Published in Eur J Immunol on August 01, 2005
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res (2007) 3.28
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics (2008) 2.17
HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One (2009) 2.16
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS One (2008) 2.06
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics (2007) 2.05
MHC class II epitope predictive algorithms. Immunology (2010) 1.72
Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One (2007) 1.72
NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics (2010) 1.37
Prediction of epitopes using neural network based methods. J Immunol Methods (2010) 1.35
A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol (2007) 1.30
HLA class I binding of HBZ determines outcome in HTLV-1 infection. PLoS Pathog (2010) 1.28
EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics (2006) 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
T-cell epitope vaccine design by immunoinformatics. Open Biol (2013) 1.20
HLA class I binding promiscuity of the CD8 T-cell epitopes of human papillomavirus type 16 E6 protein. J Virol (2006) 1.15
Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. PLoS One (2008) 1.11
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. BMC Med Genomics (2008) 1.10
An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort. J Virol (2007) 1.10
In silico analysis of six known Leishmania major antigens and in vitro evaluation of specific epitopes eliciting HLA-A2 restricted CD8 T cell response. PLoS Negl Trop Dis (2011) 1.05
High throughput T epitope mapping and vaccine development. J Biomed Biotechnol (2010) 1.04
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics (2011) 1.03
MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties. Immunogenetics (2006) 1.02
T-cell epitope prediction: rescaling can mask biological variation between MHC molecules. PLoS Comput Biol (2009) 0.99
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol (2006) 0.99
PRED(TAP): a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res (2006) 0.98
MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination. Arch Virol (2008) 0.98
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics (2008) 0.96
State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res (2010) 0.95
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome. BMC Bioinformatics (2010) 0.94
Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength. PLoS One (2011) 0.94
Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity. J Virol (2012) 0.93
Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. Immunogenetics (2011) 0.91
Specific recognition and inhibition of Ewing tumour growth by antigen-specific allo-restricted cytotoxic T cells. Br J Cancer (2011) 0.91
Epitope discovery with phylogenetic hidden Markov models. Mol Biol Evol (2010) 0.89
A modular concept of HLA for comprehensive peptide binding prediction. Immunogenetics (2006) 0.89
Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL. PLoS One (2010) 0.89
Genetic diversity of the Plasmodium vivax merozoite surface protein-5 locus from diverse geographic origins. Gene (2010) 0.89
Limited global diversity of the Plasmodium vivax merozoite surface protein 4 gene. Infect Genet Evol (2009) 0.88
High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4+ T cell responses more than 30 years post-vaccinia virus vaccination. Clin Exp Immunol (2009) 0.87
An assessment on epitope prediction methods for protozoa genomes. BMC Bioinformatics (2012) 0.87
Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning. PLoS One (2015) 0.87
First characterization of Plasmodium vivax liver stage antigen (PvLSA) using synthetic peptides. Parasit Vectors (2014) 0.86
Cross-protective peptide vaccine against influenza A viruses developed in HLA-A*2402 human immunity model. PLoS One (2011) 0.86
The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes. BMC Evol Biol (2009) 0.86
Conservation and variability of West Nile virus proteins. PLoS One (2009) 0.85
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP. PLoS One (2008) 0.85
HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses. PLoS One (2010) 0.85
Prediction of epitope-based peptides for the utility of vaccine development from fusion and glycoprotein of nipah virus using in silico approach. Adv Bioinformatics (2014) 0.84
Strategies for the identification of T cell-recognized tumor antigens in hematological malignancies for improved graft-versus-tumor responses after allogeneic blood and marrow transplantation. Biol Blood Marrow Transplant (2014) 0.84
PolyCTLDesigner: a computational tool for constructing polyepitope T-cell antigens. BMC Res Notes (2013) 0.83
Identification of MHC class II restricted T-cell-mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides. Immunology (2011) 0.82
Modelling the human immune system by combining bioinformatics and systems biology approaches. J Biol Phys (2006) 0.80
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development. BMC Bioinformatics (2013) 0.78
The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol (2017) 0.77
NetTepi: an integrated method for the prediction of T cell epitopes. Immunogenetics (2014) 0.77
Structure and Function of HLA-A*02-Restricted Hantaan Virus Cytotoxic T-Cell Epitope That Mediates Effective Protective Responses in HLA-A2.1/K(b) Transgenic Mice. Front Immunol (2016) 0.77
Computational analysis of cysteine proteases (Clan CA, Family Cl) of Leishmania major to find potential epitopic regions. Genomics Proteomics Bioinformatics (2009) 0.76
Current tools for predicting cancer-specific T cell immunity. Oncoimmunology (2016) 0.76
Spatial variation in genetic diversity and natural selection on the thrombospondin-related adhesive protein locus of Plasmodium vivax (PvTRAP). PLoS One (2014) 0.76
Therapeutics Insight with Inclusive Immunopharmacology Explication of Human Rotavirus A for the Treatment of Diarrhea. Front Pharmacol (2016) 0.76
Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int (2012) 0.75
Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes. Immunology (2012) 0.75
Computational Identification and Characterization of a Promiscuous T-Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide-Based Subunit Vaccine Design. Biomed Res Int (2017) 0.75
Computer aided prediction and identification of potential epitopes in the receptor binding domain (RBD) of spike (S) glycoprotein of MERS-CoV. Bioinformation (2014) 0.75
High-throughput identification and dendritic cell-based functional validation of MHC class I-restricted Mycobacterium tuberculosis epitopes. Sci Rep (2014) 0.75
Evaluation of the Schistosoma mansoni Y-box-binding protein (SMYB1) potential as a vaccine candidate against schistosomiasis. Front Genet (2014) 0.75
In Silico Design and Analysis of TGFαL3-SEB Fusion Protein as "a New Antitumor Agent" Candidate by Ligand-Targeted Superantigens Technique. Iran J Cancer Prev (2014) 0.75
Genome-wide identification of novel vaccine candidates for Plasmodium falciparum malaria using integrative bioinformatics approaches. 3 Biotech (2017) 0.75
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol (2005) 7.40
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
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
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
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
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
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
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol (2009) 3.56
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
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
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics (2010) 2.53
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
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
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 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
Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics (2004) 2.39
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput (2002) 2.29
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics (2008) 2.24
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother (2012) 2.23
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res (2003) 2.21
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS Comput Biol (2011) 2.14
Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope. Nat Immunol (2006) 2.11
Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics (2007) 2.05