Aaron McKenna

BASELINE uses CRISPR base editing to enable high-resolution single-cell lineage tracing in mammalian systems, recording over 4300 bits of information with high fidelity across 40 cell divisions.

PALINCODE uses ternary CRISPR bits to record cell lineage in the genome, enabling high-density lineage trees and in vivo clonal evolution analysis.

The paper introduces REMAP, a mouse model for tracking breast cancer lineage, and shows how treatment affects tumor evolution and immune response.

SCOUT models gene expression evolution on single-cell lineage trees to distinguish neutral drift from selection, validated in C. elegans and lung cancer.

This study uses FLARE to track AML cell lineage evolution under AraC treatment, revealing resistance mechanisms and validating them in a clinical cohort.

This study uses single-cell lineage tracing to show that CD8 T-cell clones exhibit differential fate commitment during acute infection, with some clones adopting memory or effector biases over time.

The paper shows that leukemia cells secrete apelin, which promotes clonal expansion of niche endothelial cells and drives leukemogenesis in zebrafish.

The paper presents an improved chromosome-scale genome assembly for the African spiny mouse using long Nanopore reads and validates it with RNA-seq data.

Circuit-seq uses Nanopore sequencing to rapidly and affordably sequence plasmids, enabling accurate and scalable validation of recombinant DNA.

This paper introduces a statistical model and method for estimating cell lineage trees using maximum-likelihood phylogenetics, showing improved accuracy over existing methods in simulations and zebrafish development.

The paper uses scRNA-seq data from mouse brain cortex to identify cell types and lineages by analyzing LOH events and gene expression patterns.

This study provides the first single-cell RNA-seq time course of zebrafish brain development, revealing the emergence of neuronal diversity and distinct neurogenic regulatory patterns across developmental stages.

The paper profiles CRISPR/Cas9-induced mutational outcomes and develops a predictive model based on sequence context to guide DSB repair outcomes.

The paper introduces a computational method to identify missing signaling pathway elements from temporal phosphoproteomic data, demonstrating its effectiveness in both human EGF response and yeast osmotic stress response.

FlashFry is a fast tool for designing CRISPR targets, allowing users to score and annotate thousands of guide sequences with customizable off-target mismatch parameters.

The paper introduces scGESTALT, a method that combines single-cell RNA sequencing with lineage tracking to identify cell types and their developmental relationships in the zebrafish brain.

This paper introduces ScanDel, a CRISPR-based method to systematically delete non-coding regions of a gene locus, revealing that distal regulatory elements are not critical for HPRT1 function.

This study introduces a genome editing method to trace whole organism lineages by accumulating mutations in DNA barcodes, showing that most adult zebrafish cells originate from few embryonic progenitors.