Duygu Ucar

Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures

The paper maps the human immune system across the lifespan using scRNA-seq and snATAC-seq, revealing unique infant immune signatures and age-related changes in immune cell populations.

Distinct senescent β-cell senotypes differentially drive islet aging and dysfunction

The paper identifies two distinct senescent β-cell subpopulations with different functional roles in islet aging and dysfunction using single-cell proteomics and transcriptomics.

Lifestyle intervention is associated with attenuation of ER stress/inflammation and enhancement of naive immune cell identity in older adults with metabolic disease

This study shows that a 6-month lifestyle intervention reduces ER stress and inflammation while enhancing naive immune cell identity in older adults with metabolic disease.

Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects

The paper analyzes single-cell transcriptomes of human islet cells across glycemic states to identify gene expression defects in beta cells associated with type 2 diabetes.

Dose-dependent interferon programs in myeloid cells after mRNA and adenovirus COVID-19 vaccination

This study compares immune responses to different COVID-19 vaccines in humans, finding distinct interferon programs in myeloid cells based on vaccine type and dose timing.

CMV-specific clonal expansion of Th1, GZMK⁺ CD8⁺, and TEMRA T cells revealed by human PBMC single cell profiling

The paper uses single-cell profiling to show CMV drives clonal expansion of GZMK CD8 and Th1 cells in humans.

Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provides Insights into Type 2 Diabetes Genetics

This study investigates how human pancreatic islet cells respond to ER and cytokine stress and identifies T2D-associated genetic variants that modulate these responses.

Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer

This study creates a single-cell aging atlas of mouse mammary tissues, identifying shared epigenomic and transcriptomic changes between aging and cancer.

Transcriptional activation of Jun and Fos members of the AP-1 complex is a conserved signature of immune aging that contributes to inflammaging

The paper identifies the transcriptional activation of Jun and Fos genes in the AP-1 complex as a conserved aging signature in immune cells, contributing to inflammaging across mouse strains and humans.

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

CoRE-ATAC is a deep learning model that classifies regulatory elements from ATAC-seq data, accurately predicting cis-RE functions across multiple cell types and identifying cell-specific variations in regulatory activity.

A read count-based method to detect multiplets and their cellular origins from snATAC-seq data

This paper introduces ATAC-DoubletDetector, a read count-based method to detect multiplets in snATAC-seq data and annotate their cellular origins, achieving 85% accuracy in annotation.

cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data

cinaR provides an R package for differential chromatin accessibility analysis and functional interpretation of ATAC-seq data, integrating multiple analysis pipelines and visualization tools.

Functional characterization of thousands of type 2 diabetes-associated and chromatin-modulating variants under steady state and endoplasmic reticulum stress

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.

BiFET: A Bias-free Transcription Factor Footprint Enrichment Test

BiFET improves TF footprint enrichment analysis by correcting biases in chromatin accessibility and GC content, increasing power and reducing false positives.

EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function

The paper provides multi-genomic maps of the EndoC-βH1 cell model to define gene regulatory programs in human pancreatic β cells and identifies allelic effects on cis-regulatory elements.

A statistical framework for the robust detection of hidden variation in single cell transcriptomes

This paper introduces IA-SVA, a method to detect hidden variation in scRNA-seq data, showing it captures technical and biological sources and improves clustering of cell subsets.

Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis-regulatory element use in human islets

The paper profiles chromatin accessibility in human islets from T2D and non-diabetic individuals to identify genetic and disease-associated changes in cis-regulatory element use.