Published in Int Immunol on July 01, 2003
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
Prediction of epitopes using neural network based methods. J Immunol Methods (2010) 1.35
Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci (2005) 1.23
Mapping the landscape of host-pathogen coevolution: HLA class I binding and its relationship with evolutionary conservation in human and viral proteins. J Virol (2010) 1.17
Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Res (2005) 1.11
A critical cross-validation of high throughput structural binding prediction methods for pMHC. J Comput Aided Mol Des (2009) 1.03
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
Discriminating self from nonself with short peptides from large proteomes. Immunogenetics (2004) 0.88
Amyloid-β peptide is a substrate of the human 20S proteasome. ACS Chem Neurosci (2010) 0.86
Human self-protein CD8+ T-cell epitopes are both positively and negatively selected. Eur J Immunol (2009) 0.83
PeptX: using genetic algorithms to optimize peptides for MHC binding. BMC Bioinformatics (2011) 0.83
Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs. Immunogenetics (2014) 0.80
Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Med (2015) 0.79
Mechanisms of HIV protein degradation into epitopes: implications for vaccine design. Viruses (2014) 0.79
Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity (2017) 0.77
Computational prediction of cleavage using proteasomal in vitro digestion and MHC I ligand data. J Zhejiang Univ Sci B (2013) 0.76
The VHSE-based prediction of proteasomal cleavage sites. PLoS One (2013) 0.76
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC Bioinformatics (2016) 0.75
Immunoinformatics Approach in Designing Epitope-based Vaccine Against Meningitis-inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae Type b). Drug Target Insights (2016) 0.75
The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated. Eur J Immunol (2015) 0.75
Proteasomal cleavage site prediction of protein antigen using BP neural network based on a new set of amino acid descriptor. J Mol Model (2013) 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
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
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
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
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
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
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 proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
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
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
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
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Hum Reprod (2010) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
Human gut microbes impact host serum metabolome and insulin sensitivity. Nature (2016) 1.85
Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance. Nat Immunol (2009) 1.83
Prediction of proteasome cleavage motifs by neural networks. Protein Eng (2002) 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
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
CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine (2006) 1.66
Continuum secondary structure captures protein flexibility. Structure (2002) 1.63
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res (2004) 1.57
Protein interaction-based genome-wide analysis of incident coronary heart disease. Circ Cardiovasc Genet (2011) 1.54
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. Immunogenetics (2013) 1.49
New weakly expressed cell cycle-regulated genes in yeast. Yeast (2005) 1.49
MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation. Eur J Immunol (2010) 1.49
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet (2013) 1.43
A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing. J Biol Chem (2011) 1.40
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol (2010) 1.35
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte. Cancer Res (2009) 1.35
HLA-B*57 Micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure, and HIV immune control. J Virol (2011) 1.31
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J Biomol Screen (2009) 1.27
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol (2007) 1.27
Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B 2705-restricted CD8+ T cells. J Virol (2010) 1.26
Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur J Immunol (2012) 1.24
HLA-A*0201-restricted CD8+ cytotoxic T lymphocyte epitopes identified from herpes simplex virus glycoprotein D. J Immunol (2008) 1.24
Heterozygote advantage fails to explain the high degree of polymorphism of the MHC. Immunogenetics (2004) 1.22
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology (2010) 1.21
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res (2009) 1.20
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PLoS One (2011) 1.20
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Brief Bioinform (2009) 1.19
Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol (2013) 1.19
Analysis and prediction of mammalian protein glycation. Glycobiology (2006) 1.18
HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. J Immunol (2011) 1.18
Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. J Immunol Methods (2010) 1.18
ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Res (2012) 1.17
ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philos Trans A Math Phys Eng Sci (2010) 1.16
Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: a novel strategy exploiting disulfide assisted protein folding. Protein Sci (2003) 1.16
Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A (2013) 1.15
The SH2 domain interaction landscape. Cell Rep (2013) 1.13
Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor. Immunol Lett (2004) 1.12
HLArestrictor--a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. Immunogenetics (2010) 1.11
Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. Proc Natl Acad Sci U S A (2012) 1.08
Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes. Genet Epidemiol (2011) 1.08
Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population. Drug Saf (2014) 1.08
Bias of purine stretches in sequenced chromosomes. Comput Chem (2002) 1.05
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. J Am Med Inform Assoc (2013) 1.04