Benjamin E. Parks

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

Scalable high-performance single cell data analysis with BPCells

BPCells enables scalable single-cell RNA-seq and ATAC-seq analysis on modest hardware by using disk-backed streaming algorithms and compressed formats.

Single-molecule chromatin configurations link transcription factor binding to expression in human cells

This study links transcription factor binding to gene expression by analyzing chromatin configurations using single-molecule footprinting in human cells.

NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells

NEAT-seq profiles nuclear proteins, chromatin accessibility, and transcriptomes in single cells, revealing TF regulatory mechanisms and linking GWAS SNPs to chromatin accessibility and target genes.

A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia

This paper develops a single-cell multi-omic framework to identify malignant regulatory signatures in mixed phenotype acute leukemia by analyzing transcriptomic and epigenetic data.