Barry L. Stoddard

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

This paper designs a chemically induced dimerization system using a de novo macrocycle and protein homodimer to control cellular processes.

This study investigates the structural and functional properties of BrxC, a conserved AAA+ ATPase in the BREX phage restriction system, revealing its role in mediating competing protein associations and DNA binding that regulate host methylation and phage restriction.

This paper introduces a generative diffusion model for de novo design of RNA and nucleoprotein complexes, validated experimentally with SHAPE-seq and electron microscopy.

This paper designs sequence-specific DNA-binding proteins computationally and validates them experimentally, achieving high specificity and affinity for target sequences.

This study identifies and characterizes the PglZ:BrxB sub-complex of BREX phage defence systems, revealing PglZ as a metal-dependent nuclease that contributes to phage defence.

The paper identifies and characterizes the BrxR protein and its gene in a BREX phage restriction system from Acinetobacter, showing its role in restriction and cis regulation.

The paper examines how mutations during transcription and genome replication can affect HR-mediated gene drive systems based on different nuclease platforms, highlighting the risk of retargeting and the need for risk assessment.