Published in BMC Bioinformatics on February 17, 2010
Prediction of epitopes using neural network based methods. J Immunol Methods (2010) 1.35
Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages. J Virol (2015) 0.88
Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping. Immunol Cell Biol (2015) 0.83
Prediction and identification of mouse cytotoxic T lymphocyte epitopes in Ebola virus glycoproteins. Virol J (2012) 0.83
PeptX: using genetic algorithms to optimize peptides for MHC binding. BMC Bioinformatics (2011) 0.83
The identification of HLA class II-restricted T cell epitopes to vaccinia virus membrane proteins. Virology (2010) 0.81
HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics (2016) 0.79
Influence of high hydrostatic pressure on epitope mapping of tobacco mosaic virus coat protein. Viral Immunol (2014) 0.76
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC Bioinformatics (2016) 0.75
Genome-wide structural modelling of TCR-pMHC interactions. BMC Genomics (2013) 0.75
Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains. 3 Biotech (2016) 0.75
A novel tuberculosis antigen identified from human tuberculosis granulomas. Mol Cell Proteomics (2015) 0.75
Measuring the accuracy of diagnostic systems. Science (1988) 27.46
Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta (1975) 17.03
SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics (1999) 14.15
A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003) 9.25
HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. Science (1992) 8.68
The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol (2005) 7.40
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
HLA class I supertypes: a revised and updated classification. BMC Immunol (2008) 3.47
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens (2003) 2.93
Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics (2002) 2.66
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res (2005) 2.40
Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol (2008) 2.30
MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res (2005) 2.05
MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res (1998) 2.02
JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics (2002) 1.75
Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics (2007) 1.74
Identifiying human MHC supertypes using bioinformatic methods. J Immunol (2004) 1.72
Methods for prediction of peptide binding to MHC molecules: a comparative study. Mol Med (2002) 1.61
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics (2008) 1.53
Learning MHC I--peptide binding. Bioinformatics (2006) 1.41
MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes (2009) 1.41
Methods and protocols for prediction of immunogenic epitopes. Brief Bioinform (2006) 1.19
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 1.18
Definition of MHC supertypes through clustering of MHC peptide-binding repertoires. Methods Mol Biol (2007) 1.09
Competition-based cellular peptide binding assays for 13 prevalent HLA class I alleles using fluorescein-labeled synthetic peptides. Hum Immunol (2003) 1.07
FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res (2002) 1.06
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
Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One (2011) 1.88
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
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 1.18
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
Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. Nucleic Acids Res (2006) 0.99
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak (2011) 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
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
GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol (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
Conformational selection in substrate recognition by Hsp70 chaperones. J Mol Biol (2012) 0.96
Local protein structure prediction using discriminative models. BMC Bioinformatics (2006) 0.95
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
Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2. FEBS Lett (2003) 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
Protein function from sequence and structure data. Appl Bioinformatics (2003) 0.89
Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics (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
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
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