Paul Glyndwr Thomas

The paper identifies an EBV-specific T cell program in MS patients that contributes to CNS autoimmunity through B cell and myeloid cell activation.

This study shows that HIV-1 DNA/rAd5 vaccination leads to distinct clonal expansion and memory precursor states in Env- and Gag-specific CD8 T cells.

This study investigates the role of mesenchymal-derived versican in modulating the innate immune response during influenza A virus infection, showing its critical role in immune cell migration and adhesion.

The paper introduces a funnel approach to identify epitope-specific CD4 T cells for influenza and SARS-CoV-2 by narrowing down potential epitopes using HLA-DR transgenic mice and ELISpot assays.

This study identifies changes in CD4+ T cell surface proteins and transcriptomes during pregnancy, highlighting perturbations in the IL-6/IL-6R axis and RUNX3 expression.

TCR2HLA infers HLA genotypes from TCR repertoires, enabling identification of immunologically relevant metaclonotypes and discovery of HLA-associated TCRs.

This paper develops a method to generate TCR knock-in mice with functional T cells by integrating TCRβ sequences into the Trb locus using AAV and CRISPR/Cas9, overcoming limitations of traditional transgenic models.

TIRTL-seq provides a scalable, cost-effective method for paired TCR repertoire sequencing, enabling accurate identification of TCR chain pairings and clonotype dynamics in large cohorts.

This paper introduces ADAPT, a deep learning framework for designing TCRs and antibodies that bind to specific pMHC targets, validated through cryo-EM structures and functional testing.

This paper introduces a computational method to predict TCR-pMHC interactions and design immunogenic peptides, achieving high accuracy and demonstrating success in T-cell activation.

This study shows that targeting RBM39 with indisulam promotes natural killer cell activity and eradicates neuroblastoma regardless of cellular state plasticity.

This study shows that IL4i1 metabolites from immune cells suppress ferroptosis in neuroblastoma cells by scavenging free radicals and activating NRF2, promoting tumor survival.

The paper identifies TCR-V gene usage patterns in T cells sorted by anti-TCR mAbs using single-cell RNAseq and finds enriched ERV1-family LTR expression in specific TRBV regions.

The paper analyzes 6 million T cells from 91 studies to identify TCR sequence convergence patterns and their association with functional and cellular T cell phenotypes.

This study compares neonatal and adult CD8+ recent thymic emigrants using single-cell multiomics, finding distinct phenotypes and functions despite similar post-thymic maturation.

This study identifies an arachidonic acid binding pocket in SMO that modulates SHH signaling, revealing context-specific allostery crucial for cardiopulmonary development.

The paper develops a model to predict HLA types from TCR repertoires using associations inferred from HLA-typed donors.

The paper shows that pre-existing immunity from H1N1 infection or vaccination can protect against lethal HPAI H5N1 clade 2.3.4.4b challenge in mice and ferrets, independent of hemagglutination inhibition titers.

This study shows diet-induced obesity in ferrets increases influenza disease severity and transmission due to altered lung microenvironment and reduced antiviral responses.

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.

The paper shows bacterial PAMPs activate TLR2/6 on fetal NPCs, enhancing proliferation and altering brain development in mice.

This study links influenza virus infection kinetics to lung injury, inflammation, and disease severity using a model-experiment framework.