Publications
There are 49 publications listed below. For more information, please visit:
2025
A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity
The alpha-variant wave of the COVID-19 pandemic provided a unique opportunity to study, at single-cell resolution, how near-universal exposure to the same pathogen can lead to …
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions
T cells recognize antigens and induce specialized gene expression programs (GEPs), enabling functions like proliferation, cytotoxicity and cytokine production. Traditionally, …
Diverse modes of T cell receptor sequence convergence define unique functional and cellular phenotypes
Single-cell techniques allow concurrent study of gene activity and T cell receptor (TCR) sequences, identifying connections between TCR structure and cell traits. Expanding on our …
Tumor location as a risk factor for severe immune-related adverse events
Immune-related adverse events (irAEs) can cause severe morbidity and mortality, and they impair treatment with immune checkpoint inhibitors (ICI). Risk factors for irAEs are not …
Immune-parenchymal multicellular niches are shared across distinct thyroid autoimmune diseases
Thyroid hormone, produced in the thyroid gland, regulates metabolism, development, and cardiac function. The thyroid is susceptible to autoimmune attack by both cellular and …
2024
Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis
Immune responses in checkpoint myocarditis across heart, blood and tumour
Immune checkpoint inhibitors are widely used anticancer therapies1 that can cause morbid and potentially fatal immune-related adverse events such as immune-related myocarditis …
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T …
Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis
Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis
It has been presumed that rheumatoid arthritis (RA) joint pain is related to inflammation in the synovium; however, recent studies reveal that pain scores in patients do not …
Longitudinal patterns and predictors of response to standard-of-care therapy in lupus nephritis: data from the Accelerating Medicines Partnership Lupus Network
Background Leveraging the Accelerating Medicines Partnership (AMP) Lupus Nephritis (LN) dataset, we evaluated longitudinal patterns, rates, and predictors of response to …
2023
Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes
Rheumatoid arthritis is a prototypical autoimmune disease that causes joint inflammation and destruction1. There is currently no cure for rheumatoid arthritis, and the …
Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States
ObjectiveRecent studies have uncovered diverse cell types and states in the rheumatoid arthritis (RA) synovium; however, limited data exist correlating these findings with …
A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma
Asthma is a chronic disease most commonly associated with allergy and type 2 inflammation. However, the mechanisms that link airway inflammation to the structural changes that …
2021
2020
Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
In late 2019 and through 2020, the COVID-19 pandemic swept the world, presenting both scientific and medical challenges associated with understanding and treating a previously …
Single-cell transcriptomics in cancer: computational challenges and opportunities
Intratumor heterogeneity is a common characteristic across diverse cancer types and presents challenges to current standards of treatment. Advancements in high-throughput …
Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal
PTPRS-targeted FLS-directed therapy synergizes with TNF inhibition in therapy of arthritis.
Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis
A genetic risk tool could be used at the first clinical visit of patients with inflammatory arthritis to increase diagnostic efficacy.
CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts
The role of stromal fibroblasts in chronic inflammation is unfolding. In rheumatoid arthritis, leukocyte-derived cytokines TNF and IL-17A work together, activating fibroblasts to …
2019
Using genetics to differentiate patients with similar symptoms: application to inflammatory arthritis in the rheumatology outpatient clinic
Slow developing complex diseases are a clinical diagnostic challenge. Since genetic information is increasingly available prior to a patient’s first visit to a clinic, it might …
Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways
Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry
Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions
How innate T cells (ITC), including invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, and γδ T cells, maintain a poised effector state has been …
2018
Mixed-effects association of single cells identifies an expanded effector CD4+T cell subset in rheumatoid arthritis
Mixed-effects regression of single-cell data accounts for confounding variation and reveals an expanded CD4+T cell population in rheumatoid arthritis.
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis
Fibroblasts regulate tissue homeostasis, coordinate inflammatory responses, and mediate tissue damage. In rheumatoid arthritis (RA), synovial fibroblasts maintain chronic …
2017
Functional genomics of stromal cells in chronic inflammatory diseases
Purpose of reviewStroma is a broad term referring to the connective tissue matrix in which other cells reside. It is composed of diverse cell types with functions such as …
UBiT2: a client-side web-application for gene expression data analysis
We present a purely client-side web-application, UBiT2 (User-friendly BioInformatics Tools), that provides installation-free, offline alignment, analysis, and visualization of …
Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples
2016
52 Genetic Loci Influencing Myocardial Mass
A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases
2015
Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci
2014
Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization
SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci
Summary: We created a fast, robust and general C++ implementation of a single-nucleotide polymorphism (SNP) set enrichment algorithm to identify cell types, tissues and pathways …
Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells
It is difficult to determine the mechanistic consequences of context-dependent genetic variants, some of which may be related to disease (see the Perspective by Gregersen). Two …