Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

TCRmodel: high resolution modeling of T cell receptors from sequence

(2018) Ragul Gowthaman et al.   NUCLEIC ACIDS RESEARCH

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires

(2018) Enkelejda Miho et al.   Frontiers in Immunology

Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

(2018) William S DeWitt et al.   eLife

A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis

(2018) Yuan Tian et al.   Frontiers in Immunology

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

(2017) Victor Greiff et al.   JOURNAL OF IMMUNOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

STCRDab: the structural T-cell receptor database

(2017) Jinwoo Leem et al.   NUCLEIC ACIDS RESEARCH

Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity

(2017) Regina S. Salvat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Post hoc assessment of the immunogenicity of bioengineered factor VIIa demonstrates the use of preclinical tools

(2017) Kasper Lamberth et al.   Science Translational Medicine

Graph-based optimization of epitope coverage for vaccine antigen design

(2017) James Theiler et al.   STATISTICS IN MEDICINE

Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires

(2017) Simon Friedensohn et al.   TRENDS IN BIOTECHNOLOGY

Design and engineering of deimmunized biotherapeutics

(2016) Karl E Griswold et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads

(2015) Regina S. Salvat et al.   BIOTECHNOLOGY AND BIOENGINEERING

Depletion of T Cell Epitopes in Lysostaphin Mitigates Anti-Drug Antibody Response and Enhances Antibacterial Efficacy In Vivo

(2015) Hongliang Zhao et al.   CHEMISTRY & BIOLOGY

HCV epitope, homologous to multiple human protein sequences, induces a regulatory T cell response in infected patients

(2015) Phyllis T. Losikoff et al.   JOURNAL OF HEPATOLOGY

Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell

(2015) Lu He et al.   VACCINE

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

(2015) Regina S. Salvat et al.   PLoS Computational Biology

Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance

(2015) Kristina Blazanovic et al.   Molecular Therapy-Methods & Clinical Development

Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage

(2014) Lu He et al.   BMC BIOINFORMATICS

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

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

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

Removing T-cell epitopes with computational protein design

(2014) C. King et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing

(2014) I. V. Zvyagin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and clonal selection in the human T-cell repertoire

(2014) Q. Qi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterizing immune repertoires by high throughput sequencing: strategies and applications

(2014) Jorg J.A. Calis et al.   TRENDS IN IMMUNOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

T-cell epitope vaccine design by immunoinformatics

(2013) A. Patronov et al.   Open Biology

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

T Cell Responses to Known Allergen Proteins Are Differently Polarized and Account for a Variable Fraction of Total Response to Allergen Extracts

(2012) C. Oseroff et al.   JOURNAL OF IMMUNOLOGY

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

(2012) Jorg J. A. Calis et al.   PLoS Computational Biology

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

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing

(2011) Jennifer Benichou et al.   IMMUNOLOGY

A Single Autoimmune T Cell Receptor Recognizes More Than a Million Different Peptides

(2011) Linda Wooldridge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TCRep 3D: An Automated In Silico Approach to Study the Structural Properties of TCR Repertoires

(2011) Antoine Leimgruber et al.   PLoS One

Therapeutic enzyme deimmunization by combinatorial T-cell epitope removal using neutral drift

(2011) J. R. Cantor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paired analysis of TCRα and TCRβ chains at the single-cell level in mice

(2010) Pradyot Dash et al.   JOURNAL OF CLINICAL INVESTIGATION

Molecular Determinants of T Cell Epitope Recognition to the Common Timothy Grass Allergen

(2010) C. Oseroff et al.   JOURNAL OF IMMUNOLOGY

Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys

(2010) Dan H Barouch et al.   NATURE MEDICINE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

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

(2009) H. S. Robins et al.   BLOOD

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

(2009) J. D. Freeman et al.   GENOME RESEARCH