Carl A. Anderson

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

The paper identifies molecular signatures of Crohn's disease using scRNA-seq data from terminal ileal biopsies, highlighting key cell types and pathways involved in disease pathogenesis.

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

This study identifies 619 IBD risk signals, resolves 81 high-confidence variants, and prioritizes 664 candidate effector genes using GWAS, eQTL, and exome sequencing.

This study uses exome and genome sequencing to identify 68 genes directly associated with inflammatory bowel disease, providing clearer genetic insights and therapeutic targets.

The paper identifies CFTR loss-of-function variants as protective against IBD using large-scale exome sequencing data and evaluates variant prioritization methods.

The paper maps eQTLs in stimulated iPSC-derived macrophages and identifies condition-specific reQTLs that colocalize with disease-associated variants.

The paper maps cell-type-specific eQTLs in IBD patients to identify effector genes and mechanisms linking genetic risk to disease.

This study uses single-cell RNA sequencing to analyze immune cell transcriptional profiles in mucosal and circulatory compartments of Crohn's disease patients, revealing tissue-specific inflammation signatures and identifying circulating T cells with mucosal-like features.

This study evaluates deep-learning methods for improving polygenic scores, finding limited benefits due to confounding effects from linkage disequilibrium.

The paper identifies inflammation-associated monocytes (IAMs) in IBD and experimental colitis, showing they express ACOD1 to limit cytokine production during inflammation.

ShaPRS improves polygenic score accuracy by leveraging shared genetic effects across traits or ancestries, enhancing performance for complex diseases and across populations.

The paper identifies low-usage splice junctions as contributors to immune-mediated disease risk by linking sQTLs to disease loci and showing their impact on gene expression in inflammation.

The paper uses network-based expansion of GWAS results to identify pleiotropic gene modules linked to multiple traits and demonstrates their application in studying inflammatory bowel disease.

The paper analyzes somatic mutations in colonic crypts of IBD patients and controls, finding higher mutation rates and clonal expansions in IBD-affected tissue.

This study uses regulatory QTLs from immune cells to fine-map causal variants for twelve immune-mediated diseases, finding smaller credible sets and higher posterior probabilities compared to traditional methods.

This study identifies HLA-DQA1*05 as a genetic risk factor for anti-drug antibody development in Crohn's disease patients treated with anti-TNF therapies.

The paper identifies 9 novel genetic loci, including low-frequency variants in TP53, associated with head circumference and intracranial volume in up to 46,000 individuals.