NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

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

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis

(2018) Yi Tian Ting et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2018) Bruno Alvarez et al.   PROTEOMICS

NetH2pan: A Computational Tool to Guide MHC Peptide Prediction on Murine Tumors

(2018) Christa I. DeVette et al.   Cancer Immunology Research

HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy

(2018) Annika Nelde et al.   OncoImmunology

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

(2018) David Gfeller et al.   JOURNAL OF IMMUNOLOGY

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes

(2018) Daniel B. Graham et al.   NATURE MEDICINE

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Footprints of antigen processing boost MHC class II natural ligand predictions

(2018) Carolina Barra et al.   Genome Medicine

A Case for a Human Immuno-Peptidome Project Consortium

(2017) Etienne Caron et al.   IMMUNITY

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

Identification of immediate early gene products of bovine herpes virus 1 (BHV-1) as dominant antigens recognized by CD8 T cells in immune cattle

(2017) Jane Hart et al.   JOURNAL OF GENERAL VIROLOGY

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

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data

(2017) Morten Nielsen et al.   JOURNAL OF PROTEOME RESEARCH

MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies

(2017) J. Patrick Murphy et al.   JOURNAL OF PROTEOME RESEARCH

Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells

(2017) Joshua D. Ooi et al.   NATURE

NNAlign: a platform to construct and evaluate artificial neural network models of receptor–ligand interactions

(2017) Morten Nielsen et al.   NUCLEIC ACIDS RESEARCH

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

(2017) Michal Bassani-Sternberg et al.   PLoS Computational Biology

Citrullination only infrequently impacts peptide binding to HLA class II MHC

(2017) John Sidney et al.   PLoS One

Mass spectrometric analysis of the HLA class I peptidome of melanoma cell lines as a promising tool for the identification of putative tumor-associated HLA epitopes

(2016) Andreas Gloger et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

The IPD-IMGT/HLA Database – New developments in reporting HLA variation

(2016) James Robinson et al.   HUMAN IMMUNOLOGY

Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing

(2016) Deepali Vasoya et al.   IMMUNOGENETICS

The Dendritic Cell Major Histocompatibility Complex II (MHC II) Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity

(2016) Cristina C. Clement et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MHC class I–associated peptides derive from selective regions of the human genome

(2016) Hillary Pearson et al.   JOURNAL OF CLINICAL INVESTIGATION

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

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

(2016) Thomas Trolle et al.   JOURNAL OF IMMUNOLOGY

Identification of MHC-Bound Peptides from Dendritic Cells Infected with Salmonella enterica Strain SL1344: Implications for a Nontyphoidal Salmonella Vaccine

(2016) Karuna P. Karunakaran et al.   JOURNAL OF PROTEOME RESEARCH

Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis

(2016) Qi Wang et al.   JOURNAL OF PROTEOME RESEARCH

Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy

(2016) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples

(2016) Tina Heyder et al.   MOLECULAR & CELLULAR PROTEOMICS

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome ProceedsViaHigh Specificity

(2016) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients’ sera

(2016) Danilo Ritz et al.   PROTEOMICS

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

High-resolution analysis of the murine MHC class II immunopeptidome

(2015) Adriana Sofron et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

(2015) Etienne Caron et al.   MOLECULAR & CELLULAR PROTEOMICS

MHC Class II Auto-Antigen Presentation is Unconventional

(2015) Scheherazade Sadegh-Nasseri et al.   Frontiers in Immunology

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

(2014) Andreas M. Hansen et al.   IMMUNOGENETICS

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

(2014) Elin Bergseng et al.   IMMUNOGENETICS

Uncovering the Peptide-Binding Specificities of HLA-C: A General Strategy To Determine the Specificity of Any MHC Class I Molecule

(2014) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

(2014) G. P. M. Mommen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive analysis of constitutive naturally processed and presentedHLA-C*04:01(Cw4) - specific peptides

(2014) R. B. Schittenhelm et al.   TISSUE ANTIGENS

MHCcluster, a method for functional clustering of MHC molecules

(2013) Martin Thomsen et al.   IMMUNOGENETICS

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

(2012) Massimo Andreatta et al.   BIOINFORMATICS

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

Designing bovine T cell vaccines via reverse immunology

(2012) Vishvanath Nene et al.   Ticks and Tick-Borne Diseases

Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities

(2011) Lasse Eggers Pedersen et al.   IMMUNOGENETICS

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

(2011) Edita Karosiene et al.   IMMUNOGENETICS

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

(2011) Massimo Andreatta et al.   PLoS One

Real-time, high-throughput measurements of peptide–MHC-I dissociation using a scintillation proximity assay

(2010) Mikkel Harndahl et al.   JOURNAL OF IMMUNOLOGICAL METHODS

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS