IEDB Publications

About the IEDB Program
1

All publications published by the IEDB team are listed by year of publication in the posts below. References are further divided into whether they are about the IEDB in general (publications under “General”) or about the IEDB Analysis Resource (publications under “Tools”).

4

You can find all publications by the IEDB team published in 2023 listed below.

General

Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans (2023)

T Cell Responses to SARS-CoV-2 (2023)

IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community (2023)

A meta-analysis of epitopes in prostate-specific antigens identifies opportunities and knowledge gaps (2023)

Correlative CD4 and CD8 T-cell immunodominance in humans and mice: Implications for preclinical testing (2023)

The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses (2023)

Pre-existing SARS-2-specific T cells are predicted to cross-recognize BA.2.86 (2023)

Tools

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins (2023)

Estimating tissue-specific peptide abundance from public RNA-Seq data (2023)

IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database (2023)

Epitope-Specific T Cell Receptor Data and Tools in the Immune Epitope Database (2023)

Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome (2023)

Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning (2023)

5

You can find all publications by the IEDB team published in 2022 listed below.

General

Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1 (2022)

Lack of evidence of significant homology of SARS-CoV-2 spike sequences to myocarditis-associated antigens (2022)

The Cancer Epitope Database and Analysis Resource (CEDAR) (2022)

Tools

Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome (2022)

Minimal Information about MHC Multimers (MIAMM) (2022)

Combined assessment of MHC binding and antigen abundance improves T cell epitope predictions (2022)

Towards the prediction of non-peptidic epitopes (2022)

A comprehensive analysis of the IEDB MHC class-I automated benchmark (2022)

Predicting the Success of Fmoc-Based Peptide Synthesis (2022)

The role of antigen expression in shaping the repertoire of HLA presented ligands (2022)

6

You can find all publications by the IEDB team published in 2021 listed below.

General

An immunologically friendly classification of non-peptidic ligands (2021)

Standardization of assay representation in the Ontology for Biomedical Investigations (2021)

Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases (2021)

SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19 (2021)

Functional HPV-specific PD-1 + stem-like CD8 T cells in head and neck cancer (2021)

Tools

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors (2021)

Allele-Specific Thresholds of Eluted Ligands for T-Cell Epitope Prediction (2021)

PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage Front Immunol (2021)

NetMHCphosPan - Pan-specific prediction of MHC class I antigen presentation of phosphorylated ligands (2021)

NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data (2021)

7

You can find all publications by the IEDB published in 2020 listed below.

General

HLA Class I Binding of Mutant EGFR Peptides in NSCLC Is Associated With Improved Survival (2020)

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2 (2020)

A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts (2020)

Epitope prediction and identification- adaptive T cell responses in humans (2020)

Tools

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system (2020)

T Cell Epitope Predictions (2020)

NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data (2020)

Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data (2020)

Comparison of HLA ligand elution data and binding predictions reveals varying prediction performance for the multiple motifs recognized by HLA-DQ2.5 (2020)

A structured model for immune exposures (2020)

Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells (2020)

Immunoinformatics: Predicting Peptide–MHC Binding (2020)

Immunopeptidomic Data Integration to Artificial Neural Networks Enhances Protein-Drug Immunogenicity Prediction (2020)

8

You can find all publications by the IEDB published in 2019 listed below.

General

The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases (2019)

Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes (2019)

A survey of known immune epitopes in the enteroviruses associated with acute flaccid myelitis (2019)

Tools

Major Histocompatibility Complex Binding, Eluted Ligands, and Immunogenicity: Benchmark Testing and Predictions (2019)

Benchmark datasets of immune receptor-epitope structural complexes (2019)

Immune Epitope Database - Analysis Resource (IEDB-AR) in 2019 (2019)

9

You can find all publications by the IEDB published in 2018 listed below.

General

Investigation of outbreak-specific nonsynonymous mutations on Ebolavirus GP in the context of known immune reactivity (2018)

FAIR principles and the IEDB: Short-term improvements and a Long-term vision of OBO-Foundry mediated machine-actionable interoperability (2018)

Identification of Errors in the IEDB Using Ontologies (2018)

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database (2018)

The Immune Epitope Database (IEDB): 2018 update (2018)

A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis (2018)

Tools

Bioinformatics Tools for the Prediction of T-Cell Epitopes (2018)

Development of a novel clustering tool for linear peptide sequences (2018)

Predicting HLA CD4 immunogenicity in human populations (2018)

Footprints of antigen processing boost MHC class II natural ligand binding predictions (2018)

Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes (2018)

ImmunomeBrowser: A tool to aggregate and visualize complex and heterogeneous epitopes in reference protein (2018)

Improved methods for predicting peptide binding affinity to MHC class II molecules (2018)

Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands (2018)

Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes (2018)

10

You can find all publications by the IEDB published in 2017 listed below.

