Publications

    2017

  1. Capellini TD, Chen H, Cao J, Doxey AC, Kiapour K, Schoor M, Kingsley DM. (2017) Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nature genetics. Advance online publication: [link]
  2. Ross A, Doxey AC, Neufeld JD. (2017) The skin microbiome of cohabitating couples. mSystems (to appear)
  3. Cheng J, Romantsov R, Engel J, Doxey AC, Rose DR, Neufeld JD, Charles T. (2017) Functional metagenomics reveals novel beta-galactosidases not predictable from gene sequences. PLoS ONE, 12:e0172545. [pubmed].
  4. Adams J, Mansfield MJ, Richard DJ, Doxey AC. (2017) Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. Bioinformatics, Advance online publication: [pubmed]
  5. Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD. (2017) Active agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environmental Microbiology, 19:1189-1208. [pubmed]
  6. 2016

  7. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y. (2016) Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microbial Genomics. Advance online publication: [doi]
  8. Lobb B, Doxey AC. (2016) Novel function discovery through sequence and structural data mining. Current Opinion in Structural Biology, 38:53-61. [pubmed]
  9. 2015

  10. Petrenko P, Lobb B, Kurtz DA, Neufeld JD, Doxey AC. (2015) MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. BMC Biology, 13:92. [pubmed]
  11. Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC. (2015) Remote homology and the functions of metagenomic dark matter. Frontiers in Genetics. [pubmed]
  12. Mansfield M, Adams J, Doxey AC. (2015) Botulinum neurotoxin homologs outside of Clostridium. FEBS Letters, 589:342-8. [pubmed]
  13. Petrenko P, Doxey AC. (2015) mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens, Bioinformatics, 31:590-2. [pubmed]
  14. Doxey AC, Kurtz DA, Lynch MDJ, Sauder LA, Neufeld JD. (2015) Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J, 9:461-71. [pubmed]
  15. 2013

  16. Guturu H*, Doxey AC*, Wenger AM, Bejerano G. (2013) Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philosophical Transactions of the Royal Society B, 368:20130029. [pubmed]
  17. Doxey AC, McConkey BJ. (2013) Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence, 4:1-14. [pubmed]
  18. 2012

  19. Bottger A, Doxey AC, Hess MW, Pfaller K, Salvenmoser W, Deutzmann R, Geissner A, Pauly B, Altstatter J, Munder S, Heim A, McConkey BJ, David CN. (2012) Horizontal gene transfer contributed to the evolution of extracellular surface structures: the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth) families. PLOS ONE, 7:e52278. [pubmed]
  20. Broom A*, Doxey AC*, Lobsanov Y, Howell PL, Rose DR, McConkey BJ, Meiering EM. (2012) Modular evolution and the origins of symmetry: design of a threefold symmetric globular protein. Structure, 20:161-71. *Co-first authors. [pubmed]
  21. Lee S, Doxey AC, McConkey BJ, Moffatt BA. (2012) Nuclear targeting of methyl-recycling enzymes is mediated by specific protein interactions in Arabidopsis thaliana. Molecular Plant, 5:231-48. [pubmed]
  22. 2006-2010

  23. Doxey AC, Cheng Z, Moffatt BA, McConkey BJ. (2010) Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC Structural Biology, 10:23. [pubmed]
  24. Doxey AC, Cheng Z, McConkey BJ. (2008) Discrimination of insoluble-carbohydrate binding proteins and their binding sites using a 3D motif detection method. BIBM 2008, pp 207-213. [available here]
  25. Doxey AC, Lynch MDJ, Muller KM, Meiering EM, McConkey BJ. (2008) Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum A neurotoxin gene cluster. BMC Evolutionary Biology, 8: 316. [pubmed]
  26. Woody OZ, Doxey AC, McConkey BJ. (2008) Assessing the evolution of gene expression using microarray data. Evolutionary Bioinformatics, 4: 139-152. [pubmed]
  27. Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ. (2007) Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states. Molecular Biology and Evolution, 24:1045-1055. [pubmed]
  28. Yaish MW, Doxey AC, McConkey BJ, Moffatt BA, Griffith M. (2006) Cold Active Winter Rye Glucanases with Ice-Binding Capacity. Plant Physiology, 141:1459-1472. [pubmed]
  29. Doxey AC, McConkey BJ. (2006) AFPredictor: a computational screening protocol for antifreeze/ice-structuring proteins. Nature protocol exchange. DOI: 10.1038/nprot.2006.213. [available here]
  30. Doxey AC, Yaish MW, Griffith M, McConkey BJ. (2006) Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Nature Biotechnology, 24:852-5. [pubmed]

Theses

  • Doxey AC. (2010) Tracing the molecular and evolutionary determinants of novel functions in protein families. Ph.D. Thesis. University of Waterloo. {Available here}.