Sean R. Johnson

Semirandom DNA adducts regulate a filamentous defence-associated reverse transcriptase

This study characterizes the DRT1 antiphage defence system, showing it generates semirandom DNA adducts that regulate filament assembly and function through structural changes.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Domainator identifies proteins involved in antiviral systems by clustering and analyzing domain-based gene neighborhoods and integrating a protein language model.

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

The paper demonstrates that positional embeddings from protein language models can improve sensitivity in homology detection without sacrificing search speed.

Discovery of novel DNA cytosine deaminase activities enables a nondestructive single-enzyme methylation sequencing method for base resolution high-coverage methylome mapping of cell-free and ultra-low input DNA

The paper discovers novel DNA cytosine deaminases and develops a nondestructive single-enzyme methylation sequencing method for high-coverage methylome mapping of low-input DNA.

Highly parallelized construction of DNA from low-cost oligonucleotide mixtures using Data-optimized Assembly Design and Golden Gate

The paper describes a method for efficiently constructing genes from low-cost oligonucleotide mixtures using Data-optimized Assembly Design and Golden Gate Assembly.

Generating novel protein sequences using Gibbs sampling of masked language models

The paper generates novel protein sequences using Gibbs sampling of BERT-style masked language models and evaluates their quality against natural sequences.