Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space

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

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

Exploring the pre-immune landscape of antigen-specific T cells

(2018) Mikhail V. Pogorelyy et al.   Genome Medicine

Footprints of antigen processing boost MHC class II natural ligand predictions

(2018) Carolina Barra et al.   Genome Medicine

Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope

(2017) Xinbo Yang 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

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes

(2017) Tyler Borrman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

(2017) Diego Chowell et al.   SCIENCE

Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8 + TCR Repertoires to Immunodominant Viral Antigens

(2017) Guobing Chen et al.   Cell Reports

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences

(2017) Asaf Madi et al.   eLife

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design

(2017) Ward Fleri et al.   Frontiers in Immunology

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

(2017) Anne-Mette Bjerregaard et al.   Frontiers in Immunology

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

(2016) Li C. Xue et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

HIV-1–Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection

(2016) Victor Y. Du et al.   JOURNAL OF IMMUNOLOGY

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

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Population tailored modification of tuberculosis specific interferon-gamma release assay

(2016) Kata Horvati et al.   JOURNAL OF INFECTION

msa: an R package for multiple sequence alignment

(2015) Ulrich Bodenhofer et al.   BIOINFORMATICS

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens

(2015) Mireia Coscolla et al.   Cell Host & Microbe

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Contacts-based prediction of binding affinity in protein–protein complexes

(2015) Anna Vangone et al.   eLife

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

An Extensive Antigenic Footprint Underpins Immunodominant TCR Adaptability against a Hypervariable Viral Determinant

(2014) Usha K. Nivarthi et al.   JOURNAL OF IMMUNOLOGY

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

(2014) O. V. Britanova et al.   JOURNAL OF IMMUNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

T-cell Receptor (TCR)-Peptide Specificity Overrides Affinity-enhancing TCR-Major Histocompatibility Complex Interactions

(2013) David K. Cole et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2013) Evan W Newell et al.   NATURE BIOTECHNOLOGY

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

T-cell receptor affinity and avidity defines antitumor response and autoimmunity in T-cell immunotherapy

(2013) S. Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the MHC-peptide matrix of central tolerance in the human thymus

(2013) Eleni Adamopoulou et al.   Nature Communications

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

Huge Overlap of Individual TCR Beta Repertoires

(2013) Mikhail Shugay et al.   Frontiers in Immunology

Bioinformatic and Empirical Analysis of Novel Hypoxia-Inducible Targets of the Human Antituberculosis T Cell Response

(2012) H. P. Gideon et al.   JOURNAL OF IMMUNOLOGY

Chromatin conformation governs T-cell receptor J  gene segment usage

(2012) W. Ndifon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The immunodominant myeloperoxidase T-cell epitope induces local cell-mediated injury in antimyeloperoxidase glomerulonephritis

(2012) J. D. Ooi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

POPISK: T-cell reactivity prediction using support vector machines and string kernels

(2011) Chun-Wei Tung et al.   BMC BIOINFORMATICS

Double- and monofunctional CD4+ and CD8+ T-cell responses to Mycobacterium tuberculosis DosR antigens and peptides in long-term latently infected individuals

(2011) Susanna Commandeur et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Structural and biophysical determinants of αβ T-cell antigen recognition

(2011) John S. Bridgeman et al.   IMMUNOLOGY

Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination

(2011) John J Miles et al.   IMMUNOLOGY AND CELL BIOLOGY

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

(2010) Marcos R. Betancourt et al.   PROTEIN SCIENCE

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope

(2009) S. Gras et al.   JOURNAL OF IMMUNOLOGY

T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity

(2008) Jennifer D. Stone et al.   IMMUNOLOGY