Cynthia A. Kalita

Psychological stress and social support are associated with opposing single-cell pro-inflammatory gene regulatory mechanisms in adults

The paper identifies opposing gene regulatory mechanisms in CD4+ T cells and monocytes associated with psychological stress and social support in African American adults using scRNA-seq and scATAC-seq.

Characterization of caffeine response regulatory variants in vascular endothelial cells

The paper identifies genetic variants that modify gene expression in response to caffeine in vascular endothelial cells and shows their potential role in cardiovascular disease.

Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

The paper introduces CWAS, a method linking genetic variation to chromatin states, identifying novel prostate cancer risk loci and regulatory mechanisms not detectable by eQTLs.

A novel method to identify cell-type specific regulatory variants and their role in cancer risk

The paper introduces DeCAF, a method to identify cell-type specific QTLs in bulk RNA-seq data, finding 3,664 genes with cfQTLs in 14 cell types and linking some to cancer risk.

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

The paper identifies gene-environment interactions in gene regulation across cell types and treatments, revealing many genes missed by GTEx.

High throughput characterization of genetic effects on DNA:protein binding and gene transcription

The paper develops a high-throughput assay to identify allele-specific effects on DNA:protein binding and gene transcription, finding significant associations with complex trait variants.

circuitSNPs: Predicting genetic effects using a Neural Network to model regulatory modules of DNase-seq footprints

circuitSNPs predicts the functional effects of genetic variants on chromatin accessibility using a neural network that models regulatory modules from DNase-seq footprints.

QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays

The paper develops QuASAR-MPRA to analyze allele-specific effects in MPRA data, finding 602 SNPs with significant allele-specific regulatory function in LCLs.

Which genetic variants in DNase I sensitive regions are functional?

The paper identifies functional genetic variants in DNase I sensitive regions by integrating sequence and footprinting data, finding they are enriched for allele-specific binding and GWAS traits.