General

Better living through ontologies at the Immune Epitope Database (2017)

Unconventional peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: Breaking Confinement (2017)

Citrullination only infrequently impacts peptide binding to HLA class II MHC (2017)

The Immune Epitope Database: How Data Are Entered and Retrieved (2017)

Deciphering the MHC-associated peptidome: a review of naturally processed ligand data (2017)

The SysteMHC Atlas project (2017)

Tools

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design (2017)

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions (2017)

GibbsCluster: unsupervised clustering and alignment of peptide sequences (2017)

BepiPred-2.0: improving sequence-based B-cell epitope predictions using conformational epitopes (2017)

Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules (2017)

Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes (2017)

Development of a strategy and computational application to select candidate protein analouges with reduced HLA binding and immunogenicity (2017)

An introduction to Deep learning on biological sequence data - Examples and solutions (2017)

NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data (2017)

An automated benchmarking platform for MHC class II binding prediction methods (2017)

11

You can find all publications by the IEDB published in 2016 listed below.

General

The Ontology for Biomedical Investigations (2016)

Ebola: an analysis of immunity at the molecular level (2016)

Immune Epitope Database and Analysis Resource (2016)

An ontology for major histocompatibility restriction (2016)

Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species (2016)

Tools

Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity (2016)

T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome (2016)

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove (2016)

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets (2016)

TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates (2016)

The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference (2016)

12

You can find all publications by the IEDB published in 2015 listed below.

General

Consequences of periodic α-to-β(3) residue replacement for immunological recognition of peptide epitopes (2015)

Reproducibility and Conflicts in Immune Epitope Data (2015)

Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present (2015)

The Use of the Immune Epitope Database to Study Autoimmune Epitope Data Related to Alopecia Areata (2015)

Tools

Automated benchmarking of peptide-MHC class I binding predictions (2015)

Antibody specific epitope prediction - emergence of a new paradigm (2015)

Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes (2015)

A Population Response Analysis Approach To Assign Class II HLA-Epitope Restrictions (2015)

LYRA, a webserver for lymphocyte receptor structural modeling (2015)

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification (2015)

Automatic Generation of Validated Specific Epitope Sets (2015)

Gapped sequence alignment using artificial neural networks: application to the MHC class I system (2015)

13

You can find all publications by the IEDB published in 2014 listed below.

General

Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks (2014)

Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB) (2014)

Substantial gaps in knowledge of Bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy (2014)

The immune epitope database (IEDB) 3.0 (2014)

Tools

Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery (2014)

NetTepi: an integrated method for the prediction of T cell epitopes. Immunogenetics (2014)

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions (2014)

14

You can find all publications by the IEDB published in 2013 listed below.

General

Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation (2013)

Query enhancement through the practical application of ontology: the IEDB and OBI (2013)

A molecular view of multiple sclerosis and experimental autoimmune encephalitis: What can we learn from the epitope data? (2013)

Tools

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments (2013)

NetMHCstab - predicting stability of peptide:MHC-I complexes; impacts for CTL epitope discovery (2013)

Evaluation of peptide selection approaches for epitope-based vaccine design (2013)

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 (2013)

Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource (2013)

Properties of MHC class I presented peptides that enhance immunogenicity (2013)

HLA Class I Alleles Are Associated with Peptide-Binding Repertoires of Different Size, Affinity, and Immunogenicity (2013)

15

You can find all publications by the IEDB published in 2012 listed below.

General

A Meta-Analysis of the Existing Knowledge of Immunoreactivity against Hepatitis C Virus (HCV) (2012)

The Immune Epitope Database: A Historical Retrospective of the First Decade (2012)

A comparison of epitope repertoires associated with myasthenia gravis in humans and nonhuman hosts (2012)

Strategies to Query and Display Allergy-Derived Epitope Data from the Immune Epitope Database (2012)

Tools

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? (2012)

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions (2012)

Immune epitope database analysis resource (2012)

Structural analysis of B-cell epitopes in antibody:protein complexes (2012)

16

You can find all publications by the IEDB published in 2011 listed below.

