P. G. Thomas

Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling

This paper introduces copepodTCR, a tool for designing and interpreting TCR specificity assays, which efficiently identifies antigen-specific TCRs using combinatorial peptide pooling and Bayesian modeling.

Conserved developmental rewiring of the TCR signalosome drives tolerance in innate-like lymphocytes

The paper identifies a conserved mechanism, RePrESS, by which autoreactive innate-like T cells maintain tolerance through rewiring of the TCR signalosome.

Mucosal and systemic immune dynamics associated with COVID-19 outcomes: a longitudinal prospective clinical study

This study examines mucosal and systemic immune dynamics in a diverse cohort of children and adults with COVID-19, identifying immune markers associated with disease severity and outcomes.

Utility of nasal swabs for assessing mucosal immune responses towards SARS-CoV-2

This study shows nasal swabs can assess mucosal immune responses to SARS-CoV-2, revealing distinct cytokine and antibody profiles compared to systemic responses.

Establishing thresholds for cytokine storm and defining their relationship to disease severity in respiratory viral infections

This study identifies cytokine thresholds and their relationship to disease severity in respiratory viral infections, showing that hypercytokinemia is not strongly linked to severity and that certain cytokines may predict long COVID risk.

Integrated Drivers of Basal and Acute Immunity in Diverse Human Populations

The paper examines factors influencing immunity across diverse populations, finding ancestry and age significantly affect immune responses and disease severity.

Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells

The paper identifies HHV-6 reactivation in CAR T cells using single-cell sequencing and links it to clinical neurotoxicity observed in patients.

Improved metabolic syndrome and timing of weight loss is crucial for influenza vaccine-induced immunity in obese mice

This study shows pre-vaccination weight loss improves influenza vaccine efficacy in obese mice, while post-vaccination weight loss does not.

Neuroblastoma formation requires unconventional CD4 T cells and myeloid amino acid metabolism

This study identifies unconventional CD4 T cells and myeloid amino acid metabolism as critical for neuroblastoma formation using a mouse model and spatial transcriptomics.

TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features

The paper introduces meta-clonotypes for TCR analysis, identifies HLA-restricted SARS-CoV-2 TCR features, and develops tcrdist3 for repertoire analysis.

Preexisting memory CD4 T cells in nÏave individuals confer robust immunity upon hepatitis B vaccination

The paper shows preexisting memory CD4 T cells in unvaccinated individuals correlate with stronger hepatitis B vaccine responses and predicts immune outcomes using TCR sequencing and machine learning.

Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA)

The paper introduces CoNGA, a graph-theoretic method to analyze relationships between TCR sequences and gene expression in T cells, revealing known and novel associations across human and mouse datasets.

Novel Vβ specific germline contacts shape an elite controller T cell response

The paper identifies Vβ2-specific germline contacts that contribute to a focused T cell response against a parasite-derived peptide presented by H-2Ld, enhancing HIV control.

Dynamic metabolic reprogramming in dendritic cells: an early response to influenza infection that is essential for effector function

This paper identifies dynamic metabolic reprogramming in dendritic cells during influenza infection, showing it is essential for effector function and immune response initiation.