMed Central
CAS
PubMed
Google Scholar
Neuhierl B, Feederle R, Hammerschmidt W, Delecluse HJ: Glycoprotein gp110 of Epstein-Barr virus determines viral tropism and efficiency of infection. Proceedings of the National Academy of Sciences of the United States of America. 2002, 99: 15036-15041. 10.1073/pnas.232381299.
PubMed Central
CAS
PubMed
Google Scholar
Loret S, Guay G, Lippé R: Comprehensive characterization of extracellular herpes simplex virus type 1 virions. Journal of Virology. 2008, 82: 8605-8618. 10.1128/JVI.00904-08.
PubMed Central
CAS
PubMed
Google Scholar
Padula ME, Sydnor ML, Wilson DW: Isolation and preliminary characterization of herpes simplex virus 1 primary enveloped virions from the perinuclear space. Journal of Virology. 2009, 83: 4757-4765. 10.1128/JVI.01927-08.
PubMed Central
CAS
PubMed
Google Scholar
Sollner J, Grohmann R, Rapberger R, Perco P, Lukas A, Mayer B: Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. Immunome Research. 2008, 4: 1-10.1186/1745-7580-4-1.
PubMed Central
PubMed
Google Scholar
Dosztányi Z, Mészáros B, Simon I: ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009, 25 (20): 2745-2746. 10.1093/bioinformatics/btp518.
PubMed Central
PubMed
Google Scholar
Panchenko AR, Kondrashov F, Bryant S: Prediction of functional sites by analysis of sequence and structure conservation. Protein Science: A Publication of the Protein Society. 2004, 13: 884-892.
CAS
Google Scholar
Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T: Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Research. 2009, 37: 5959-5968. 10.1093/nar/gkp634.
PubMed Central
CAS
PubMed
Google Scholar
Sankararaman S, Kolaczkowski B, Sjölander K: INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Research. 2009, 37: W390-395. 10.1093/nar/gkp339.
PubMed Central
CAS
PubMed
Google Scholar
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH: CDD: a Conserved Domain Database for protein classification. Nucleic Acids Research. 2005, 33: D192-196. 10.1093/nar/gki069.
PubMed Central
CAS
PubMed
Google Scholar
Rawlings ND, Barrett AJ, Bateman A: MEROPS: the peptidase database. Nucleic Acids Research. 2009
Google Scholar
Toussaint NC, Dönnes P, Kohlbacher O: A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Computational Biology. 2008, 4: e1000246-10.1371/journal.pcbi.1000246.
PubMed Central
PubMed
Google Scholar
Basha G, Lizée G, Reinicke AT, Seipp RP, Omilusik KD, Jefferies WA: MHC class I endosomal and lysosomal trafficking coincides with exogenous antigen loading in dendritic cells. PloS One. 2008, 3: e3247-10.1371/journal.pone.0003247.
PubMed Central
PubMed
Google Scholar
Kotturi MF, Assarsson E, Peters B, Grey H, Oseroff C, Pasquetto V, Sette A: Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?. Immunome Research. 2009, 5: 3-10.1186/1745-7580-5-3.
PubMed Central
PubMed
Google Scholar
Assarsson E, Sidney J, Oseroff C, Pasquetto V, Bui H, Frahm N, Brander C, Peters B, Grey H, Sette A: A quantitative analysis of the variables affecting the repertoire of T cell specificities recognized after vaccinia virus infection. Journal of Immunology (Baltimore, Md.: 1950). 2007, 178: 7890-7901.
CAS
Google Scholar
Overstreet MG, Freyberger H, Cockburn IA, Chen YC, Tse SW, Zavala F: CpG-enhanced CD8+ T cell responses to peptide immunization are severely inhibited by B cells. Eur J Immunol. 2010, 40: 124-133. 10.1002/eji.200939493.
PubMed Central
CAS
PubMed
Google Scholar
Ishizuka J, Grebe K, Shenderov E, Peters B, Chen Q, Peng Y, Wang L, Dong T, Pasquetto V, Oseroff C, Sidney J, Hickman H, Cerundolo V, Sette A, Bennink JR, McMichael A, Yewdell JW: Quantitating T cell cross-reactivity for unrelated peptide antigens. Journal of Immunology (Baltimore, Md.: 1950). 2009, 183: 4337-4345.
CAS
Google Scholar
Verma D, Swaminathan S: Epstein-Barr virus SM protein functions as an alternative splicing factor. Journal of Virology. 2008, 82: 7180-7188. 10.1128/JVI.00344-08.
PubMed Central
CAS
PubMed
Google Scholar
Seib KL, Dougan G, Rappuoli R: The key role of genomics in modern vaccine and drug design for emerging infectious diseases. PLoS Genetics. 2009, 5: e1000612-10.1371/journal.pgen.1000612.
PubMed Central
PubMed
Google Scholar
Peters B, Sidney J, Bourne P, Bui H, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A: The immune epitope database and analysis resource: from vision to blueprint. PLoS Biology. 2005, 3: e91-10.1371/journal.pbio.0030091.
PubMed Central
PubMed
Google Scholar
de Jesus O, Smith PR, Spender LC, Elgueta Karstegl C, Niller HH, Huang D, Farrell PJ: Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. The Journal of General Virology. 2003, 84: 1443-1450. 10.1099/vir.0.19054-0.
