Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules

Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets

(2020) Michelle P. Aranha et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

(2020) Cangzhi Jia et al.   BIOINFORMATICS

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

(2020) Fuyi Li et al.   BRIEFINGS IN BIOINFORMATICS

Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly from deglycosylated precursors

(2020) Shutao Mei et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

(2020) Quanzhong Liu et al.   BRIEFINGS IN BIOINFORMATICS

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma

(2020) Pouya Faridi et al.   Cancer Immunology Research

Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome

(2019) Kevin Michael Boehm et al.   BMC BIOINFORMATICS

Performance evaluation of MHC class-I binding prediction tools based on an experimentally validated MHC-peptide binding dataset

(2019) Maria Bonsack et al.   Cancer Immunology Research

DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction

(2019) Zhonghao Liu et al.   Scientific Reports

Positive-unlabelled learning of glycosylation sites in the human proteome

(2019) Fuyi Li et al.   BMC BIOINFORMATICS

ACME: Pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks

(2019) Yan Hu et al.   BIOINFORMATICS

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

IEDB-AR: immune epitope database—analysis resource in 2019

(2019) Sandeep Kumar Dhanda et al.   NUCLEIC ACIDS RESEARCH

MHCSeqNet: a deep neural network model for universal MHC binding prediction

(2019) Poomarin Phloyphisut et al.   BMC BIOINFORMATICS

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

(2019) Jennifer G. Abelin et al.   IMMUNITY

Modification of the cyclopropyl moiety of abacavir provides insight into the structure activity relationship between HLA‐B*57:01 binding and T‐cell activation

(2019) Paul J. Thomson et al.   ALLERGY

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

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

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

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

(2018) Fuyi Li et al.   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Biased Dropout and Crossmap Dropout: Learning towards effective Dropout regularization in convolutional neural network

(2018) Alvin Poernomo et al.   NEURAL NETWORKS

A Tomato Nucleotide Binding Sites−Leucine-Rich Repeat Gene Is Positively Involved in Plant Resistance to Phytophthora infestans

(2018) Ning Jiang et al.   PHYTOPATHOLOGY

The Peptide Repertoire of HLA-B27 may include Ligands with Lysine at P2 Anchor Position

(2018) Shira Yair-Sabag et al.   PROTEOMICS

Immunopeptidomics Special Issue

(2018) Nicola Ternette et al.   PROTEOMICS

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

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

Employing proteomics in the study of antigen presentation: an update

(2018) Sri H. Ramarathinam et al.   Expert Review of Proteomics

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

(2018) David Gfeller 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

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

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

HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome

(2018) Patricia T. Illing et al.   Nature Communications

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

The molecular basis for peptide repertoire selection in the human leukocyte antigen (HLA) C*06:02 molecule

(2017) Jesse I. Mobbs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization

(2017) Qing Yu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural and regulatory diversity shape HLA-C protein expression levels

(2017) Gurman Kaur et al.   Nature Communications

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

‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization

(2017) Markus Müller et al.   Frontiers in Immunology

PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity

(2017) Geng Liu et al.   GigaScience

Identification of the core regulators of the HLA I-peptide binding process

(2017) Yu-Hang Zhang et al.   Scientific Reports

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection

(2016) Miguel Marcilla et al.   JOURNAL OF PROTEOME RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

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

(2016) Juliane Liepe et al.   SCIENCE

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

(2016) Shelly Kalaora et al.   Oncotarget

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

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

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

A comprehensive analysis of peptides presented by HLA-A1

(2015) K. Giam et al.   TISSUE ANTIGENS

Revisiting the Arthritogenic Peptide Theory: Quantitative Not Qualitative Changes in the Peptide Repertoire of HLA-B27 Allotypes

(2015) Ralf B. Schittenhelm et al.   Arthritis & Rheumatology

Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome

(2015) Ingrid M. M. Schellens et al.   PLoS One

Naturally Processed Non-canonical HLA-A*02:01 Presented Peptides

(2014) Chopie Hassan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue

(2013) Miguel Marcilla et al.   MOLECULAR & CELLULAR PROTEOMICS

Immune self-reactivity triggered by drug-modified HLA-peptide repertoire

(2012) Patricia T. Illing et al.   NATURE

Immune epitope database analysis resource

(2012) Y. Kim et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Identification by random forest method of HLA class I amino acid substitutions associated with lower survival at day 100 in unrelated donor hematopoietic cell transplantation

(2011) S R Marino et al.   BONE MARROW TRANSPLANTATION

Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools

(2011) L. Zhang et al.   BRIEFINGS IN BIOINFORMATICS

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

(2011) Edita Karosiene et al.   IMMUNOGENETICS

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

Major histocompatibility complex class I binding predictions as a tool in epitope discovery

(2010) Claus Lundegaard et al.   IMMUNOLOGY

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

Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype

(2008) Nina Hillen et al.   EUROPEAN JOURNAL OF IMMUNOLOGY