Andrew C. Doxey

The paper develops a new S-acylation prediction tool, SAPPTree, by integrating sequence and structural features from experimentally confirmed sites to improve prediction accuracy.

This study uses comparative proteomics to identify Ca2+-dependent adhesins involved in biofilm development in Pseudoalteromonas tunicata.

The paper identifies clostridial neurotoxin genes in ancient DNA samples, finding TeNT and botulinum neurotoxin genes in 1.6% of datasets.

The paper identifies a novel botulinum neurotoxin-like gene cluster in Furfurilactobacillus sp. OKN36, encoding a toxin with structural similarities to clostridial neurotoxins but significant sequence divergence.

The paper uses AlphaFold 3 and DALI to predict structures and functions of viral genes in cyanophages, identifying 28 new structural homologs including cyanobacteriochrome.

AnnoView provides a web tool for exploring and comparing gene neighborhoods across microbial genomes, supporting both large databases and user-uploaded datasets.

The paper identifies a novel botulinum neurotoxin-like gene cluster in Bacillus toyonensis, showing it shares structural and functional features with known BoNTs.

The paper identifies two divergent botulinum neurotoxin homologs in Paeniclostridium ghonii and characterizes their structural and functional features.

The paper identifies ancient Clostridium tetani genomes and TeNT variants from archaeological remains, revealing new species and a pathogenic toxin variant.

This paper identifies intronic regulatory elements of ACE2 that respond to immune signaling and oxidative stress, influencing ACE2 expression and viral susceptibility.

AnnoTree visualizes and explores functional annotations across 24,000 bacterial genomes, revealing widespread phylogenetic patchiness in gene families.

The paper identifies new relatives of botulinum neurotoxins in environmental bacteria, revealing their evolutionary origins and divergence from related toxin families.

The paper analyzes ABC transporter gene expression in human airway epithelial cells under cigarette smoke, COPD, and asthma conditions, identifying differentially expressed transporters and validating findings with an in vitro model.

This study compares the effects of cannabis and tobacco smoke on human airway epithelial cells, showing similar impairments in barrier function and antiviral responses, with no benefit from formoterol/budesonide treatment.