Predicting recognition between T cell receptors and epitopes with TCRGP

TCRBuilder: multi-state T-cell receptor structure prediction

(2020) Wing Ki Wong et al.   BIOINFORMATICS

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

(2019) Neerja Thakkar et al.   BMC BIOINFORMATICS

An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data

(2019) Lu Cheng et al.   Nature Communications

Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires

(2019) Sofie Gielis et al.   Frontiers in Immunology

Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors

(2019) Anja Mösch et al.   Frontiers in Genetics

Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers

(2019) Hongyi Zhang et al.   CLINICAL CANCER RESEARCH

mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion

(2018) Emmi Jokinen et al.   BIOINFORMATICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

High-throughput determination of the antigen specificities of T cell receptors in single cells

(2018) Shu-Qi Zhang et al.   NATURE BIOTECHNOLOGY

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition

(2017) Nicolas De Neuter et al.   IMMUNOGENETICS

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

(2017) Ryan O Emerson et al.   NATURE GENETICS

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis

(2017) P. Savola et al.   Nature Communications

High-throughput pairing of T cell receptor α and β sequences

(2015) Bryan Howie et al.   Science Translational Medicine

High-resolution analysis of the human T-cell receptor repertoire

(2015) Eliana Ruggiero et al.   Nature Communications

Hepatocellular carcinoma epidemiology

(2014) Cristina Bosetti et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

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

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Learning a peptide-protein binding affinity predictor with kernel ridge regression

(2013) Sébastien Giguère et al.   BMC BIOINFORMATICS

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly diverse TCRα chain repertoire of pre-immune CD8+T cells reveals new insights in gene recombination

(2012) Raphael Genolet et al.   EMBO JOURNAL

Gaussian Processes for Personalized e-Health Monitoring With Wearable Sensors

(2012) L. Clifton et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

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

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

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

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

The Variational Gaussian Approximation Revisited

(2008) Manfred Opper et al.   NEURAL COMPUTATION