Yoav Gilad

The paper examines regulatory variation in iPSCs and differentiated cells, finding lower individual variation in iPSCs and identifying shared chromatin regions for some cell type-specific QTLs.

The paper uses gene expression in dendritic cells to predict tuberculosis susceptibility, finding differentially expressed genes and genetic polymorphisms associated with TB risk.

The paper reduces mitochondrial reads in ATAC-seq using CRISPR/Cas9 and a modified protocol, improving peak calling and reducing costs.

This study identifies genotype as the major source of variation in scRNA-seq data and highlights technical replicate variation, suggesting a framework for effective study design.

The paper identifies genetic variants associated with upper airway microbiome composition, highlighting mucosal immunity genes' role in shaping microbial communities.

This study identifies 7,273 new human coding sequences using ribosome footprint profiling and validates their functionality through selective constraint and translation correlation analysis.

This study compares regulatory differences in iPSCs and finds that genetic variation, not cell type of origin, primarily drives these differences.

The paper identifies genes specifically regulated by mycobacterial infection in macrophages, suggesting they may contribute to inter-individual susceptibility to tuberculosis.

The paper introduces msCentipede, a model that improves transcription factor binding site inference by better modeling DNase I cleavage pattern heterogeneity and spatial structure.

This study shows that bacterial infection rapidly alters DNA methylation in human dendritic cells, affecting enhancer elements and gene expression related to immune responses.

WASP improves the discovery of molecular QTLs by providing robust allele-specific read mapping and analysis, showing lower error rates and higher power than existing methods.

This study shows that reprogramming LCLs to iPSCs recovers donor-specific gene expression signatures, suggesting iPSCs better reflect genetic influences on gene regulation than LCLs.

This study maps eQTL and analyzes gene expression variation in wild baboons, finding strong genetic contributions and similarities with human data.

The paper generates a panel of chimpanzee iPSCs and compares their regulatory variation with somatic cells and human iPSCs, finding reduced species-specific differences in iPSCs.

The paper investigates how epigenetic marks contribute to gene expression differences between primate species using lymphoblastoid cell lines.

The paper quantifies how RNA degradation affects gene expression measurements and shows that a linear model controlling for RNA Integrity Number (RIN) can correct for these effects.