Deep generative models for T cell receptor protein sequences

Memory CD4+ T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus

(2018) Nicolas De Neuter et al.   GENES AND IMMUNITY

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

(2018) Yuval Elhanati et al.   IMMUNOLOGICAL REVIEWS

A Diverse Lipid Antigen–Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis

(2018) William S. DeWitt et al.   JOURNAL OF IMMUNOLOGY

High-throughput immune repertoire analysis with IGoR

(2018) Quentin Marcou et al.   Nature Communications

Method for identification of condition-associated public antigen receptor sequences

(2018) Mikhail V Pogorelyy et al.   eLife

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

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

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

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

(2017) Ryan O Emerson et al.   NATURE GENETICS

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

(2017) Felix Breden et al.   Frontiers in Immunology

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

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

(2015) Bryan Howie et al.   Science Translational Medicine

Quantifying selection in immune receptor repertoires

(2014) Yuval Elhanati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating the ratio of CD4+ to CD8+ T cells using high-throughput sequence data

(2013) Ryan Emerson et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

nestly--a framework for running software with nested parameter choices and aggregating results

(2012) C. O. McCoy et al.   BIOINFORMATICS

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

(2012) A. Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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