Lindsey A. Criswell

Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

The paper identifies five SNPs in the DDX6-CXCR5 locus associated with autoimmune diseases and shows their functional effects on gene regulation in immune and epithelial cells.

Transcriptomic analysis reveals immune signatures associated with specific cutaneous manifestations of lupus in systemic lupus erythematosus

The paper identifies immune signatures in SLE cutaneous subtypes using transcriptomics, revealing subtype-specific pathways and potential therapeutic targets.

Single-cell RNA sequencing of peripheral blood defines two immunological subtypes of Sjögren's disease

The paper identifies two immunological subtypes of Sjögren's disease using single-cell RNA sequencing, highlighting distinct IFN-I signatures and transitional B cell characteristics.

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes

The paper identifies cell-specific transposable element (TE) gene expression associations with SLE phenotypes, finding 731 differentially expressed TEs linked to antiviral pathways and IFN signaling.

Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis

This paper identifies 13 biomarkers for rheumatoid arthritis using cross-tissue transcriptomic data and machine learning, validated across multiple datasets and showing clinical utility.

Calling differential DNA methylation at cell-type resolution: addressing misconceptions and best practices

The paper benchmarks two methods for detecting cell-type-specific differential DNA methylation, finding TCA superior to CellDMC and discussing best practices for cell-type resolution analysis.

Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus

This study identifies ethnicity-specific transcriptomic subgroups in SLE patients using RNA-seq data and correlates them with disease activity.

Landscape of stimulation-responsive chromatin across diverse human immune cells

The paper maps stimulation-responsive chromatin changes in immune cells and identifies variants linked to autoimmunity.

Complement component 4 genes contribute sex-specific vulnerability in diverse illnesses

This study identifies C4 genes in the MHC locus as sex-specific contributors to risk for lupus, Sjogrens syndrome, and schizophrenia, with stronger effects in men than women.

Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology

The paper demonstrates a method to infer cell-type-specific DNA methylation from bulk data, revealing novel associations with leukocyte composition and rheumatoid arthritis.

Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes

The paper introduces demuxlet, an algorithm that uses natural genetic variation to multiplex single-cell RNA-seq samples, enabling accurate sample identification and doublet detection in pooled experiments.