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

The C-terminal extension landscape of naturally presented HLA-I ligands

(2018) Philippe Guillaume et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Bruno Alvarez et al.   PROTEOMICS

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

(2018) David Gfeller et al.   Frontiers in Immunology

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01

(2017) Soumya G. Remesh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices

(2017) Moreno Di Marco et al.   JOURNAL OF IMMUNOLOGY

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 peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands

(2017) Hugo G. Hilton et al.   Cell Reports

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

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

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

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

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

Purification of soluble HLA class I complexes from human serum or plasma deliver high quality immuno peptidomes required for biomarker discovery

(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

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

Crystal structure of HLA-B*5801, a protective HLA allele for HIV-1 infection

(2016) Xiaolong Li et al.   Protein & Cell

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

(2016) Curtis McMurtrey et al.   eLife

The Peptidome of Behçet's Disease-Associated HLA-B*51:01 Includes Two Subpeptidomes Differentially Shaped by Endoplasmic Reticulum Aminopeptidase 1

(2016) Pablo Guasp et al.   Arthritis & Rheumatology

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

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

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

(2012) Massimo Andreatta et al.   BIOINFORMATICS

Uncovering new aspects of protein interactions through analysis of specificity landscapes in peptide recognition domains

(2012) David Gfeller   FEBS LETTERS

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

(2012) TaeHyung Kim et al.   NUCLEIC ACIDS RESEARCH

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

The multiple-specificity landscape of modular peptide recognition domains

(2011) D. Gfeller et al.   Molecular Systems Biology

Structural Basis for T Cell Alloreactivity among Three HLA-B14 and HLA-B27 Antigens

(2009) Pravin Kumar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human Leukocyte Antigen Class I-Restricted Activation of CD8+ T Cells Provides the Immunogenetic Basis of a Systemic Drug Hypersensitivity

(2008) Diana Chessman et al.   IMMUNITY