John A. Hawkins

Direct detection of CRISPR mutations and transcriptional responses at single cell resolution in vivo

This paper introduces scPT-seq, a method to detect CRISPR mutations and transcriptional responses at single-cell resolution in vivo, revealing clonal markers and lineage dynamics in Drosophila intestine.

Plasmodium falciparum egress disrupts endothelial junctions and activates JAK-STAT signaling in a microvascular 3D blood-brain barrier model

This study shows that Plasmodium falciparum egress products disrupt BBB endothelial junctions and activate JAK-STAT signaling, leading to increased permeability and suggesting therapeutic targets.

Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq

This paper introduces SDR-seq, a multiomic scDNA-scRNA-seq method to link genotypes with gene expression, showing variants affect expression in iPSCs and B-cell lymphoma.

Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

The paper profiles cleavage specificity and kinetics of CRISPR nucleases using NucleaSeq and CHAMP, finding engineered Cas9s show improved specificity while wtCas12a has similar specificity to wtCas9 in vitro.

Error-correcting DNA barcodes for high-throughput sequencing

The paper introduces and validates FREE barcodes, which correct DNA synthesis and sequencing errors, including insertions and deletions, improving accuracy and efficiency in high-throughput sequencing.