Browsing Science (Faculty of) by Supervisor "Doxey, Andrew"
Now showing items 1-11 of 11
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Bioinformatic insights into the diversity and evolution of bacterial toxins
(University of Waterloo, 2020-01-24)Bacterial toxins are a broad category of molecules ranging from small organic compounds and peptides to large multi-domain or multi-meric enzymes. Several important diseases are caused primarily by bacterial toxins including ... -
Bioinformatic Insights into the Impacts of External Stimuli on the Human Airway
(University of Waterloo, 2021-12-21)The airway epithelium represents a critical component of the human lung that helps orchestrate defences against inhaled substances including air pollution, allergens, bacteria, and viruses. To manage these continuous ... -
Comparative metagenomics of PHA synthase genes in soil
(University of Waterloo, 2017-01-19)Polyhydroxyalkanoates (PHAs) are biopolymers produced naturally by bacteria. They are of considerable scientific interest as fundamental components of bacterial carbon metabolism and have biotechnological applications as ... -
Deciphering the Toxicity Effects of 5′-Methylthioadenosine Accumulation in Arabidopsis thaliana
(University of Waterloo, 2021-09-29)Metabolic constraints imposed by extreme environmental fluctuations are an inescapable reality for sessile organisms such as plants. To survive, they finely tune their metabolic activity to adapt their growth to the ... -
Experimental characterization of a catalytically active flagellin variant in Clostridium haemolyticum
(University of Waterloo, 2017-04-18)The bacterial flagellum is made up of approximately 20,000 subunits of the monomeric protein, flagellin, and plays a role in cell motility and pathogenesis. The extreme sequence diversity within the hypervariable region ... -
Exploring functional annotation through genomic and metagenomic data mining
(University of Waterloo, 2020-09-09)Functional profiling of genomes and metagenomes, as well as data mining for novel proteins, all rely on computational methods for functional annotation of protein sequences. Standard methods assign protein function based ... -
Genome analysis reveals unexpected absence of oxygen metabolic capacity in helminths
(University of Waterloo, 2022-07-06)Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms must be able to switch between aerobic and anaerobic metabolisms depending on their life-cycle stage. ... -
Large-scale phylogenomic visualization and analysis of functional traits in bacteria
(University of Waterloo, 2019-01-24)The growth of genomic information in public databases has dramatically improved our view of the tree of life and at the same time expanded our knowledge of protein diversity. Through the use of automated annotation pipelines, ... -
Micromeda: a genome property prediction pipeline and web visualization tool
(University of Waterloo, 2020-05-07)Understanding the distribution of biochemical pathways across microorganisms is critical to understanding these organism's evolution, ecology, and industrial applicability. Advances in genome sequencing and pathway databases ... -
Petabase-scale Data Mining Identifies Novel Clostridial Species and Neurotoxins Associated with Ancient Human DNA
(University of Waterloo, 2022-09-08)Analyzing microbial genomes found in archaeological samples can provide insights into the origins of modern infectious diseases. A large-scale metagenomic analysis of archeological samples discovered bacterial species ... -
Structure-aided detection of functional innovation in protein phylogenies
(University of Waterloo, 2016-01-19)Detection of positive selection in proteins is both a common and powerful approach for investigating the molecular basis of adaptation. In this thesis, I explore the use of protein three- dimensional (3D) structure to ...