Yoav Gilad

The paper identifies genetic variants associated with cardiotoxic responses to chemotherapeutic drugs using single-cell RNA-seq and eQTL analysis.

CrossFilt improves cross-species genomic analysis by filtering reads that map reciprocally between species, leading to more accurate gene expression comparisons.

This paper shows that gene expression dispersion, not just mean expression, is a genetically controlled regulatory feature reflecting fidelity across species and cell types.

This study identifies context-specific gene regulatory effects in human brain organoids under oxygen stress, revealing 1,745 trait-associated genes with regulatory responses only under hypoxic or hyperoxic conditions.

The paper identifies response eQTLs associated with environmental exposures in human cells and finds they overlap with disease-associated loci not explained by steady-state eQTLs.

The paper identifies expression quantitative trait loci in 29 cell-types from heterogeneous differentiating cultures and characterizes regulatory dynamics across differentiation trajectories.

The paper identifies diet-responsive eQTLs in baboons exposed to high cholesterol and fat diets, showing their relevance to human metabolic GWAS genes.

This paper develops a guided differentiation protocol to generate cardiac cell aggregates (cardiac HDCs) from iPSCs, enabling the study of cardiac cell diversity through single-cell RNA-sequencing.

This study uses single-cell RNA-sequencing of embryoid bodies to compare gene expression across humans and chimpanzees, identifying conserved and species-specific regulatory genes.

This study uses an in vitro model to compare gene regulation in human and chimpanzee skeletal cells, identifying differentially expressed genes that may contribute to skeletal trait differences.

The paper identifies lineage-specific dynamic eQTLs during human cardiomyocyte differentiation using single-cell RNA-seq and deconvolves bulk RNA-seq data to attribute dynamic effects to specific lineages.

The paper uses human embryoid bodies to study inter-individual regulatory differences across diverse cell types using single-cell RNA-sequencing.

The paper identifies gene-environment interactions in gene regulation across cell types and treatments, revealing many genes missed by GTEx.

The paper characterizes gene expression responses to biomechanical strain in an in vitro model of osteoarthritis using iPSC-chondrocytes and identifies inter-individual expression differences in response to mechanical strain.

This study identifies divergence in alternative polyadenylation (APA) between humans and chimpanzees as a contributor to gene regulatory differences, particularly in protein expression.

The paper identifies dynamic eQTLs in cardiomyocytes under hypoxic stress, showing how genetic variation affects gene expression differently across conditions.

This study compares gene expression variability and eQTLs in humans and chimpanzees, finding shared genetic and non-genetic determinants of inter-individual expression differences.

The paper identifies genetic variants affecting alternative polyadenylation (APA) and shows their impact on gene expression, protein levels, and disease risk.

The paper develops a method to quantify cell cycle progression in scRNA-seq data using a small number of genes, showing it can predict cell cycle phase within 14% accuracy.

The paper compares gene expression and DNA methylation across tissues and species in primates, finding that only 7-11% of inter-species expression differences are explained by methylation, with higher explanation in tissue-specific genes.

The paper compares Drop-seq and DroNc-seq in profiling cardiomyocyte differentiation, finding similar cell types and trajectories in both methods.

This study uses Hi-C and RNA-seq to analyze 3D chromatin interactions and gene expression in human and chimpanzee iPSCs, finding that lower-order interactions are conserved while higher-order structures like TADs are not, and that inter-species differences in 3D structure correlate with gene expression differences.

This study identifies variance QTLs (vQTLs) in human iPSCs using scRNA-seq, finding that genetic variants affect gene expression variance but with smaller phenotypic impact than mean expression QTLs.

The paper compares hypoxia responses in human and chimpanzee iPSC-derived cardiomyocytes, finding conserved transcriptional responses and species-specific regulatory differences.

The paper compares chromatin accessibility and transcription factor binding in human and chimpanzee induced pluripotent stem cells, finding widespread conservation and suggesting the pluripotent state is evolutionarily constrained.

This study compares endoderm differentiation in humans and chimpanzees using iPSCs, finding high conservation of gene regulatory trajectories despite species-specific expression differences.

The paper compares gene expression and regulatory differences between human and chimpanzee iPSC-derived cardiomyocytes and primary heart tissues to assess their utility for comparative genomic studies.

This study assesses genetic influences on inter-individual variation in three human phosphoproteomes and identifies genetic associations with phosphopeptide variation.

This study identifies genetic variants influencing the transcriptomic response to doxorubicin in cardiomyocytes and links them to anthracycline-induced cardiotoxicity risk.

The paper examines H3K9me3 marking of transposable elements in human and chimpanzee induced pluripotent stem cells, finding limited species-specificity and no strong link to gene expression divergence.