Discrimination of Insoluble-Carbohydrate Binding Proteins and Their Binding Sites Using a 3D Motif Detection Method. - Andrew C. Doxey; Zhenyu Cheng 002; Brendan J. McConkey (BIBM, 2008)

mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. - Pavel Petrenko; Andrew C. Doxey (Bioinform., 2015)

Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. - Jeremy Adams; Michael J. Mansfield; Daniel J. Richard; Andrew C. Doxey (Bioinform., 2017)

Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties. - Lee H. Bergstrand; Josh D. Neufeld; Andrew C. Doxey (Bioinform., 2019)

PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. - Benjamin Jean-Marie Tremblay; Briallen Lobb; Andrew C. Doxey (Bioinform., 2021)

Gene function prediction using an AnnoTree-based genomic language model. - Huagang Tan; Gabriel Moreno-Hagelsieb; Andrew C. Doxey (BIBM, 2024)

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods. - Xin Wei; Huagang Tan; Briallen Lobb; William Zhen; Zijing Wu; Donovan H. Parks; Josh D. Neufeld; Gabriel Moreno-Hagelsieb; Andrew C. Doxey (Briefings Bioinform., 2024)