Ali Naji

Deep learning representations of human Immune Health for precision immunology

The paper develops MAESTRO, a self-supervised deep learning framework to transform immune profiles into embeddings capturing immune health, enabling clinical prediction and precision immunotherapy.

Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes

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.

SEL1L-HRD1 ER-Associated Degradation Facilitates Prohormone Convertase 2 Maturation and Glucagon Production in Islet α Cells

This study identifies SEL1L-HRD1 ERAD as a regulator of PC2 maturation and glucagon production in islet α cells by degrading misfolded proPC2.

Epigenetic adaptation of beta cells across lifespan and disease: age-related demethylation is advanced in type 2 diabetes

The paper examines age-related DNA methylation changes in beta and alpha cells using HPAP data, finding accelerated demethylation in T2D beta cells.

Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset

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

Single-cell multiome analysis supports α-to-β transdifferentiation in human pancreas

The paper identifies transitional cell states between alpha and beta cells in human islets using single-cell multiome data, suggesting potential for alpha-to-beta transdifferentiation.

Human Vascularized Macrophage-Islet Organoids to Model Immune-Mediated Pancreatic β cell Pyroptosis upon Viral Infection

The paper develops vascularized macrophage-islet organoids to study immune-mediated β cell pyroptosis during viral infection and identifies TNFSF12-TNFRSF12A as a key mechanism.

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

This study identifies heightened TNF pathway activity and chromatin remodeling in pancreatic lymph node CD4+ T cells from T1D patients, supporting the use of TNF inhibitors in clinical trials.

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics data, showing improved performance over existing methods in diabetic tissue analysis.

Modeling Type 1 Diabetes progression from single-cell transcriptomic measurements in human islets

This study uses single-cell transcriptomics and machine learning to predict T1D development in autoantibody-positive donors and identifies shared gene signatures across cell types.

Computational workflow and interactive analysis of single-cell expression profiling of islets generated by the Human Pancreas Analysis Program

The paper presents a computational workflow and interactive tool for analyzing single-cell RNA-seq data from pancreatic islets of diabetic and non-diabetic donors.

Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

This study integrates single-cell gene expression and chromatin accessibility data from human pancreatic islets to identify T1D risk mechanisms involving multiple cell types and genetic variants.

The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

The paper uses 3D chromatin maps to identify cell-type-specific regulatory architecture of type 2 diabetes risk by analyzing pancreatic cell types.

Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes

Exome-by-phenome-wide rare variant gene burden association with electronic health record phenotypes

This study identifies robust gene-phenotype associations by analyzing rare loss-of-function variants in exome-wide data linked to electronic health records.

Discovery of 318 novel loci for type-2 diabetes and related micro- and macrovascular outcomes among 1.4 million participants in a multi-ethnic meta-analysis.

Multi-ethnic type 2 diabetes (T2D) meta-analysis of 228,499 cases and 1,178,783 controls finds 318 previously unreported loci, 804 expression-colocalized genes, and 13 SNP-by-T2D vascular-outcome interactions.