Suna Önengüt-Gümüşcü

Genetic drivers of protein changes over time: Findings, considerations, and approaches in TOPMed cohorts and UK Biobank

The paper identifies genetic drivers of protein change over time using longitudinal proteomics data from MESA, UK Biobank, and CARDIA, finding that baseline adjustment improves replication but may introduce biases.

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

Prediction of Polygenic Risks by Screening Thousands of Polygenic Scores

The paper introduces SECRET, a method to develop polygenic scores for traits with limited data, showing improved prediction power over existing methods.

HLA-focused type 1 diabetes genetic risk prediction in populations of diverse ancestry

This paper develops ancestry-specific and combined HLA-focused genetic risk scores for type 1 diabetes and evaluates their performance across diverse populations.

LAG3+ CD8+ T cell Subset Drives HR+/HER2- Breast Cancer Reduction in Bispecific Antibody Armed Activated T Cell Therapy

This study identifies LAG3+ CD8+ T cells as key effectors in bispecific antibody armed T cell therapy for HR+/HER2- breast cancer and shows how checkpoint inhibitors can enhance their anti-tumor function.

Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes

The paper identifies shifts in isoform usage in Tregs associated with Type 1 Diabetes by comparing gene expression between cases and controls.

Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal

The paper introduces the T1D Knowledge Portal, a resource for querying genetic and functional data related to type 1 diabetes to aid in hypothesis generation and target discovery.

Evaluation of a scalable approach to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells

The paper evaluates a scalable approach using scRNA-seq to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells from mouse bone marrow-derived stromal cells.

Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

The paper uses single-cell ATAC-seq to analyze coronary artery cells from CAD patients, identifying regulatory mechanisms and risk variants associated with disease.

Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

This study identifies causal variants, cells, genes, and drug targets for type 1 diabetes using large-scale genetic and functional genomic analyses.

Systems genetics analyses in Diversity Outbred mice inform human bone mineral density GWAS and identify Qsox1 as a novel determinant of bone strength

The paper uses Diversity Outbred mice to analyze bone traits and identify novel genes associated with bone strength, informing human GWAS findings.

Enhanced genetic analysis of type 1 diabetes by selecting variants on both effect size and significance, and by integration with autoimmune thyroid disease

The paper identifies 302 new genetic signals for type 1 diabetes and autoimmune thyroid disease by combining effect size and significance, showing that only 28% of genome-wide significant signals have large effects.

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples

This paper introduces 10cRNA-seq, an in situ method for sequencing 10 microdissected cells, showing improved sensitivity and reliability compared to scRNA-seq.

Genome-wide association study of diabetic kidney disease highlights biology involved in renal basement membrane collagen

This study identifies 16 genome-wide significant loci associated with diabetic kidney disease, including a protective variant in the COL4A3 gene.

Fine-mapping identifies causal variants for RA and T1D in DNASE1L3, SIRPG, MEG3, TNFAIP3 and CD28/CTLA4 loci

This study fine-maps RA and T1D loci outside the MHC, identifying causal variants and confirming their functional impact through allele-specific binding and enhancer activity.