Dr. Andrew Doxey

Division of Respirology

Dr. Andrew Doxey

PhD Bioinformatics, BSc Biology

Assistant Clinica Professor (Adjunct), Division of Respirology, Department of Medicine






Research Interests

Andrew Doxey is a bioinformatician with research interests in biological data mining, protein function prediction, and comparative and evolutionary genomics.

The Doxey Lab develops computational methods to predict novel molecular or systems-level functions from genomes and other “omics” datasets. Current efforts are focused largely on uncharacterized proteins from newly sequenced microbial genomes and metagenomes.

The Doxey Lab combines both “dry” (computational) and “wet” (biochemical/molecular) approaches, and works closely with a diverse range of local and international collaborators.

Selected Publications

  1. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Mendler K, Chen H, Parks DH, Hug LA, Doxey AC. bioRxiv (2018) 463455. [link]
  2. Identification of a diphtheria toxin like gene family beyond the Corynebacterium genus. Mansfield MJ, Sugiman-Marangos S, Melnyk RA, Doxey AC. FEBS Lett. (2018) 592:2693-2705. [doi]
  3. Metagenomic Sequencing of Wastewater from a South African Research Farm. Lobb B, Adegoke AA, Ma K, Doxey AC, Aiyegoro OA. Microbiol Res Announc. (2018) 7:e01323-18. [link]
  4. Genomic insights into the evolution and ecology of botulinum neurotoxins. Mansfield MJ, Doxey AC. Pathog Dis. (2018) 76. [doi]
  5. The impact of cigarette smoke exposure, and COPD or asthma status on ABC transporter gene expression in human airway epithelial cells. Aguiar JA, Tamminga A, Lobb B, Huff RD, Nguyen J, Kim Y, Dvorkin-Gheva A, Stampfli MR, Doxey AC, Hirota JA. bioRxiv (2018) 369355. [doi]
  6. Draft genome sequences of two novel cellulolytic Streptomyces strains isolated from South African rhizosphere soil. Adegboye MF, Lobb B, Babalola OO, Doxey AC, Ma K. Genome Announc. (2018) 6:e00632-18. [doi]
  7. Discovery of novel bacterial toxins by genomics and computational biology. Doxey AC*, Mansfield MJ, Montecucco C*. (co-corresponding authors) Toxicon. (2018) 147:2-12. [pubmed]
  8. Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. 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] Press coverage: ScienceDailyGenEngNewsHarvardMedical
  9. Metagenomic analysis of aerobic proteobacterial methylotrophs in Movile Cave ecosystem. Kumaresan D, Stephenson J, Doxey AC, Bandukwala H, Brooks E, Hillebrand-Voiclueseu A, Whiteley AS and Murrell JC. Microbiome. (2018) 6:1. [pubmed]
  10. Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height. Guo M, Liu Z, Willen J, Shaw CP, Richard D, Jagoda E, Doxey AC, Hirschhorn, Capellini TD. eLife (2017) 6:e29329. [link]
  11. Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution. Kuc C, Richard DJ, Johnson S, Bragg L, Servos MR, Doxey AC, Craig PM. Scientific Reports (2017) 7:16843. [link]
  12. Newly identified relatives of botulinum neurotoxins shed light on their molecular evolution. Mansfield MJ, Wentz TG, Zhang S, Lee EJ, Dong M, Sharma SK, Doxey AC. bioRxiv preprint [link]
  13. Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. 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] Press coverage: ScienceDailyPhys.Org
  14. Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Capellini TD, Chen H, Cao J, Doxey AC, Kiapour K, Schoor M, Kingsley DM. Nature Genetics. (2017) 49:1202–1210. [pubmed] Press coverage: ScienceDaily,New York Times, GenomeWeb Highlighted in Nature Genetics News and Views Access the recommendation on F1000Prime
  15. Estrogen receptor beta is a novel target in acute myeloid leukemia. 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]
  16. Transcriptome analysis of PHB cycle mutants reveals discrete loci connecting nitrogen utilization and carbon storage in Sinorhizobium meliloti D'Alessio M, Nordeste R, Doxey AC, Charles TC. mSystems. (2017) 2:e00035-17. [pubmed]
