Golnaz Vahedi

Nutrient-sensitive histone propionylation regulates T cell fate and function

This study shows that histone propionylation, influenced by nutrient availability, regulates T cell fate and antitumor immunity.

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

The paper shows lineage-determining transcription factors position enhancers and promoters to enable multi-enhancer regulation of oncogenes in lymphoma and T-cell leukemia.

OLIVE Provides Rapid Visualization and Analysis of Chromatin Tracing Experiments

OLIVE provides a web-based tool for visualizing and analyzing chromatin tracing data, enabling interactive exploration and quantitative analysis of three-dimensional chromatin structures.

Inference of multi-enhancer interactions in T lymphocytes using Hi-Cociety

Hi-Cociety infers 3D enhancer communities from Hi-C data in T lymphocytes, identifying key regulatory modules and cell-type-specific chromatin organization differences.

Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells

The paper uses single-allele chromatin tracing to show that genomic clustering of paralogous transcription factors enables developmental robustness in T cells by allowing compensatory interactions when regulatory elements are lost.

TET2 regulates early and late transitions in exhausted CD8+ T-cell differentiation and limits CAR T-cell function

This study shows that targeting TET2 in CAR T-cells improves their anti-tumor responses by limiting terminal exhaustion and enhancing therapeutic potential.

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

This study identifies heightened TNF pathway activity and chromatin remodeling in pancreatic lymph node CD4+ T cells from T1D patients, supporting the use of TNF inhibitors in clinical trials.

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics data, showing improved performance over existing methods in diabetic tissue analysis.

Modeling Type 1 Diabetes progression from single-cell transcriptomic measurements in human islets

This study uses single-cell transcriptomics and machine learning to predict T1D development in autoantibody-positive donors and identifies shared gene signatures across cell types.

High-throughput Oligopaint screen identifies druggable regulators of genome folding

The paper develops HiDRO, a high-throughput imaging pipeline, to screen the human druggable genome and identifies >300 factors regulating chromatin folding, including GSK3A as a regulator of TAD interactions.

Dynamic enhancer interactome promotes senescence and aging

The paper investigates how enhancer interactomes reconfigure during senescence and aging, identifying hyper-connected enhancer communities linked to gene expression and potential therapeutic targets.

Computational workflow and interactive analysis of single-cell expression profiling of islets generated by the Human Pancreas Analysis Program

The paper presents a computational workflow and interactive tool for analyzing single-cell RNA-seq data from pancreatic islets of diabetic and non-diabetic donors.

A multi-enhancer hub at the Ets1 locus controls T cell differentiation and allergic inflammation through 3D genome topology

Stripenn detects architectural stripes from chromatin conformation data using computer vision

Stripenn detects and quantifies architectural stripes from chromatin conformation data using computer vision, outperforming existing methods in biological applications.

Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes

Exome-by-phenome-wide rare variant gene burden association with electronic health record phenotypes

This study identifies robust gene-phenotype associations by analyzing rare loss-of-function variants in exome-wide data linked to electronic health records.

TooManyCells identifies and visualizes relationships of single-cell clades

TooManyCells identifies and visualizes cell clades using graph-based tools, outperforming existing methods in detecting rare populations in single-cell RNA-seq data.

A cosine similarity-based method to infer variability of chromatin accessibility at the single-cell level

PRISM quantifies single-cell chromatin accessibility variation, outperforming existing methods by accounting for technical biases and revealing masked heterogeneity.