Kenneth Barr

Genetic Determinants of Cell-Type-Specific Responses to Cardiotoxic Chemotherapeutic Agents

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

CrossFilt: A Cross-species Filtering Tool that Eliminates Alignment Bias in Comparative Genomics Studies

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

Beyond the mean: genetic control of gene expression fidelity and dispersion

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

Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures

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

Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity

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.

Embryoid bodies facilitate comparative analysis of gene expression in humans and chimpanzees across dozens of cell types

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.

Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation

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.

Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

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

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

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

Fully Interpretable Deep Learning Model of Transcriptional Control

The paper presents a fully interpretable deep learning model for understanding DNA regulatory codes in gene expression, validated on Drosophila embryo data.

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

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.

An in silico analysis of robust but fragile gene regulation links enhancer length to robustness

The paper analyzes gene regulation robustness in Drosophila using a sequence-level model, finding that enhancer length correlates with robustness to genetic perturbation.