  17. The skin microbiome of cohabitating couples. Ross A, Doxey AC, Neufeld JD. mSystems. (2017) 2:e00043-17. [pubmed] Press coverage: [New York Times][Popular Science][ScienceDaily]
  18. Functional metagenomics reveals novel beta-galactosidases not predictable from gene sequences. Cheng J, Romantsov R, Engel J, Doxey AC, Rose DR, Neufeld JD, Charles T. PLoS One. (2017) 12:e0172545. [pubmed]
  19. Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. Adams J, Mansfield MJ, Richard DJ, Doxey AC. Bioinformatics. (2017) 33:1338-1345. [pubmed]
  20. Active agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD. Environmental Microbiology. (2017) 12:e0172545. [pubmed]
  21. Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y Microbial Genomics. (2016) 2, doi: 10.1099/mgen.0.000080. [DOI]
  22. Novel function discovery through sequence and structural data mining. Lobb B, Doxey AC. Current Opinion in Structural Biology. (2016) 38:53-61. [pubmed]
  23. MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. Petrenko P, Lobb B, Kurtz DA, Neufeld JD, Doxey AC. BMC Biology. (2015) 13:92. [pubmed] Blog: [Microbe.net]
  24. Remote homology and the functions of metagenomic dark matter. 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. Doxey AC*, Kurtz D, Sauder L, Lynch MDJ, Neufeld JD*. (co-corresponding authors) ISME Journal. (2015) 9, 461–471. [pubmed] Press coverage: [ScienceDaily]
  26. Botulinum neurotoxin homologs in non-Clostridium species. Mansfield M, Adams J, Doxey AC. FEBS Letters. (2015) 589:342-8. [pubmed]
  27. mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. Petrenko P, Doxey AC. Bioinformatics. (2015) 31:590-2. [pubmed] Resource: mimicme.uwaterloo.ca
  28. Prediction of molecular mimicry candidates in human pathogenic bacteria. Doxey AC, McConkey BJ. Virulence. (2013) 4:1-14. [pubmed]
  29. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Guturu H*, Doxey AC*, Wenger AM, Bejerano G. Philosophical Transactions of the Royal Society B. (2013) 368:20130029. [pubmed] Resource: mimicme.uwaterloo.ca
  30. 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. 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]
  31. Modular evolution and the origins of symmetry: design of a threefold symmetric globular protein. 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
  32. Nuclear targeting of methyl-recycling enzymes is mediated by specific protein interactions in Arabidopsis thaliana. Lee S, Doxey AC, McConkey BJ, Moffatt BA. Molecular Plant. (2012) 5:231-48. [pubmed]
  33. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. Doxey AC, Cheng Z, Moffatt BA, McConkey BJ. BMC Structural Biology. (2010) 10:23. [pubmed]
  34. Discrimination of insoluble-carbohydrate binding proteins and their binding sites using a 3D motif detection method. Doxey AC, Cheng Z, McConkey BJ. BIBM. (2008) pp 207-213. [available here]
  35. Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum A neurotoxin gene cluster. Doxey AC, Lynch MDJ, Muller KM, Meiering EM, McConkey BJ. BMC Evolutionary Biology. (2008) 8:316. [pubmed]
  36. Assessing the evolution of gene expression using microarray data. Woody OZ, Doxey AC, McConkey BJ. Evolutionary Bioinformatics. (2008) 4:139-152. [pubmed]
  37. Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states. Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ. Molecular Biology and Evolution. (2007) 24:1045-1055. [pubmed]
  38. Cold Active Winter Rye Glucanases with Ice-Binding Capacity. Yaish MW, Doxey AC, McConkey BJ, Moffatt BA, Griffith M. Plant Physiology. (2006) 141:1459-1472. [pubmed]
  39. Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Doxey AC, Yaish MW, Griffith M, McConkey BJ. Nature Biotechnology. (2006) 24:852-5. [pubmed]