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个人简介

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. Bioinformatics Computational Biology Molecular Genetics International Society for Computational Biology American Association for the Advancement of Science 2010 PhD Bioinformatics, University of Waterloo 2005 BSc Biology, University of Waterloo

研究领域

Due to continual advances in sequencing and other “omics” technologies, biology is experiencing a big data revolution. Computational methods are required not only to interpret newly sequenced genomes, but search through a vast quantity of existing biological information to reveal previously uncharacterized functionality. The Doxey lab is interested in both the development and application of computational methods to predict novel molecular functions (protein-coding and non-coding) from genomic, structural, and other high-throughput datasets. We explore three separate but overlapping areas: Predicting novel protein families and functions: We develop methods that combine sequence analysis with structural bioinformatics to predict and experimentally validate protein functions of interest. Currently, we are focusing efforts on predicting new families and functions of bacterial flagellins, clostridial toxins, and proteolytic enzymes. Predicting evolutionary adaptations in genes and genomes: We combine sequence analysis, phylogenetics and structural modeling to pinpoint adaptive events in genes and genomes. We are interested in inferring mechanisms of neofunctionalization and functional divergence in protein families as well as non-coding regulatory elements. Comparative functional metagenomics: The Doxey Lab is also developing computational approaches to functionally annotate metagenomes and detect biologically relevant differences between them. Recent work includes the development of the MetAnnotate framework for combined taxonomic and functional profiling of metagenomic datasets. Professor Doxey actively seeks eager and talented graduate or undergraduate students interested in bioinformatics, genomics, or molecular biology.

近期论文

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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 {biorxiv preprint here}. 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] Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD. (2016) Active agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environmental Microbiology, Advance online publication: [pubmed] 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] Lobb B, Doxey AC. (2016) Novel function discovery through sequence and structural data mining. Current Opinion in Structural Biology, 38:53-61. [pubmed] 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] Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC. (2015) Remote homology and the functions of metagenomic dark matter. Frontiers in Genetics. [pubmed] Mansfield M, Adams J, Doxey AC. (2015) Botulinum neurotoxin homologs outside of Clostridium. FEBS Letters, 589:342-8. [pubmed] 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] 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] 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] Doxey AC, McConkey BJ. (2013) Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence, 4:1-14. [pubmed] 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] 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] 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] 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] 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] 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] Woody OZ, Doxey AC, McConkey BJ. (2008) Assessing the evolution of gene expression using microarray data. Evolutionary Bioinformatics, 4: 139-152. [pubmed] 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] 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] 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] 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]

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