Susan Kales

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

The paper identifies non-coding variants associated with clonal hematopoiesis and demonstrates their regulatory impact on gene expression and clonal expansion.

The paper identifies ~2,000 cis-regulatory elements (CREs) across 27 dsDNA viruses using reporter assays and machine learning, revealing their regulatory features and associated transcription factors.

The paper expands the DNA motif lexicon of transcriptional regulatory code by identifying composite elements and using a deep learning model to predict their activity and impact of variants.

The paper analyzes 3,313 genetically engineered mouse lines to identify gene essentiality as the main factor affecting Cas9-based genome editing success.

This paper designs synthetic cis-regulatory elements (CREs) that outperform natural ones in driving cell type-specific gene expression using deep learning and experimental validation.

The paper identifies three regulatory variants associated with IVD expression and linked to GWAS signals, showing synergistic and opposing effects through functional experiments.

The paper identifies 1,500 human variants affecting RE1 silencers using a modified MPRA assay and shows how REST binding motifs influence silencing.

This paper identifies causal SNPs and their target genes in JIA risk haplotypes using MPRA and CRISPRi, finding 84 SNPs that alter gene expression and regulate multiple genes in TRAF1 and LNPEP/ERAP2 loci.

HCR-FlowFISH identifies cis-regulatory elements and their target genes by quantifying gene expression changes after CRISPR perturbations, using >270,000 perturbations to detect CREs for multiple genes.

The paper identifies functional β cell transcriptional variants from T2D GWAS SNPs using MPRA, showing strong correlation with chromatin accessibility and revealing regulatory features under stress conditions.