David R. Edgell

The paper introduces Murmurent, an agentic AI environment that supports biomedical research collaboration by providing infrastructure, specialized agents, memory, traceability, SOP enforcement, and multi-user capacity.

The paper analyzes homing endonuclease genes, identifies their activity levels, and reconstructs ancestral forms showing improved function and structural insights.

The paper develops PHYCUT, a CRISPR/Cas9 system for multiplex genome editing in the diatom Phaeodactylum tricornutum, demonstrating its use to reduce fucosylation of secreted proteins.

The paper improves deep learning models for predicting sgRNA/Cas9 activity by optimizing data curation and filtering, resulting in better generalization across species and data types.

This study shows how buffer conditions affect cleavage preferences of chimeric gene editors, revealing non-targeted cleavage in low salt environments.

The paper introduces STALEMATE, a biocontainment system that reduces genetic escape rates in engineered bacteria by entangling genetic sequences, achieving rates below 10^-10 in mice.

This study uses machine learning to predict SaCas9 activity in bacteria, revealing that PAM adenine methylation and flanking sequences significantly influence activity.

The paper shows Ku suppresses RNA-mediated innate immune responses in human cells, enabling primate-specific Alu element expansion by reducing dsRNA-induced inflammation.

This paper introduces a method for targeted gene editing using RNA-templated DNA repair pathways in human cells, achieving high efficiency and fidelity.

The paper develops a transfer learning model, crisprHAL, to improve SpCas9/sgRNA activity prediction using small high-quality datasets.

The paper develops thermoregulated meganucleases to degrade DNA at 18°C, preventing the spread of engineered genetic material outside the mammalian gut.

This study establishes a conditional Ku70 knockout system in human cells to investigate the causes of Ku essentiality, finding that loss of Ku affects multiple cellular processes beyond DNA repair and telomere maintenance.

This paper presents a telomere-to-telomere genome assembly of Phaeodactylum tricornutum using Oxford Nanopore long reads, identifying 25 nuclear chromosomes and improving genetic engineering opportunities.

This paper develops a conjugation-based system for genome engineering in D. radiodurans, enabling stable plasmid introduction and gene deletion protocols.

The paper identifies type IV conjugation systems in metagenomic data and shows they differ between age and geographic cohorts, suggesting their use as biomarkers and highlighting limitations of current binning methods.

The paper develops a method to generate designer algal mitochondrial genomes using yeast and E. coli hosts for efficient DNA cloning and testing.

The paper characterizes Cas9-generated auxotrophs in Phaeodactylum tricornutum, showing they can be complemented by plasmid-based genes and exhibit metabolic changes.

The paper develops S. meliloti strains and vectors to transfer high G+C content DNA to multiple hosts.