Aidan Keith

Multiplex programming of mappable, molecularly tagged genomic deletions

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.

High-throughput identification of chromatin-opening transcription factors

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

Small molecule activation of the tumor suppressor kinase LKB1

This study develops small molecules that activate the tumor suppressor kinase LKB1 and shows their therapeutic benefits in cancer cell lines.

Gigabase-scale deletion scanning of the human genome

This paper introduces Shred-seq, a method to scan large-scale deletions in the human genome, revealing essential regions including noncoding sequences and establishing a lower bound for viability.

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

The paper develops monoclonal embryoids with genetic barcoding to overcome clonal complexity bottlenecks in mosaic organoid screens, enabling more accurate quantification of genetic perturbation effects.

Massively multiplex single-molecule oligonucleosome footprinting

The paper introduces a single-molecule sequencing method to measure nucleosome positions on chromatin fibers and reveals heterogeneous patterns of oligonucleosome occupancy across epigenomic domains.

A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

This study evaluates how experimental design, orientation, and sequence context affect MPRA results, finding significant differences in regulatory activity measurements.

Functional Testing of Thousands of Osteoarthritis-Associated Variants for Regulatory Activity

The paper functionally tests osteoarthritis-associated variants to identify regulatory activity, finding six SNPs with differential effects, including rs4730222 increasing HBP1 isoform expression.

Functional Characterization of Enhancer Evolution in the Primate Lineage

The paper characterizes the evolutionary-functional trajectories of liver enhancers in primates by analyzing sequence mutations and their impact on regulatory activity.