Published in PLoS Biol on March 01, 2005
The immune epitope database 2.0. Nucleic Acids Res (2009) 6.07
Modeling biomedical experimental processes with OBI. J Biomed Semantics (2010) 5.36
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A (2009) 4.47
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
Memory T cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. J Clin Invest (2008) 4.30
ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res (2007) 3.96
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol (2008) 3.71
HLA class I supertypes: a revised and updated classification. BMC Immunol (2008) 3.47
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res (2007) 3.28
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun (2007) 3.02
The yellow fever virus vaccine induces a broad and polyfunctional human memory CD8+ T cell response. J Immunol (2009) 2.68
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci U S A (2007) 2.67
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A (2008) 2.43
The biocurator: connecting and enhancing scientific data. PLoS Comput Biol (2006) 2.41
Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol (2008) 2.30
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res (2007) 2.25
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics (2008) 2.17
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res (2008) 2.07
Preexisting immunity to pandemic (H1N1) 2009. Emerg Infect Dis (2009) 1.85
Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Proc Natl Acad Sci U S A (2008) 1.77
Automating document classification for the Immune Epitope Database. BMC Bioinformatics (2007) 1.76
Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One (2007) 1.72
Research resources: curating the new eagle-i discovery system. Database (Oxford) (2012) 1.64
Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity. J Immunol (2009) 1.57
The curation guidelines of the immune epitope database and analysis resource. Cytometry A (2008) 1.56
Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J Biomed Biotechnol (2010) 1.55
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics (2007) 1.47
SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res (2009) 1.42
MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes (2009) 1.41
Curation of complex, context-dependent immunological data. BMC Bioinformatics (2006) 1.36
Immunoinformatics comes of age. PLoS Comput Biol (2006) 1.35
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. J Immunol (2013) 1.32
Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun (2009) 1.30
Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity. J Immunol (2010) 1.29
Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. J Immunol (2008) 1.28
HLA-DR1001 presents "altered-self" peptides derived from joint-associated proteins by accepting citrulline in three of its binding pockets. Arthritis Rheum (2010) 1.27
Recent advances in B-cell epitope prediction methods. Immunome Res (2010) 1.26
Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis (2008) 1.23
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology (2010) 1.21
Coping with loss of perfection in the MHC class I peptide repertoire. Curr Opin Immunol (2008) 1.21
Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection. PLoS Pathog (2007) 1.20
Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection. Infect Immun (2008) 1.19
Epitope discovery in West Nile virus infection: Identification and immune recognition of viral epitopes. Proc Natl Acad Sci U S A (2008) 1.18
Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. J Immunol Methods (2010) 1.18
AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res (2009) 1.18
Mathematical and computational approaches can complement experimental studies of host-pathogen interactions. Cell Microbiol (2009) 1.15
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res (2005) 1.15
Gliadin activates HLA class I-restricted CD8+ T cells in celiac disease intestinal mucosa and induces the enterocyte apoptosis. Gastroenterology (2008) 1.15
The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. J Immunol (2012) 1.13
Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum. Expert Rev Vaccines (2008) 1.13
Emerging vaccine informatics. J Biomed Biotechnol (2011) 1.12
Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics (2009) 1.12
Highly conserved cross-reactive CD4+ T-cell HA-epitopes of seasonal and the 2009 pandemic influenza viruses. Influenza Other Respir Viruses (2010) 1.11
Pathema: a clade-specific bioinformatics resource center for pathogen research. Nucleic Acids Res (2009) 1.11
OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res (2009) 1.10
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. BMC Med Genomics (2008) 1.10
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res (2007) 1.10
Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinformatics (2010) 1.08
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. J Immunol Methods (2010) 1.07
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol (2010) 1.07
Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol (2010) 1.07
HLA class I molecules consistently present internal influenza epitopes. Proc Natl Acad Sci U S A (2009) 1.07
Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. J Immunol (2010) 1.06
On evaluating MHC-II binding peptide prediction methods. PLoS One (2008) 1.04
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics (2011) 1.03
Viruses selectively mutate their CD8+ T-cell epitopes--a large-scale immunomic analysis. Bioinformatics (2009) 1.03
Use of hepadnavirus core proteins as vaccine platforms. Expert Rev Vaccines (2009) 1.01
Design and utilization of epitope-based databases and predictive tools. Immunogenetics (2010) 1.00
Genome-wide screening of human T-cell epitopes in influenza A virus reveals a broad spectrum of CD4(+) T-cell responses to internal proteins, hemagglutinins, and neuraminidases. Hum Immunol (2009) 1.00
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol (2006) 0.99
MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. BMC Bioinformatics (2010) 0.98
Early HLA-B*57-restricted CD8+ T lymphocyte responses predict HIV-1 disease progression. J Virol (2012) 0.98
The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. Immunogenetics (2008) 0.97
Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PLoS One (2010) 0.97
HLA-DM constrains epitope selection in the human CD4 T cell response to vaccinia virus by favoring the presentation of peptides with longer HLA-DM-mediated half-lives. J Immunol (2012) 0.97
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics (2008) 0.96
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
Mining for the antibody-antigen interacting associations that predict the B cell epitopes. BMC Struct Biol (2010) 0.95
Data management: it starts at the bench. Nat Immunol (2009) 0.95
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. BMC Bioinformatics (2010) 0.95
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome. BMC Bioinformatics (2010) 0.94
Dana-Farber repository for machine learning in immunology. J Immunol Methods (2011) 0.93
Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. Schizophr Bull (2013) 0.93
Concept and application of a computational vaccinology workflow. Immunome Res (2010) 0.93
HLA class I molecules reflect an altered host proteome after influenza virus infection. Hum Immunol (2010) 0.92
Vaccinia peptides eluted from HLA-DR1 isolated from virus-infected cells are recognized by CD4+ T cells from a vaccinated donor. J Proteome Res (2008) 0.92
A human CD4+ T cell epitope in the influenza hemagglutinin is cross-reactive to influenza A virus subtypes and to influenza B virus. J Virol (2012) 0.92
Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. Clin Dev Immunol (2013) 0.91
Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model. Virology (2008) 0.91
Cytotoxic T cell recognition of an HIV-1 reverse transcriptase variant peptide incorporating the K103N drug resistance mutation. AIDS Res Ther (2006) 0.91
Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90
PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC Genomics (2008) 0.90
Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA). Cell Stress Chaperones (2010) 0.90
Multiple, non-conserved, internal viral ligands naturally presented by HLA-B27 in human respiratory syncytial virus-infected cells. Mol Cell Proteomics (2010) 0.88
Protein sequence database for pathogenic arenaviruses. Immunome Res (2007) 0.88
Human major histocompatibility complex (MHC) class I molecules with disulfide traps secure disease-related antigenic peptides and exclude competitor peptides. J Biol Chem (2008) 0.87
Learning a peptide-protein binding affinity predictor with kernel ridge regression. BMC Bioinformatics (2013) 0.87
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. BMC Bioinformatics (2011) 0.85
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins (2003) 5.88
Fine dissection of a nine amino acid glycoprotein epitope, a major determinant recognized by lymphocytic choriomeningitis virus-specific class I-restricted H-2Db cytotoxic T lymphocytes. J Exp Med (1988) 4.75
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
Adjuvant-enhanced antibody responses in the absence of toll-like receptor signaling. Science (2006) 6.47
Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med (2004) 6.33
The immune epitope database 2.0. Nucleic Acids Res (2009) 6.07
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Cutting edge: the conversion of arginine to citrulline allows for a high-affinity peptide interaction with the rheumatoid arthritis-associated HLA-DRB1*0401 MHC class II molecule. J Immunol (2003) 4.64
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res (2008) 4.53
A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol (2006) 4.52
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A (2009) 4.47
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol (2004) 4.20
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One (2007) 3.99
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIV antibody responses. Immunity (2013) 3.72
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol (2008) 3.71
Spindle checkpoint protein dynamics at kinetochores in living cells. Curr Biol (2004) 3.67
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
Rational HIV immunogen design to target specific germline B cell receptors. Science (2013) 3.55
HLA class I supertypes: a revised and updated classification. BMC Immunol (2008) 3.47
Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines. J Exp Med (2004) 3.43
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics (2005) 2.99
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics (2005) 2.91
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med (2005) 2.75
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics (2008) 2.69
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci U S A (2007) 2.67
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics (2010) 2.53
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics (2009) 2.50
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol (2008) 2.48
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A (2008) 2.43
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
A roadmap for the immunomics of category A-C pathogens. Immunity (2005) 2.36
Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci U S A (2013) 2.32
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance. J Immunol (2008) 2.25
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother (2012) 2.23
Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides. J Virol (2004) 2.21
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity. Cancer Cell (2013) 2.18
Asthma disease management: regression to the mean or better? Am J Manag Care (2004) 2.15
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation. Proc Natl Acad Sci U S A (2005) 2.11
Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol (2007) 2.10
Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09