Dan M. Park

Efficient biological design via genomic in-context learning

This paper demonstrates that in-context learning in the genome language model Evo 2 enables efficient biological sequence design without additional training.

Unobserved Sequence Space Has Many Functional Proteins

The paper shows that unobserved protein sequence space contains many functional proteins, challenging the assumption that existing proteins cover most functional space.

A family portrait of lanmodulin selectivity for enhanced rare-earth separations

The paper develops a high-throughput assay to measure lanmodulin selectivity for rare-earth elements, identifying variants with enhanced separation capabilities.

Creating overlapping genes by alternate-frame insertion

This paper introduces a method to create overlapping genes by inserting an inner gene into an outer gene, demonstrating functionality and applications in synthetic biology.

GENTANGLE: integrated computational design of gene entanglements

GENTANGLE is a computational tool for designing overlapping gene pairs in microbial genomes, enabling safer genetic engineering through gene entanglements.

Prolonging Genetic Circuit Stability through Adaptive Evolution of Overlapping Genes

This paper demonstrates how sequence entanglement and adaptive evolution can stabilize synthetic genetic circuits by altering mutational landscapes and reducing circuit burden.

Comprehensive analysis of kill switch toxins in plant-beneficial Pseudomonas fluorescens reveals drivers of lethality, stability, and escape

The paper compares eight toxins in Pseudomonas fluorescens to assess their lethality, stability, and genetic escape, identifying factors that influence kill switch effectiveness.