Published in Bioinformatics on February 12, 2004
Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol (2013) 5.23
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
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
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
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 MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
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
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
Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol (2008) 2.30
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
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. Nucleic Acids Res (2012) 1.81
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res (2010) 1.78
MHC class II epitope predictive algorithms. Immunology (2010) 1.72
Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol (2012) 1.44
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics (2006) 1.41
Protection against P. aeruginosa with an adenovirus vector containing an OprF epitope in the capsid. J Clin Invest (2005) 1.35
Prediction of epitopes using neural network based methods. J Immunol Methods (2010) 1.35
Immunoinformatics comes of age. PLoS Comput Biol (2006) 1.35
Plant-produced idiotype vaccines for the treatment of non-Hodgkin's lymphoma: safety and immunogenicity in a phase I clinical study. Proc Natl Acad Sci U S A (2008) 1.34
SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res (2006) 1.33
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics (2009) 1.30
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics (2006) 1.22
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology (2010) 1.21
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PLoS One (2011) 1.20
T-cell epitope vaccine design by immunoinformatics. Open Biol (2013) 1.20
Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol (2013) 1.19
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules. PLoS One (2012) 1.18
Prediction of MHC class II binding peptides based on an iterative learning model. Immunome Res (2005) 1.17
PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands. Nucleic Acids Res (2005) 1.14
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS Comput Biol (2010) 1.07
Safety and immunotoxicity assessment of immunomodulatory monoclonal antibodies. MAbs (2010) 1.06
Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools. Immunome Res (2007) 1.06
A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol (2008) 1.06
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinformatics (2007) 1.05
Modeling the bound conformation of Pemphigus vulgaris-associated peptides to MHC Class II DR and DQ alleles. Immunome Res (2006) 1.04
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
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
MHC motif viewer. Immunogenetics (2008) 0.99
MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. BMC Bioinformatics (2010) 0.98
Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One (2010) 0.98
State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res (2010) 0.95
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. BMC Bioinformatics (2010) 0.95
A probabilistic meta-predictor for the MHC class II binding peptides. Immunogenetics (2007) 0.95
Potential T cell epitopes of Mycobacterium tuberculosis that can instigate molecular mimicry against host: implications in autoimmune pathogenesis. BMC Immunol (2012) 0.93
Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities. Immunogenetics (2011) 0.91
Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput (2010) 0.91
An assessment on epitope prediction methods for protozoa genomes. BMC Bioinformatics (2012) 0.87
Prediction of MHC binding peptide using Gibbs motif sampler, weight matrix and artificial neural network. Bioinformation (2008) 0.87
Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning. PLoS One (2015) 0.87
An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches. Immunome Res (2010) 0.86
Mutated BCR-ABL generates immunogenic T-cell epitopes in CML patients. Clin Cancer Res (2012) 0.86
Cross-protective peptide vaccine against influenza A viruses developed in HLA-A*2402 human immunity model. PLoS One (2011) 0.86
Designing of interferon-gamma inducing MHC class-II binders. Biol Direct (2013) 0.86
Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes. PLoS One (2010) 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
pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res (2010) 0.83
In vitro and in vivo activities of antimicrobial peptides developed using an amino acid-based activity prediction method. Antimicrob Agents Chemother (2014) 0.81
PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinformatics (2013) 0.81
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. BMC Bioinformatics (2012) 0.81
Modelling the human immune system by combining bioinformatics and systems biology approaches. J Biol Phys (2006) 0.80
Predicting MHC-II binding affinity using multiple instance regression. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.80
Discovery of novel cross-protective Rickettsia prowazekii T-cell antigens using a combined reverse vaccinology and in vivo screening approach. Vaccine (2014) 0.77
The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density. PLoS One (2012) 0.77
GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes. PLoS One (2012) 0.77
The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep (2017) 0.77
T cell epitope mapping of the e-protein of West Nile virus in BALB/c mice. PLoS One (2014) 0.76
Improving peptide-MHC class I binding prediction for unbalanced datasets. BMC Bioinformatics (2008) 0.76
Predictor for the effect of amino acid composition on CD4+ T cell epitopes preprocessing. J Immunol Methods (2013) 0.76
HLA class I-restricted MYD88 L265P-derived peptides as specific targets for lymphoma immunotherapy. Oncoimmunology (2016) 0.75
Insights from the predicted epitope similarity between Mycobacterium tuberculosis virulent factors and its human homologs. Bioinformation (2015) 0.75
Immunoinformatics Features Linked to Leishmania Vaccine Development: Data Integration of Experimental and In Silico Studies. Int J Mol Sci (2017) 0.75
Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. Bioinformatics (2015) 0.75
Accurate prediction of major histocompatibility complex class II epitopes by sparse representation via ℓ 1-minimization. BioData Min (2014) 0.75
Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes. Front Immunol (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
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
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
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
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit (2007) 2.02
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Hum Reprod (2010) 1.97
PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS One (2013) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res (2010) 1.94