Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

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

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

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

Characterization of the peptide binding specificity of the HLA class I alleles B*38:01 and B*39:06

(2016) John Sidney et al.   IMMUNOGENETICS

Preparation and functionalization of linear and reductively degradable highly branched cyanoacrylate-based polymers

(2016) Houliang Tang et al.   JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

The "cancer immunogram"

(2016) C. U. Blank et al.   SCIENCE

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

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

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

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

Automated benchmarking of peptide-MHC class I binding predictions

(2015) Thomas Trolle et al.   BIOINFORMATICS

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy

(2015) S. Walz et al.   BLOOD

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

The first step of peptide selection in antigen presentation by MHC class I molecules

(2015) Malgorzata A. Garstka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

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

(2014) Yohan Kim et al.   BMC BIOINFORMATICS

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

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

(2013) S. Paul et al.   JOURNAL OF IMMUNOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

Analysis Tool Web Services from the EMBL-EBI

(2013) Hamish McWilliam et al.   NUCLEIC ACIDS RESEARCH

In Silico and in Vitro Elucidation of BH3 Binding Specificity toward Bcl-2

(2012) Nir London et al.   BIOCHEMISTRY

A few useful things to know about machine learning

(2012) Pedro Domingos   COMMUNICATIONS OF THE ACM

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

Machine learning competition in immunology – Prediction of HLA class I binding peptides

(2011) Guang Lan Zhang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Dana-Farber repository for machine learning in immunology

(2011) Guang Lan Zhang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

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

Large-scale characterization of peptide-MHC binding landscapes with structural simulations

(2011) C. Yanover et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soluble plasma HLA peptidome as a potential source for cancer biomarkers

(2010) M. Bassani-Sternberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

(2009) Hao Zhang et al.   BIOINFORMATICS

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

(2009) Yohan Kim et al.   BMC BIOINFORMATICS

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

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

Prediction of MHC-Peptide Binding: A Systematic and Comprehensive Overview

(2009) Esther Lafuente et al.   CURRENT PHARMACEUTICAL DESIGN

Naturally Presented Peptides on Major Histocompatibility Complex I and II Molecules Eluted from Central Nervous System of Multiple Sclerosis Patients

(2009) Nicolas Fissolo et al.   MOLECULAR & CELLULAR PROTEOMICS

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH

Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers

(2008) G. M. Grotenbreg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA