Published in Bioinformatics on July 15, 2006
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
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics (2008) 2.17
SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics (2006) 1.59
Human CD1 dimeric proteins as indispensable tools for research on CD1-binding lipids and CD1-restricted T cells. J Immunol Methods (2009) 1.07
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics (2011) 1.03
Accurate prediction of DnaK-peptide binding via homology modelling and experimental data. PLoS Comput Biol (2009) 1.01
Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods (2007) 0.98
Large-scale characterization of peptide-MHC binding landscapes with structural simulations. Proc Natl Acad Sci U S A (2011) 0.92
Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90
Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning. PLoS One (2015) 0.87
Quantum chemical analysis of MHC-peptide interactions for vaccine design. Mini Rev Med Chem (2010) 0.86
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. BMC Bioinformatics (2012) 0.81
Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides. Clin Dev Immunol (2013) 0.80
DINC: a new AutoDock-based protocol for docking large ligands. BMC Struct Biol (2013) 0.77
DockTope: a Web-based tool for automated pMHC-I modelling. Sci Rep (2015) 0.76
Current tools for predicting cancer-specific T cell immunity. Oncoimmunology (2016) 0.76
DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles. BMC Struct Biol (2017) 0.75
Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation. J Comput Aided Mol Des (2016) 0.75
Tools to define the melanoma-associated immunopeptidome. Immunology (2017) 0.75
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (2011) 3.05
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49
Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Computational epigenetics. Bioinformatics (2007) 1.92
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75
Learning multiple evolutionary pathways from cross-sectional data. J Comput Biol (2005) 1.74
Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68
Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics (2007) 1.65
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
Computational analysis of human protein interaction networks. Proteomics (2007) 1.53
Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (2005) 1.41
EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett (2004) 1.38
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
Permutation importance: a corrected feature importance measure. Bioinformatics (2010) 1.32
Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. J Virol (2006) 1.28
Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics (2005) 1.27
An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26
Survey on the PABC recognition motif PAM2. Biochem Biophys Res Commun (2004) 1.26
Structural and functional analysis of ataxin-2 and ataxin-3. Eur J Biochem (2004) 1.24
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23
Confirmation of human protein interaction data by human expression data. BMC Bioinformatics (2005) 1.23
Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways. Hum Mol Genet (2005) 1.21
Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta (2007) 1.21
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J Infect Dis (2005) 1.19
Microarrays: how many do you need? J Comput Biol (2003) 1.19
Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer (2012) 1.19
Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics (2005) 1.18
Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther (2007) 1.17
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics (2004) 1.16
Tenofovir resistance and resensitization. Antimicrob Agents Chemother (2003) 1.10
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics (2012) 1.08
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis (2009) 1.07
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One (2008) 1.07
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening. Chemistry (2007) 1.05
IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci (2007) 1.04
Classification with correlated features: unreliability of feature ranking and solutions. Bioinformatics (2011) 1.03
Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Bioinformatics (2008) 1.03
Methods for optimizing antiviral combination therapies. Bioinformatics (2003) 1.02
Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus. Genome Biol (2008) 1.00
Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng (2003) 1.00
Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hepatitis C virus genotype 1-infected patients. J Virol (2013) 1.00
Effects of alkali cations and halide anions on the DOPC lipid membrane. J Phys Chem A (2009) 0.99
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak (2011) 0.99
Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. Nucleic Acids Res (2006) 0.99
An integrative approach for predicting interactions of protein regions. Bioinformatics (2008) 0.98
Moment invariants as shape recognition technique for comparing protein binding sites. Bioinformatics (2007) 0.98
GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol (2007) 0.98
Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer. Mol Cancer (2007) 0.98
Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination. Retrovirology (2007) 0.98
Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods Mol Biol (2010) 0.98
Local protein structure prediction using discriminative models. BMC Bioinformatics (2006) 0.95
Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2. FEBS Lett (2003) 0.94
MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol (2009) 0.94
Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas. Int J Cancer (2007) 0.94
Predicting response to antiretroviral treatment by machine learning: the EuResist project. Intervirology (2012) 0.93
Structural and functional comparison of the non-structural protein 4B in flaviviridae. J Mol Graph Model (2007) 0.93
Alignment of non-covalent interactions at protein-protein interfaces. PLoS One (2008) 0.93
Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120. J Infect Dis (2010) 0.92
Dynamics of NRTI resistance mutations during therapy interruption. AIDS Res Hum Retroviruses (2009) 0.91
Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol (2013) 0.90
Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level. Clin Vaccine Immunol (2007) 0.90
Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90
Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics (2006) 0.89
Membrane-proximal tryptophans of synaptobrevin II stabilize priming of secretory vesicles. J Neurosci (2012) 0.89
Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C. Antivir Ther (2006) 0.89
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. Bioinformatics (2003) 0.89
Pyranose oxidase identified as a member of the GMC oxidoreductase family. Bioinformatics (2003) 0.89
Protein function from sequence and structure data. Appl Bioinformatics (2003) 0.89
Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART. J Clin Virol (2006) 0.88
Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment. Neoplasia (2005) 0.88
Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients. Med Microbiol Immunol (2010) 0.88
Integrating expression data with domain interaction networks. Bioinformatics (2008) 0.88