Published in J Immunol on August 15, 2003
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
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
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci U S A (2007) 2.67
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics (2007) 2.05
HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24. PLoS One (2007) 1.77
MHC class II epitope predictive algorithms. Immunology (2010) 1.72
Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci (2004) 1.55
An analysis of the epitope knowledge related to Mycobacteria. Immunome Res (2007) 1.53
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
Immunoinformatics comes of age. PLoS Comput Biol (2006) 1.35
The specificity of trimming of MHC class I-presented peptides in the endoplasmic reticulum. J Immunol (2009) 1.30
EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics (2006) 1.26
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. BMC Bioinformatics (2009) 1.23
Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci (2005) 1.23
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology (2010) 1.21
Phase-dependent immune evasion of herpesviruses. J Virol (2007) 1.20
Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol (2013) 1.19
Tumor neoantigens: building a framework for personalized cancer immunotherapy. J Clin Invest (2015) 1.13
Emerging vaccine informatics. J Biomed Biotechnol (2011) 1.12
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
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. J Immunol Methods (2010) 1.07
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
Viruses selectively mutate their CD8+ T-cell epitopes--a large-scale immunomic analysis. Bioinformatics (2009) 1.03
A detailed analysis of the murine TAP transporter substrate specificity. PLoS One (2008) 1.00
Signal peptides and trans-membrane regions are broadly immunogenic and have high CD8+ T cell epitope densities: Implications for vaccine development. Mol Immunol (2011) 0.99
PRED(TAP): a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res (2006) 0.98
A panel of artificial APCs expressing prevalent HLA alleles permits generation of cytotoxic T cells specific for both dominant and subdominant viral epitopes for adoptive therapy. J Immunol (2009) 0.97
A peptide filtering relation quantifies MHC class I peptide optimization. PLoS Comput Biol (2011) 0.95
State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res (2010) 0.95
Single residue within the antigen translocation complex TAP controls the epitope repertoire by stabilizing a receptive conformation. Proc Natl Acad Sci U S A (2010) 0.92
Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California. J Infect Dis (2012) 0.90
Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins. J Virol (2011) 0.88
Discriminating self from nonself with short peptides from large proteomes. Immunogenetics (2004) 0.88
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
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
Proteome sampling by the HLA class I antigen processing pathway. PLoS Comput Biol (2012) 0.85
HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses. PLoS One (2010) 0.85
Intra- and inter-clade cross-reactivity by HIV-1 Gag specific T-cells reveals exclusive and commonly targeted regions: implications for current vaccine trials. PLoS One (2011) 0.84
Predicting alloreactivity in transplantation. J Immunol Res (2014) 0.84
Bacteria modulate the CD8+ T cell epitope repertoire of host cytosol-exposed proteins to manipulate the host immune response. PLoS Comput Biol (2011) 0.84
Human self-protein CD8+ T-cell epitopes are both positively and negatively selected. Eur J Immunol (2009) 0.83
Whole-genome immunoinformatic analysis of F. tularensis: predicted CTL epitopes clustered in hotspots are prone to elicit a T-cell response. PLoS One (2011) 0.83
PolyCTLDesigner: a computational tool for constructing polyepitope T-cell antigens. BMC Res Notes (2013) 0.83
Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. Drug Des Devel Ther (2014) 0.82
Dendritic cells restore CD8+ T cell reactivity to autologous HIV-1. J Virol (2014) 0.82
Targeting neoantigens to augment antitumour immunity. Nat Rev Cancer (2017) 0.81
A computational assay to design an epitope-based Peptide vaccine against saint louis encephalitis virus. Bioinform Biol Insights (2013) 0.81
Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs. Immunogenetics (2014) 0.80
Optimal viral immune surveillance evasion strategies. Theor Popul Biol (2011) 0.79
Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation. J Immunol (2010) 0.78
Reconstitution of CD8 T Cells Protective against Cytomegalovirus in a Mouse Model of Hematopoietic Cell Transplantation: Dynamics and Inessentiality of Epitope Immunodominance. Front Immunol (2016) 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
TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence. Immunome Res (2010) 0.77
Estimate of within population incremental selection through branch imbalance in lineage trees. Nucleic Acids Res (2015) 0.76
Identification and validation of T-cell epitopes in outer membrane protein (OMP) of Salmonella typhi. Bioinformation (2014) 0.76
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
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC Bioinformatics (2016) 0.75
Short communication: HIV-1 Nef protein carries multiple epitopes suitable for induction of cellular immunity for an HIV vaccine in Africa. AIDS Res Hum Retroviruses (2014) 0.75
Immunoinformatics Features Linked to Leishmania Vaccine Development: Data Integration of Experimental and In Silico Studies. Int J Mol Sci (2017) 0.75
Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. J Biol Chem (2017) 0.75
ImmunoNodes - graphical development of complex immunoinformatics workflows. BMC Bioinformatics (2017) 0.75
Prediction and in vitro verification of potential CTL epitopes conserved among PRRSV-2 strains. Immunogenetics (2017) 0.75
Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies. Immunogenetics (2014) 0.75
Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME. Arch Toxicol (2013) 3.00
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol (2010) 2.05
Finding one's way in proteomics: a protein species nomenclature. Chem Cent J (2009) 1.75
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst Biol (2007) 1.71
Characterizing the N-terminal processing motif of MHC class I ligands. J Immunol (2008) 1.68
Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities. Eur J Biochem (2002) 1.48
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels. Proc Natl Acad Sci U S A (2007) 1.32
MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics (2003) 1.31
Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome. Nat Struct Mol Biol (2009) 1.30
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Mol Syst Biol (2007) 1.28
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol (2010) 1.19
Structural biology of mammalian lipoxygenases: enzymatic consequences of targeted alterations of the protein structure. Biochem Biophys Res Commun (2005) 1.19
FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics (2011) 1.16
The virtual liver: state of the art and future perspectives. Arch Toxicol (2014) 1.05
Quantifying the contribution of the liver to glucose homeostasis: a detailed kinetic model of human hepatic glucose metabolism. PLoS Comput Biol (2012) 0.96
Detection of low-frequency human antigen-specific CD4(+) T cells using MHC class II multimer bead sorting and immunoscope analysis. Eur J Immunol (2004) 0.95
Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics. J Mol Biol (2008) 0.94
CySBML: a Cytoscape plugin for SBML. Bioinformatics (2012) 0.91
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems (2003) 0.91
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. BMC Syst Biol (2007) 0.91
Oxygen consumption rates during three different neuronal activity states in the hippocampal CA3 network. J Cereb Blood Flow Metab (2012) 0.90
CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. BMC Syst Biol (2012) 0.90
Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks. Genome Inform (2010) 0.90
Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation. J Mol Biol (2002) 0.89
Enzymatic features of the glucose metabolism in tumor cells. FEBS J (2011) 0.88
Computational lipidology: predicting lipoprotein density profiles in human blood plasma. PLoS Comput Biol (2008) 0.88
Evaluation of 41 candidate gene variants for obesity in the EPIC-Potsdam cohort by multi-locus stepwise regression. PLoS One (2013) 0.87
IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. Biophys J (2010) 0.87
Dual role of oxygen during lipoxygenase reactions. FEBS J (2005) 0.86
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. BMC Syst Biol (2012) 0.86
Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced α-Ketoglutarate Dehydrogenase Activities on ATP Production and Generation of Reactive Oxygen Species. Int J Cell Biol (2012) 0.85
A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles. PLoS One (2009) 0.85
Computational design of reduced metabolic networks. Chembiochem (2004) 0.85
Hepatitis B virus HBx peptide 116-138 and proteasome activator PA28 compete for binding to the proteasome alpha4/MC6 subunit. Biol Chem (2003) 0.84
In vitro phototoxicity testing: development and validation of a new concentration response analysis software and biostatistical analyses related to the use of various prediction models. Altern Lab Anim (2002) 0.84
Pruning genome-scale metabolic models to consistent ad functionem networks. Genome Inform (2007) 0.83
Stimulation of plasminogen activation by recombinant cellular prion protein is conserved in the NH2-terminal fragment PrP23-110. Thromb Haemost (2003) 0.83
Both lysine-clusters of the NH2-terminal prion-protein fragment PrP23-110 are essential for t-PA mediated plasminogen activation. Thromb Haemost (2004) 0.82
Quantifying the contribution of defective ribosomal products to antigen production: a model-based computational analysis. J Immunol (2005) 0.82
Kinetic modeling of human hepatic glucose metabolism in type 2 diabetes mellitus predicts higher risk of hypoglycemic events in rigorous insulin therapy. J Biol Chem (2012) 0.81
Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis. BMC Med Genet (2012) 0.80
Metannogen: annotation of biological reaction networks. Bioinformatics (2011) 0.80
Composition of metabolic flux distributions by functionally interpretable minimal flux modes (MinModes). Genome Inform (2006) 0.80
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes. Biosystems (2011) 0.79
A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling. J Theor Biol (2007) 0.79
The influence of the chloride currents on action potential firing and volume regulation of excitable cells studied by a kinetic model. J Theor Biol (2011) 0.78
Metabolic gradients as key regulators in zonation of tumor energy metabolism: a tissue-scale model-based study. Biotechnol J (2013) 0.78
Uncovering metabolic objectives pursued by changes of enzyme levels. Ann N Y Acad Sci (2009) 0.78
Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast. Genome Inform (2007) 0.77
A hypothetical model of cargo-selective rab recruitment during organelle maturation. Cell Biochem Biophys (2012) 0.76
Assessment of hepatic detoxification activity: proposal of an improved variant of the (13)c-methacetin breath test. PLoS One (2013) 0.76
The high energy demand of neuronal cells caused by passive leak currents is not a waste of energy. Cell Biochem Biophys (2013) 0.76
Computer aided optimization of carbon atom labeling for tracer experiments. Genome Inform (2008) 0.75
Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks. Genome Inform (2005) 0.75
Rapid degradation of solid-phase bound peptides by the 20S proteasome. J Pept Sci (2013) 0.75