Leah Claire Kottyan

This study identifies HIF-2 as a critical factor for the survival of cytokine-activated human NK cells, showing it is induced by IL-2/IL-15 and not hypoxia, and its inhibition reduces NK cell viability.

This study develops an EBV-infected tonsil organoid model to study B cell states and antiviral responses during primary infection, revealing unique transcriptional programs and immune interactions.

The paper systematically identifies effector functions of pathogen ORFs across multiple pathways, revealing new roles for known effectors and uncharacterized proteins.

The paper identifies a new bZIP protein motif, BPabZIP, that facilitates nucleosome displacement and binding near nucleosomes in human cells.

The paper characterizes gene regulatory networks in human airway epithelial cells and identifies cell type-specific responses to type I interferon.

This study uses single nucleus RNA sequencing to identify altered angiogenic signaling in JDM muscle, highlighting vascular and IFN pathways.

This study identifies gene regulatory networks in human memory CD4+ T cells that drive rapid recall, linking specific transcription factors to immune-mediated disease risk.

This study shows that EBNA2 activity is increased in MS patients, altering gene expression and chromatin accessibility in EBV-transformed B cells.

The paper presents a genetic resource of 15,684 individuals of African ancestry, demonstrating its utility in replicating and discovering disease associations.

The paper identifies CpG sites and pathways associated with gestational age and epigenetic age acceleration, and links perinatal exposures to these epigenetic changes.

This study evaluates over 3,000 congenital heart disease-risk variants using SNP Bind-n-Seq and MPRA to identify variants with allelic TF binding and regulatory activity.

This study shows that Ddx3x is essential for B-cell development in mice, with loss leading to developmental blocks and defects in immunoglobulin rearrangement.

This study shows HCMV infection disrupts chromatin organization and reduces TEAD1 activity through multiple mechanisms, linking it to genetic risk loci for eye and ear development.

The paper develops a pipeline for integrated breast cancer risk assessment using polygenic risk scores and other factors in the eMERGE study, showing high concordance between API and UI results.

This study identifies nuclear factor I (NFI) as a driver of dysregulated purine metabolism in DIPG, showing that targeting ATIC reduces tumor progression in mice.

The paper uses a polygenic risk score for colorectal cancer in a PheWAS to find genetic correlations with other phenotypes from electronic health records.

The paper examines how covariates affect polygenic score performance across European and African cohorts, finding significant differences in R2 and interaction effects, and proposes methods to improve model performance.

This study uses structural information of antibodies to identify convergent antibodies in bulk IgH data, improving disease prediction for food sensitization and matching HIV prediction performance.

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

The paper selects and validates ten polygenic risk scores for clinical use in diverse populations, focusing on chronic diseases and addressing disparities in predictive performance.

This study shows that macrophage epigenetic changes from early life injury influence pain responses later in life, with a focus on sex-specific effects.

maxATAC provides deep learning models for predicting transcription factor binding sites from ATAC-seq data, improving prediction in primary and single-cell contexts.

This study identifies 20 genome-wide significant loci associated with serum IgA levels and finds genetic correlations with various immune and metabolic traits.

This study evaluates how ancestry, GWAS sample size, and LD reference panels affect BMI PRS performance across different age groups and ancestries.

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

This paper develops a trans-ancestry polygenic risk score for type 2 diabetes and validates it across diverse populations to improve equitable risk prediction.

This paper introduces polygenic risk vectors (PRV) to improve genetic risk stratification for cardio-metabolic diseases by combining additive and dominant genetic effects, outperforming traditional polygenic risk scores.

This study identifies epigenetic and transcriptional dysregulation in CD4+ T cells of atopic dermatitis patients, linking genetic risk variants to altered chromatin accessibility and NFKB1 binding.

This study shows EBNA2 alters chromatin structure and gene expression at autoimmune risk loci, linking viral infection to genetic risk mechanisms in autoimmune diseases.