Mark A. Atkinson

This paper identifies 23 candidate causal genes for critical COVID-19 by integrating severity-stratified, longitudinal cis-eQTL mapping with GWAS signals from 1,031 patients.

This study identifies transcriptional impairments in mitochondrial and protein homeostasis pathways in islets during type 1 diabetes pathogenesis, independent of T-cell infiltration.

The paper maps the morphological and functional maturation of human endocrine pancreas from birth to age 10 using pediatric tissue samples and imaging techniques.

This paper introduces SMILE, a diffusion model for converting H&E stains to multiplex IHC images, showing superior performance in pancreatic islet analysis and breast cancer stain conversion.

This study uses spatial transcriptomics to identify inflammation signatures in pancreas and lymph node tissues of T1D patients, highlighting LTB and other genes involved in disease pathogenesis.

The paper identifies TCR subsequence motifs associated with type 1 diabetes using deep learning and shows their enrichment in T1D individuals based on HLA risk alleles.

This study integrates histopathological data from the human pancreas across T1D stages to identify novel histopathological correlates, particularly in the prodromal stage.

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

The paper uses 3D imaging to analyze pancreatic islets in healthy and type 1 diabetes (T1D) individuals, finding that islet size and composition influence their loss in T1D.

The paper uses single-islet proteomics to analyze pseudo-temporal immune responses and beta-cell dysfunction in stage 1 T1D, identifying key pathways involved in islet dysfunction.

This study shows that ImmTAAI, a beta cell-targeted PD-1 agonist, inhibits T cell activity in human type 1 diabetes by increasing T cell motility and reducing cytokine secretion.

The paper presents a 3D multi-omic framework to detect and characterize ovarian cancer precursors in fallopian tubes, identifying TP53 mutations in microscopic lesions.

The paper quantifies macrophage infiltration in pancreatic tissue of type 1 diabetes donors and finds increased infiltration and HLA-II expression in islet regions, suggesting a role in disease progression.

This study uses single-cell multiomics and spatial transcriptomics to identify gene regulatory programs in pancreatic cell types that drive type 1 diabetes progression.

This study shows that beta cell dysfunction occurs in type 1 diabetes independently of T cell infiltration, using human pancreas tissue slices from recently diagnosed patients.

Laser-microdissected islets of 3 multiple-autoantibody-positive stage 1 type 1 diabetes donors versus matched controls show 202 altered proteins: immune and glycolytic up, translation and ER-stress proteins down.

This study identifies aberrant immune regulation and stem-like CD8+ T cells in pancreatic lymph nodes during type 1 diabetes development using mass cytometry and single-cell RNA sequencing.

The paper analyzes immune cell changes in human pancreas-draining lymphatic tissues before and after T1D onset, identifying proinflammatory patterns and genetic risk correlations.

The paper integrates 3D imaging with nuclear segmentation to analyze nuclear morphology in human tissue, revealing spatial patterns and interactions in disease progression.

The paper uses imaging mass cytometry to analyze human pancreatic samples and identifies early β-cell dysfunction and immune changes in type 1 diabetes progression.

The paper identifies a multi-omics recovery factor predictive of long COVID using data from the IMPACC study, showing it can predict LC risk early after infection.

The paper introduces CRAWDAD, a tool for analyzing cell-type spatial relationships across scales in spatially resolved omics data, and demonstrates its application on simulated and real datasets.

This study identifies sex-specific cytokine, chemokine, and growth factor differences in T1D patients and progressors, highlighting potential implications for personalized treatment.

This study identifies immune subtypes in hospitalized COVID-19 patients linked to clinical outcomes and long COVID risk through longitudinal multi-omics analysis.

This study investigates viral reactivation in COVID-19 patients, finding associations between reactivation of specific virus families and clinical outcomes, including mortality and PASC symptoms.

This paper develops ENTPD3-specific CAR Tregs to control T1D by targeting beta cells and shows their efficacy in preventing disease progression in a mouse model.

This study shows that m6A methylation, regulated by METTL3, controls the innate immune response in β-cells during T1D onset by modulating OAS mRNA stability.

The paper examines islet and acinar cell secretion in different pancreatic regions across diabetes stages, finding reduced insulin secretion and beta-cell volume in T1D with normal enzyme secretion.

geneBasis selects an optimal gene panel from scRNA-seq data by iteratively adding genes that maximize manifold distance, outperforming existing methods in resolving cell types and states.

This study uses imaging mass cytometry to analyze pancreatic cells in T2D patients and controls, revealing changes in islet structure, cell composition, and immune cell infiltration.