NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions
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Title
NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions
Authors
Keywords
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Journal
MOLECULAR & CELLULAR PROTEOMICS
Volume 18, Issue 12, Pages 2459-2477
Publisher
American Society for Biochemistry & Molecular Biology (ASBMB)
Online
2019-10-03
DOI
10.1074/mcp.tir119.001658
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Note: Only part of the references are listed.- 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
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- (2012) Massimo Andreatta et al. BIOINFORMATICS
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- 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
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- 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
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