Publications

    2017

  1. Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella.
  2. Eckhard U, Bandukwala H, Mansfield MJ, Marino G, Cheng J, Wallace I, Holyoak T, Charles TC, Austin JW, Overall CM, Doxey AC.

    Nature Communications. (2017, in press)


  3. Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk.
  4. Capellini TD, Chen H, Cao J, Doxey AC, Kiapour K, Schoor M, Kingsley DM.

    Nature Genetics. (2017) 49:1202–1210 [pubmed]


  5. Estrogen receptor beta is a novel target in acute myeloid leukemia.
  6. Rota SG, Roma A, Dude I, Ma C, Stevens R, MacEachern J, Gracyzk J, Espiritu SM, Nekkar P, Minden MD, Kreinin E, Hess D, Doxey AC, Spagnuolo PA.

    Molecular Cancer Therapy. (2017, in press)


  7. Transcriptome analysis of PHB cycle mutants reveals discrete loci connecting nitrogen utilization and carbon storage in Sinorhizobium meliloti
  8. D'Alessio M, Nordeste R, Doxey AC, Charles TC.

    mSystems. (2017, in press)


  9. The skin microbiome of cohabitating couples.
  10. Ross A, Doxey AC, Neufeld JD.

    mSystems. (2017) 2:e00043-17.


  11. Functional metagenomics reveals novel beta-galactosidases not predictable from gene sequences.
  12. Cheng J, Romantsov R, Engel J, Doxey AC, Rose DR, Neufeld JD, Charles T.

    PLoS One. (2017) 12:e0172545. [pubmed]


  13. Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function.
  14. Adams J, Mansfield MJ, Richard DJ, Doxey AC.

    Bioinformatics. (2017) 33:1338-1345. [pubmed]


  15. Active agricultural soil denitrifiers possess extensive nitrite reductase gene diversity.
  16. Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD.

    Environmental Microbiology. (2017) 12:e0172545. [pubmed]


    2016

  17. Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.
  18. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y.

    Microbial Genomics. (2016) 2, doi: 10.1099/mgen.0.000080. [DOI]


  19. Novel function discovery through sequence and structural data mining.
  20. Lobb B, Doxey AC.

    Current Opinion in Structural Biology. (2016) 38:53-61. [pubmed]


    2015

  21. MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.
  22. Petrenko P, Lobb B, Kurtz DA, Neufeld JD, Doxey AC.

    BMC Biology. (2015) 13:92. [pubmed]


  23. Remote homology and the functions of metagenomic dark matter.
  24. Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC.

    Frontiers in Genetics (2015) 6:234. [pubmed]


  25. Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.
  26. Doxey AC*, Kurtz D, Sauder L, Lynch MDJ, Neufeld JD*. (co-corresponding authors)

    ISME Journal. (2015) 9, 461–471. [pubmed]


  27. Botulinum neurotoxin homologs in non-Clostridium species.
  28. Mansfield M, Adams J, Doxey AC.

    FEBS Letters. (2015) 589:342-8.. [pubmed]


  29. mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens.
  30. Petrenko P, Doxey AC.

    Bioinformatics. (2015) 31:590-2. [pubmed]

    Resource: mimicme.uwaterloo.ca


    2013

  31. Prediction of molecular mimicry candidates in human pathogenic bacteria.
  32. Doxey AC, McConkey BJ.

    Virulence. (2013) 4:1-14. [pubmed]


  33. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.
  34. Guturu H*, Doxey AC*, Wenger AM, Bejerano G.

    Philosophical Transactions of the Royal Society B. (2013) 368:20130029. [pubmed]

    Resource: mimicme.uwaterloo.ca


    2012

  35. 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.
  36. 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.

    PLoS One. (2012) 7:e52278. [pubmed]


  37. Modular evolution and the origins of symmetry: design of a threefold symmetric globular protein.
  38. Broom A*, Doxey AC*, Lobsanov Y, Howell PL, Rose DR, McConkey BJ, Meiering EM.

    Structure. (2012) 20:161-71. [pubmed]

    • Access the recommendation on F1000Prime


  39. Nuclear targeting of methyl-recycling enzymes is mediated by specific protein interactions in Arabidopsis thaliana.
  40. Lee S, Doxey AC, McConkey BJ, Moffatt BA.

    Molecular Plant. (2012) 5:231-48. [pubmed]


    2006-2012

  41. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.
  42. Doxey AC, Cheng Z, Moffatt BA, McConkey BJ.

    BMC Structural Biology. (2010) 10:23. [pubmed]


  43. Discrimination of insoluble-carbohydrate binding proteins and their binding sites using a 3D motif detection method.
  44. Doxey AC, Cheng Z, McConkey BJ.

    BIBM. (2008) pp 207-213. [available here]


  45. Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum A neurotoxin gene cluster.
  46. Doxey AC, Lynch MDJ, Muller KM, Meiering EM, McConkey BJ.

    BMC Evolutionary Biology. (2008) 8:316. [pubmed]


  47. Assessing the evolution of gene expression using microarray data.
  48. Woody OZ, Doxey AC, McConkey BJ.

    Evolutionary Bioinformatics. (2008) 4:139-152. [pubmed]


  49. Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states.
  50. Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ.

    Molecular Biology and Evolution. (2007) 24:1045-1055. [pubmed]


  51. Cold Active Winter Rye Glucanases with Ice-Binding Capacity.
  52. Yaish MW, Doxey AC, McConkey BJ, Moffatt BA, Griffith M.

    Plant Physiology. (2006) 141:1459-1472. [pubmed]


  53. Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.
  54. Doxey AC, Yaish MW, Griffith M, McConkey BJ.

    Nature Biotechnology. (2006) 24:852-5. [pubmed]