Published in BMC Bioinformatics on September 14, 2009
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics (2012) 1.49
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Structural analysis of B-cell epitopes in antibody:protein complexes. Mol Immunol (2012) 1.28
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EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics (2010) 1.21
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SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction. BMC Genomics (2010) 1.12
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Structure of allergens and structure based epitope predictions. Methods (2013) 0.86
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B-cell epitope prediction through a graph model. BMC Bioinformatics (2012) 0.81
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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
Positive-unlabeled learning for the prediction of conformational B-cell epitopes. BMC Bioinformatics (2015) 0.80
Prediction and characterization of novel epitopes of serotype A foot-and-mouth disease viruses circulating in East Africa using site-directed mutagenesis. J Gen Virol (2015) 0.79
Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. Biomed Res Int (2015) 0.78
Mapping the epitopes of a neutralizing antibody fragment directed against the lethal factor of Bacillus anthracis and cross-reacting with the homologous edema factor. PLoS One (2013) 0.78
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The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol (2017) 0.77
EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. BMC Bioinformatics (2014) 0.77
Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull. PLoS One (2015) 0.76
A meta-learning approach for B-cell conformational epitope prediction. BMC Bioinformatics (2014) 0.76
Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences. BMC Genomics (2017) 0.75
Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int (2012) 0.75
PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types. PLoS One (2016) 0.75
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. BMC Bioinformatics (2017) 0.75
An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res (2016) 0.75
Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction. J Biol Chem (2016) 0.75
DRREP: deep ridge regressed epitope predictor. BMC Genomics (2017) 0.75
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Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. Mol Cell (2006) 4.11
The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A (2009) 4.11
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50
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A structural EM algorithm for phylogenetic inference. J Comput Biol (2002) 2.67
An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res (2007) 2.21
Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog (2009) 1.94
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86
Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol (2009) 1.80
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FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res (2012) 1.52
A combined empirical and mechanistic codon model. Mol Biol Evol (2006) 1.52
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Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc Natl Acad Sci U S A (2013) 1.51
The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol (2010) 1.44
Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep (2012) 1.41
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Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins (2007) 1.31
A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (2005) 1.30
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29
The "alternative" choice of constitutive exons throughout evolution. PLoS Genet (2007) 1.27
DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci U S A (2013) 1.25
Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23
In silico identification of functional regions in proteins. Bioinformatics (2005) 1.18
The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release. J Virol (2004) 1.18
Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16
A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16
Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol (2011) 1.15
Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res (2011) 1.10
Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics (2007) 1.10
GLOOME: gain loss mapping engine. Bioinformatics (2010) 1.08
Deep Panning: steps towards probing the IgOme. PLoS One (2012) 1.08
SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution. Hum Mol Genet (2010) 1.07
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol (2008) 1.05
The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers. New Phytol (2014) 1.04
Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. J Struct Biol (2011) 1.02
The DFNA15 deafness mutation affects POU4F3 protein stability, localization, and transcriptional activity. Mol Cell Biol (2003) 0.99
Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells. PLoS One (2010) 0.98
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study. Genome Biol Evol (2011) 0.98
Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection. Mol Biol Evol (2011) 0.97
Evolution of the metazoan protein phosphatase 2C superfamily. J Mol Evol (2006) 0.93
State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol Biol (2013) 0.92
An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst Biol (2010) 0.91
Uncovering the co-evolutionary network among prokaryotic genes. Bioinformatics (2012) 0.90
Native homing endonucleases can target conserved genes in humans and in animal models. Nucleic Acids Res (2011) 0.90
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Synonymous site conservation in the HIV-1 genome. BMC Evol Biol (2013) 0.82
A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Eukaryot Cell (2011) 0.82
CoPAP: Coevolution of presence-absence patterns. Nucleic Acids Res (2013) 0.80
Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms. BMC Evol Biol (2006) 0.80
The operonic location of auto-transcriptional repressors is highly conserved in bacteria. Mol Biol Evol (2011) 0.79
Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes. Biochem Mol Biol Educ (2012) 0.79
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans. Biol Direct (2008) 0.78
An evolutionary space-time model with varying among-site dependencies. Mol Biol Evol (2005) 0.78
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics (2007) 0.76