Caleb A. Lareau

The paper introduces PHAGE-ATAC, a method for simultaneous single-cell measurement of surface proteins, chromatin accessibility, and mtDNA-based clonal tracing, and demonstrates its application in human immune cells.

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.

This study identifies 5,552 blood-cell trait-variant associations across 746,667 individuals from 5 global populations, including 71 novel loci and ancestry-specific variants not found in European ancestry populations.

This study identifies 5,106 new genetic variants associated with blood cell traits using large-scale GWAS, highlighting the polygenic and monogenic basis of hematopoiesis.

The paper identifies and quantifies barcode multiplets in 10x Chromium scATAC-seq data, showing their potential to confound single-cell analyses.

The paper benchmarks 10 scATAC-seq analysis methods on synthetic and real datasets, finding SnapATAC, Cusanovich2018, and cisTopic perform best in separating cell populations across varying coverage and noise levels.

This study identifies 14 genome-wide significant loci and a polygenic signature for myeloproliferative neoplasms, implicating hematopoietic stem cell function and self-renewal in disease risk.

The paper describes SECURE-ABE and -CBE base editors with reduced RNA off-target activities and improved DNA editing precision.

The paper performs a pooled loss-of-function screen in hematopoietic cells to identify genes underlying GWAS loci associated with red blood cell traits, finding 77 genes at 38 loci with biological relevance.

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

This study fine-maps genetic variants associated with blood cell traits and identifies cell types and causal mechanisms using single-cell chromatin accessibility data from the UK Biobank.

The paper uses gene expression data and GWAS summary statistics to identify disease-relevant tissues and cell types by detecting heritability enrichments in gene-specific expression regions.

The paper challenges the claim that CRISPR-Cas9 induces off-target mutations by showing that the observed variants are likely pre-existing genetic differences between treated mice and the control.

The paper introduces hichipper, a preprocessing tool for HiChIP data that includes quality control, bias correction, and DNA loop calling.

diffloop identifies and analyzes differential DNA loops between samples using ChIA-PET data, linking loop changes to epigenetic and gene expression differences.

The paper uses single-cell chromatin accessibility to map the continuous regulatory variation in human hematopoietic differentiation and identifies epigenomic heterogeneity within cell populations.