Publications

See here for our publications at google scholar

    Preprints

  1. Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses.
  2. Banerjee A, El-Sayes N, Budylowski P, Richard D, Maan H, Aguiar JA, Baid K, D’Agostino MR, Ang JA, Tremblay BJM, Afkhami A, Karimzadeh M, Irving AT, Yip L, Ostrowski M, Hirota JA, Kozak R, Capellini TD, Miller MS, Wang B, Mubareka S, McGeer AJ, McArthur AG, Doxey AC, Mossman K.

    bioRxiv (2020). [doi]


  3. Potentiation of Long-Acting β2-Agonist and Glucocorticoid Responses in Human Airway Epithelial Cells by Modulation of Intracellular cAMP.
  4. Kim Y, Hou V, Huff RD, Aguiar JA, Revill S, Tiessen N, Cao Q, Miller MS, Inman MD, Ask K, Doxey AC, Hirota JA.

    bioRxiv (2020). [doi]


    2020

  5. PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling.
  6. Tremblay BJM, Lobb B, Doxey AC.

    Bioinformatics (2020) Forthcoming.


  7. Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2.
  8. Banerjee A, Doxey AC, Mossman K, Irving AT.

    Trends in Ecology and Evolution (2020) epub online ahead of print. [doi]


  9. Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis.
  10. Eckhard U. Blöchl C, Jenkins B, Mansfield M, Huber C, Doxey AC, Brandstetter H.

    Scientific Reports (2020) 10(1):19052. [pubmed]


  11. Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell® culture inserts.
  12. Chandiramohan A, Dabaghi M, Aguiar JA, Tiessen N, Stewart M, Cao Q, Nguyen JP, Makhdami N, Cox G, Doxey AC, Hirota JA.

    ERJ Open (2020) epub ahead of print. [link]


  13. High throughput sequencing of microRNA in rainbow trout plasma, mucus, and surrounding water following acute stress.
  14. Ikert H, Lynch MDJ, Doxey AC, Giesy JP, Servos MR, Katzenback BA, Craig PM.

    Frontiers in Physiology (2020) To appear.


  15. Predicting the recombination potential of SARS-CoV-2 and MERS-CoV.
  16. Banerjee A, Doxey AC, Tremblay BJM, Mansfield MJ, MacKay K, MacKenzie K, Poinar H, Hirota J, McArthur AG, Miller MS, Mubareka S, Mossman K.

    Journal of General Virology (2020) 101(12):1251-1260. [pubmed]


  17. Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue.
  18. Aguiar JA, Tremblay BJM, Mansfield MJ, Woody O, Lobb B, Banerjee A, Chandiramohan A, Tiessen N, Dvorkin-Gheva A, Revill S, Miller M, Carlsten C, Organ L, Joseph C, John A, Jenkins G, Mossman K, Ask K, Doxey AC, Hirota JA.

    European Respiratory Journal (2020) 2001123. [pubmed]


  19. Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B.
  20. Mansfield MJ, Tremblay J-M, Zeng J, Wei X, Hodgins H, Worley J, Bry L, Dong M, Doxey AC.

    PLOS Pathogens (2020). epub ahead of print. [pubmed]


  21. Slr4, a newly identified S-layer protein from marine Gammaproteobacteria is a major biofilm matrix component.
  22. Ali S, Jenkins B, Cheng J, Lobb B, Egan S, Charles TC, McConkey BJ, Austin J, Doxey AC.

    Molecular Microbiology (2020). epub ahead of print. [pubmed]


  23. Expression of the endocannabinoid system in the human airway epithelial cells: Impact of sex and chronic respiratory disease status.
  24. Fantauzzi MF, Aguiar JA, Tremblay BJM, Yanagihara T, Chandiramohan A, Revill S, Hyung MR, Carlsten C, Ask K, Stämpfli M, Doxey AC, Hirota JA.

    ERJ Open Research (2020) 6: 00128-2020. [link]


  25. ABCF1 regulates dsDNA-induced immune responses in human airway epithelial cells.
  26. Cao QT, Aguiar JA, Tremblay BJM, Abbas N, Tiessen AA, Makhdami N, Revill S, Cox G, Ask K, Doxey AC, Hirota JA.

    Frontiers in Cellular and Infection Microbiology (2020) 10:487. [pubmed]


  27. Time-series resolution of the fish necrobiome reveals a microbial succession involving toxigenic pathogens.
  28. Lobb B, Hodgson R, Lynch MDJ, Mansfield MJ, Cheng J, Charles TC, Neufeld JD, Craig PM, Doxey AC.

    mSystems (2020) 5(2):e00145-20. [link]


  29. Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae.
  30. Bano L, Kiel M, Sales G, Doxey AC, Mansfield MJ, Schiiavone M, Rossetto O, Pirazzini M, Dobrindt U, Montecucco C.

    Microbiology Resource Announcements (2020) 9:e01575-19. [link]


  31. High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.
  32. Spasov E, Tsuji JM, Hug LA, Doxey AC, Sauder LA, Parker WJ, Neufeld JD.

    ISME J (2020) 14(7):1857-1872. [pubmed]


  33. An assessment of genome annotation coverage across the bacterial tree of life.
  34. Lobb BA, Tremblay B, Moreno-Hagelsieb G, Doxey AC.

    Microbial Genomics (2020) 6(3). [doi]


  35. The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus.
  36. Orrell KE, Mansfield MJ, Doxey AC, Melnyk RA.

    Nature Communications (2020) 11:432. [doi]


  37. Effect of long-acting β-agonists/glucocorticoids on human airway epithelial cell cytokine, transcriptomic and oxidative stress responses to cannabis smoke.
  38. Huff RD, Aguiar JA, Tse W, Stämpfli MR, McConkey BJ, Doxey AC, Hirota JA.

    ERJ Open Research (2020) 6: 00265-2019. [doi]


    2019

  39. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.
  40. Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC.

    Nucleic Acids Research (2019) 47:4442–4448. [link]


  41. A study of Nitric Oxide dynamics in a growing biolm using a density dependent reaction-diffusion model.
  42. Ghasemi M, Jenkins B, Doxey AC, Sivaloganathan S.

    Journal of Theoretical Biology (2019) 485:110053. [pubmed]


  43. Metagenomic and chemical characterization of soil cobalamin production.
  44. Lu X, Heal KR, Ingalls AE, Doxey AC, Neufeld JD.

    ISME J (2019) 14:53–66. [link]


  45. Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke.
  46. Aguiar JA, Huff RD, Tse W, Stampfli MR, McConkey BJ, Doxey AC*, Hirota JA*.

    Physiology Reports (2019) 7(20):e14249. [link]


  47. Pygenprop: a python library for interactive programmatic exploration and comparison of organism Genome Properties.
  48. Bergstrand L, Neufeld JD*, Doxey AC*.

    Bioinformatics (2019) 35(23):5063-5065. [pubmed]


  49. Exploring the evolution of virulence factors through bioinformatic data mining.
  50. Doxey AC, Mansfield MJ, Lobb BA.

    mSystems (2019) 4:e00162-19. [link]


  51. Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins.
  52. Mansfield MJ, Wentz T, Zhang S, Lee EJ, Dong M, Sharma S, Doxey AC.

    Scientific Reports (2019) 9:1634. [link]


  53. The impact of cigarette smoke exposure, and COPD or asthma status on ABC transporter gene expression in human airway epithelial cells.
  54. Aguiar JA, Tamminga A, Lobb B, Huff RD, Nguyen J, Kim Y, Dvorkin-Gheva A, Stampfli MR, Doxey AC, Hirota JA.

    Scientific Reports (2019) 9:153. [link]


  55. Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
  56. Brown P, RELISH Consortium*, & Zhou Y.

    Database (2019) 2019:baz085. [doi]


    2018

  57. Identification of a diphtheria toxin like gene family beyond the Corynebacterium genus.
  58. Mansfield MJ, Sugiman-Marangos S, Melnyk RA, Doxey AC.

    FEBS Lett. (2018) 592:2693-2705. [doi]


  59. Metagenomic Sequencing of Wastewater from a South African Research Farm.
  60. Lobb B, Adegoke AA, Ma K, Doxey AC, Aiyegoro OA.

    Microbiol Res Announc. (2018) 7:e01323-18. [link]


  61. Genomic insights into the evolution and ecology of botulinum neurotoxins.
  62. Mansfield MJ, Doxey AC.

    Pathog Dis. (2018) 76. [doi]


  63. Draft genome sequences of two novel cellulolytic Streptomyces strains isolated from South African rhizosphere soil.
  64. Adegboye MF, Lobb B, Babalola OO, Doxey AC, Ma K.

    Genome Announc. (2018) 6:e00632-18. [doi]


  65. Discovery of novel bacterial toxins by genomics and computational biology.
  66. Doxey AC*, Mansfield MJ, Montecucco C*. (co-corresponding authors)

    Toxicon. (2018) 147:2-12. [pubmed]


  67. Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium.
  68. Zhang S, Lebreton F, Mansfield MJ, Miyashita S, Zhang J, Schwartzman JA, Tao L, Masuyer G, Martinez-Carranza M, Stenmark P, Gilmore MS, Doxey AC*, Dong M*. (co-corresponding authors)

    Cell Host & Microbe. (2018) 23:1-8. [link]


  69. Metagenomic analysis of aerobic proteobacterial methylotrophs in Movile Cave ecosystem.
  70. Kumaresan D, Stephenson J, Doxey AC, Bandukwala H, Brooks E, Hillebrand-Voiclueseu A, Whiteley AS and Murrell JC.

    Microbiome. (2018) 6:1. [pubmed]


    2017

  71. Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height.
  72. Guo M, Liu Z, Willen J, Shaw CP, Richard D, Jagoda E, Doxey AC, Hirschhorn, Capellini TD.

    eLife (2017) 6:e29329. [link]


  73. Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution.
  74. Kuc C, Richard DJ, Johnson S, Bragg L, Servos MR, Doxey AC, Craig PM.

    Scientific Reports (2017) 7:16843. [link]


  75. Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella.
  76. 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) 8:521. [link]


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

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


  79. Estrogen receptor beta is a novel target in acute myeloid leukemia.
  80. 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) 16:2618-2626. [pubmed]


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

    mSystems. (2017) 2:e00035-17. [pubmed]


  83. The skin microbiome of cohabitating couples.
  84. Ross A, Doxey AC, Neufeld JD.

    mSystems. (2017) 2:e00043-17. [pubmed]


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

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


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

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


  89. Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity.
  90. Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD.

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


    2016

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

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


  93. Novel function discovery through sequence and structural data mining.
  94. Lobb B, Doxey AC.

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


    2015

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

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


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

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


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

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


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

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


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

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

    Resource: mimicme.uwaterloo.ca


    2013

  105. Prediction of molecular mimicry candidates in human pathogenic bacteria.
  106. Doxey AC, McConkey BJ.

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


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

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

    Resource: mimicme.uwaterloo.ca


    2012

  109. 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.
  110. 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]


  111. Modular evolution and the origins of symmetry: design of a threefold symmetric globular protein.
  112. 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


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

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


    2006-2012

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

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


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

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


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

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


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

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


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

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


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

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


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

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