General

Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation (2011)

Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data (2011)

A Model for Collaborative Curation, The IEDB and ChEBI Curation of Non-peptidic Epitopes (2011)

Tools

A computational pipeline to generate MHC binding motifs (2011)

Prediction of epitopes using neural network based methods (2011)

17

You can find all publications by the IEDB published in 2010 listed below.

General

Molecular determinants of T cell epitope recognition to the common Timothy grass allergen (2010)

Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population (2010)

Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity (2010)

Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens (2010)

Modeling biomedical experimental processes with OBI (2010)

IEDB-3D: structural data within the immune epitope database (2010)

Meta-analysis of all immune epitope data in the Flavivirus genus: inventory of current immune epitope data status in the context of virus immunity and immunopathology (2010)

Tools

NetCTLpan: pan-specific MHC class I pathway epitope predictions (2010)

The MHC motif viewer: a visualization tool for MHC binding motifs (2010)

Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource (2010)

MHC class II epitope predictive algorithms (2010)

Design and utilization of epitope-based databases and predictive tools (2010)

Peptide binding predictions for HLA DR, DP and DQ molecules (2010)

Limitations of Ab initio predictions of peptide binding to MHC class II molecules (2010)

18

You can find all publications by the IEDB published in 2009 listed below.

General

Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B08 and HLA-B2705, bind peptides with sequence similarity (2009)

Diverse recognition of conserved orthopoxvirus CD8+ T cell epitopes in vaccinated rhesus macaques (2009)

Definition of epitopes and antigens recognized by vaccinia specific immune responses: their conservation in variola virus sequences, and use as a model system to study complex pathogens (2009)

Classification of the universe of immune epitope literature: representation and knowledge gaps (2009)

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population (2009)

Meta-analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine-related issues (2009)

The Immune Epitope Database 2.0 (2009)

Tools

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods (2009)

NetMHCpan, a method for MHC class I binding prediction beyond humans (2009)

Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior (2009)

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: Application to MHC-peptide binding (2009)

19

You can find all publications by the IEDB published in 2008 listed below.

General

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries (2008)

HLA class I supertypes: a revised and updated classification (2008)

Immunodominant epitopes in herpes simplex virus type 2 glycoprotein D are recognized by CD4 lymphocytes from both HSV-1 and HSV-2 seropositive subjects (2008)

The Curation Guidelines of the Immune Epitope Database and Analysis Resource (2008)

Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum (2008)

Tools

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11 (2008)

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan (2008)

ElliPro: a new structure-based tool for the prediction of antibody epitopes (2008)

B-cell epitope prediction (2008)

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach (2008)

Immune epitope database analysis resource (IEDB-AR) (2008)

20

You can find all publications by the IEDB published in 2007 listed below.

General

Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide library (2007)

An analysis of the epitope knowledge related to Mycobacteria (2007)

Ab and T cell epitopes of influenza A virus, knowledge and opportunities (2007)

Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database (2007)

Immune epitope mapping in the post-genomic era: lessons for vaccine development (2007)

Automating document classification for the Immune Epitope Database (2007)

Tools

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB) (2007)

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines (2007)

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools (2007)

Modeling the adaptive immune system: predictions and simulations (2007)

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence (2007)

Integrating epitope data into the emerging web of biomedical knowledge resources (2007)

Antibody-protein interactions: benchmark datasets and prediction tools evaluation (2007)

21

You can find all publications by the IEDB published 2003-2006 listed below.

General

The biocurator: connecting and enhancing scientific data (2006)

The Immune Epitope Database and Analysis Resource (2006)

Curation of complex, context-dependent immunological data (2006)

Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity (2005)

The design and implementation of the immune epitope database and analysis resource (2005)

The Immune Epitope Database and Analysis Resource: From Vision to Blueprint (2005)

An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities (2005)

A Roadmap for the Immunomics of Category A–C Pathogens (2005)

The immune epitope database and analysis resource: from vision to blueprint (2004)

Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition (2004)

In silico prediction of peptides binding to multiple HLA-DR molecules accurately identifies immunodominant epitopes from gp43 of Paracoccidioides brasiliensis frequently recognized in primary peripheral blood mononuclear cell responses from sensitized individuals (2003)

Tools

Predicting population coverage of T-cell epitope-based diagnostics and vaccines (2006)

A community resource benchmarking predictions of peptide binding to MHC-I molecules (2006)

A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules (2005)

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method (2005)