Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

(2018) Marvin H. Gee et al.   CELL

In vivo genome editing of the albumin locus as a platform for protein replacement therapy

(2015) R. Sharma et al.   BLOOD

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

New approaches for predicting T cell–mediated drug reactions: A role for inducible and potentially preventable autoimmunity

(2015) Aaron W. Michels et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex

(2015) Dennis X Beringer et al.   NATURE IMMUNOLOGY

Destructin-1 is a collagen-degrading endopeptidase secreted byPseudogymnoascus destructans, the causative agent of white-nose syndrome

(2015) Anthony J. O’Donoghue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution mapping of epitopes on the C2 domain of factor VIII by analysis of point mutants using surface plasmon resonance

(2014) P.-C. T. Nguyen et al.   BLOOD

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

(2014) Yohan Kim et al.   BMC BIOINFORMATICS

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

(2014) Asaf Madi et al.   GENOME RESEARCH

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells

(2014) Evan W Newell et al.   NATURE BIOTECHNOLOGY

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Divergent paths for the selection of immunodominant epitopes from distinct antigenic sources

(2014) AeRyon Kim et al.   Nature Communications

Optimized atomic statistical potentials: assessment of protein interfaces and loops

(2013) Guang Qiang Dong et al.   BIOINFORMATICS

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

B-Cell Depletion and Immunomodulation before Initiation of Enzyme Replacement Therapy Blocks the Immune Response to Acid Alpha-Glucosidase in Infantile-Onset Pompe Disease

(2013) Melissa E. Elder et al.   JOURNAL OF PEDIATRICS

Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

(2013) Evan W Newell et al.   NATURE BIOTECHNOLOGY

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

CD4+ T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions

(2013) Eric Shifrut et al.   Frontiers in Immunology

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Global identification of peptidase specificity by multiplex substrate profiling

(2012) Anthony J O'Donoghue et al.   NATURE METHODS

Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection

(2011) Yiyuan Yin et al.   EMBO JOURNAL

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

(2011) R. L. Warren et al.   GENOME RESEARCH

Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B

(2011) Julian P. Vivian et al.   NATURE

Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One

(2011) Javed Mohammed Khan et al.   PLoS One

Prediction of protease substrates using sequence and structure features

(2010) David T. Barkan et al.   BIOINFORMATICS

MHC Class II epitope predictive algorithms

(2010) Morten Nielsen et al.   IMMUNOLOGY

A reductionist cell-free major histocompatibility complex class II antigen processing system identifies immunodominant epitopes

(2010) Isamu Z Hartman et al.   NATURE MEDICINE

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

(2010) Hao Zhang et al.   PLoS One

BIOINFORMATIC APPROACHES FOR PREDICTING SUBSTRATES OF PROTEASES

(2010) JIANGNING SONG et al.   Journal of Bioinformatics and Computational Biology

Viruses selectively mutate their CD8+ T-cell epitopes--a large-scale immunomic analysis

(2009) T. Vider-Shalit et al.   BIOINFORMATICS

Lineages of human T-cell clones, including T helper 17/T helper 1 cells, isolated at different stages of anti-factor VIII immune responses

(2009) R. A. Ettinger et al.   BLOOD

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types

(2008) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach

(2008) Peng Wang et al.   PLoS Computational Biology