Graham McVicker

GenVarLoader accelerates deep learning applications in personalized genomics by improving data loading speed and compression.

DNACipher predicts variant effects across cell types and assays, identifying imVars at most GWAS loci with support from experimental data.

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

Superb-seq captures single-cell Cas9 edits and transcriptomes, revealing on- and off-target effects on gene expression in over 34,000 cells.

This study identifies how chromatin structure heterogeneity in B-ALL correlates with transcriptional subtypes and developmental stages, revealing its role in disease progression.

The paper analyzes single-cell CRISPR perturbations to show enhancers act multiplicatively with limited evidence for epistatic interactions.

The paper identifies a distal enhancer for GATA3 involved in allergic diseases by combining GWAS signals with deletion mapping in T helper 2 cells.

The paper identifies cell type-specific gene regulatory changes in the amygdala of rats with varying cocaine addiction-like behaviors, linking them to energy metabolism, GABAergic inhibition, and chromatin accessibility.

This study evaluates variant callers on ATAC-seq data to discover SNVs and indels, finding VarCA outperforms individual callers in both bulk and single-cell data.

RELICS is a Bayesian method for analyzing tiling CRISPR screens to discover functional genomic sequences with higher resolution than existing approaches.

The paper identifies cell type-specific enhancer-promoter connectivity in the human brain and links these to disease risk variants in Alzheimer's and psychiatric disorders.

BreakCA identifies indels in regulatory regions using ChIP-seq and ATAC-seq, finding recurrent indels in neuroblastoma cell lines that may be oncogenic.