NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

T Cell Epitope Predictions

(2020) Bjoern Peters et al.   Annual Review of Immunology

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

(2020) Birkir Reynisson et al.   JOURNAL OF PROTEOME RESEARCH

Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data

(2019) Christian Garde et al.   IMMUNOGENETICS

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

(2019) Jennifer G. Abelin et al.   IMMUNITY

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

(2019) Bruno Alvarez et al.   MOLECULAR & CELLULAR PROTEOMICS

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets

(2019) Xiaoshan M. Shao et al.   Cancer Immunology Research

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

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

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

(2018) Bruno Alvarez et al.   PROTEOMICS

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

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

(2018) Sinu Paul et al.   Frontiers in Immunology

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

Footprints of antigen processing boost MHC class II natural ligand predictions

(2018) Carolina Barra et al.   Genome Medicine

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

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

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

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

Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics

(2016) Andrew F. Jarnuczak et al.   JOURNAL OF PROTEOME RESEARCH

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

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) Edita Karosiene et al.   IMMUNOGENETICS

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