Browsing Theses by Subject "Bioinformatics"
Now showing items 1-14 of 14
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Algorithms for Characterizing Peptides and Glycopeptides with Mass Spectrometry
(University of Waterloo, 2013-09-26)The emergence of tandem mass spectrometry (MS/MS) technology has significantly accelerated protein identification and quantification in proteomics. It enables high-throughput analysis of proteins and their quantities in a ... -
Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters
(University of Waterloo, 2015-10-30)Bioinformatics is a rapidly expanding field of research due to multiple recent advancements: 1) the advent of machine intelligence, 2) the increase of computing power, 3) our better understanding of the underlying biomolecular ... -
Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction
(University of Waterloo, 2004)This thesis investigates the correlations between short protein peptide sequences and local tertiary structures. In particular, it introduces a novel algorithm for partitioning short protein segments into clusters of ... -
Effective Strategies for Improving Peptide Identification with Tandem Mass Spectrometry
(University of Waterloo, 2011-12-21)Tandem mass spectrometry (MS/MS) has been routinely used to identify peptides from protein mixtures in the field of proteomics. However, only about 30% to 40% of current MS/MS spectra can be identified, while many of them ... -
Finding Similar Protein Structures Efficiently and Effectively
(University of Waterloo, 2014-04-24)To assess the similarities and the differences among protein structures, a variety of structure alignment algorithms and programs have been designed and implemented. We introduce a low-resolution approach and a ... -
Improving Spatial Resolution of and Error Estimation for Radical Probe Mass Spectrometry
(University of Waterloo, 2015-09-23)The function of a protein depends on the structure of the protein. A commonly used analytical technique for studying protein structure is radical-probe mass spectrometry (RP-MS). RP-MS oxidizes a protein of interest then ... -
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 ... -
Optimization of SPME coating characteristics for metabolomics and targeted analysis with LC/MS
(University of Waterloo, 2015-09-23)Metabolomics data provides complementary information to proteomics, genomics, and transcriptomics, in addition to enabling the tracking of the dynamic reactions in living systems. Metabolomics is widely used in various ... -
The Power Landmark Vector Learning Framework
(University of Waterloo, 2008-05-12)Kernel methods have recently become popular in bioinformatics machine learning. Kernel methods allow linear algorithms to be applied to non-linear learning situations. By using kernels, non-linear learning problems can ... -
Sequence Analysis of the Bacterial Protein Elongation Factor P
(University of Waterloo, 2008-01-24)In 1975, Elongation Factor P (EF-P) protein was first discovered in the bacterium Escherichia coli. EF-P is believed to facilitate the translation of proteins by stimulating peptide bond synthesis for a number of different ... -
SPIDER: Reconstructive Protein Homology Search with De Novo Sequencing Tags
(University of Waterloo, 2011-04-21)In the field of proteomic mass spectrometry, proteins can be sequenced by two independent yet complementary algorithms: de novo sequencing which uses no prior knowledge and database search which relies upon existing protein ... -
Tracing the molecular and evolutionary determinants of novel functions in protein families
(University of Waterloo, 2010-03-29)This thesis explores the limits of homology-based inference of protein function and evolution, where overall similarity between sequences can be a poor indicator of functional similarity or evolutionary relationships. Each ... -
Training of Template-Specific Weighted Energy Function for Sequence-to-Structure Alignment
(University of Waterloo, 2008-09-26)Threading is a protein structure prediction method that uses a library of template protein structures in the following steps: first the target sequence is matched to the template library and the best template structure ... -
Using Metagenomic Approaches to Determine Antimicrobial Resistance Diversity and Prevalence within Four Landfills
(University of Waterloo, 2023-08-21)Antibiotics are one of the many hazardous substances present in municipal solid waste (MSW) landfills. Antibiotics can contaminate the leachate generated in landfills, which poses a threat to human health as leachate ...