CAS
PubMed
Google Scholar
Dolan A, Addison C, Gatherer D, Davison AJ, McGeoch DJ: The genome of Epstein-Barr virus type 2 strain AG876. Virology. 2006, 350: 164-170. 10.1016/j.virol.2006.01.015.
CAS
PubMed
Google Scholar
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A: Comparative protein structure modeling using Modeller. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. 2006, Chapter 5:Unit 5.6
Google Scholar
Berman H, Henrick K, Nakamura H: Announcing the worldwide Protein Data Bank. Nature Structural Biology. 2003, 10: 980-10.1038/nsb1203-980.
CAS
PubMed
Google Scholar
Weichenberger CX, Sippl MJ: NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. Bioinformatics (Oxford, England). 2006, 22: 1397-1398. 10.1093/bioinformatics/btl128.
CAS
Google Scholar
DeLano W: The PyMOL User's Manual. DeLano Scientific. 2002, Palo Alto, CA, USA
Google Scholar
Mészáros B, Simon I, Dosztányi Z: Prediction of protein binding regions in disordered proteins. PLoS Computational Biology. 2009, 5: e1000376-10.1371/journal.pcbi.1000376.
PubMed Central
PubMed
Google Scholar
Sweredoski MJ, Baldi P: COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Engineering, Design & Selection: PEDS. 2009, 22: 113-120. 10.1093/protein/gzn075.
PubMed Central
CAS
Google Scholar
El-Manzalawy Y, Dobbs D, Honavar V: Predicting flexible length linear B-cell epitopes. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 2008, 7: 121-132.
PubMed Central
PubMed
Google Scholar
Haste Andersen P, Nielsen M, Lund O: Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Science: A Publication of the Protein Society. 2006, 15: 2558-2567.
Google Scholar
Ponomarenko J, Bui H, Li W, Fusseder N, Bourne PE, Sette A, Peters B: ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008, 9: 514-10.1186/1471-2105-9-514.
PubMed Central
PubMed
Google Scholar
Jones DT: Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics (Oxford, England). 2007, 23: 538-544. 10.1093/bioinformatics/btl677.
CAS
Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology. 2001, 305: 567-580. 10.1006/jmbi.2000.4315.
CAS
PubMed
Google Scholar
Sonnhammer EL, von Heijne G, Krogh A: A hidden Markov model for predicting transmembrane helices in protein sequences. Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 1998, 6: 175-182.
CAS
Google Scholar
Adamczak R, Porollo A, Meller J: Accurate prediction of solvent accessibility using neural networks-based regression. Proteins. 2004, 56: 753-767. 10.1002/prot.20176.
CAS
PubMed
Google Scholar
Adamczak R, Porollo A, Meller J: Combining prediction of secondary structure and solvent accessibility in proteins. Proteins. 2005, 59: 467-475. 10.1002/prot.20441.
PubMed
Google Scholar
Julenius K, Mølgaard A, Gupta R, Brunak S: Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology. 2005, 15: 153-164. 10.1093/glycob/cwh151.
CAS
PubMed
Google Scholar
Prediction of N-glycosylation sites in human proteins. [http://www.cbs.dtu.dk/services/NetNGlyc/]
Matthews BW: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica Et Biophysica Acta. 1975, 405: 442-451.
CAS
PubMed
Google Scholar
Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (Oxford, England). 2000, 16: 412-424. 10.1093/bioinformatics/16.5.412.
CAS
Google Scholar
Buus S, Lauemøller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S: Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens. 2003, 62: 378-384. 10.1034/j.1399-0039.2003.00112.x.
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O: Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Science: A Publication of the Protein Society. 2003, 12: 1007-1017.
CAS
Google Scholar
Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M: Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics. 2007, 8: 424-10.1186/1471-2105-8-424.
PubMed Central
PubMed
Google Scholar
Nielsen M, Lundegaard C, Lund O: Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 2007, 8: 238-10.1186/1471-2105-8-238.
PubMed Central
PubMed
Google Scholar
Nielsen M, Lundegaard C, Lund O, Keşmir C: The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 2005, 57: 33-41. 10.1007/s00251-005-0781-7.
CAS
PubMed
Google Scholar
Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M: NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics. 2009, 61: 1-13. 10.1007/s00251-008-0341-z.
PubMed Central
CAS
PubMed
Google Scholar
Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O: Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Computational Biology. 2008, 4: e1000107-10.1371/journal.pcbi.1000107.
PubMed Central
PubMed
Google Scholar
Senger M, Rice P, Bleasby A, Uludag M: Soaplab: open source web services framework for Bioinformatics programs. In The 10th Annual Bioinformatics Open Source Conference. Satellite Workshop of the Joint 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2009) and 7th European Conference on Computational Biology, ECC B. 2009, 168: 27-28.
Google Scholar
Holland RCG, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ: BioJava. Bioinformatics. 2008, 24: 2096-2097. 10.1093/bioinformatics/btn397.
PubMed Central
CAS
PubMed
Google Scholar
Drummond A, Strimmer K: PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics. 2001, 17: 662-663. 10.1093/bioinformatics/17.7.662.
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
PubMed Central
CAS
PubMed
Google Scholar
Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology. 1999, 292: 195-202. 10.1006/jmbi.1999.3091.
CAS
PubMed
Google Scholar