A5069661844- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Probiotics and Fermented Foods
- Antimicrobial Peptides and Activities
- vaccines and immunoinformatics approaches
- Microbial Natural Products and Biosynthesis
- Escherichia coli research studies
- S100 Proteins and Annexins
- Essential Oils and Antimicrobial Activity
- Microbial Metabolic Engineering and Bioproduction
- Intraperitoneal and Appendiceal Malignancies
- Oral microbiology and periodontitis research
- Image Processing Techniques and Applications
- Epigenetics and DNA Methylation
- Pancreatitis Pathology and Treatment
- Cell Image Analysis Techniques
- Banana Cultivation and Research
- Immune responses and vaccinations
- Mycobacterium research and diagnosis
- Sepsis Diagnosis and Treatment
- Neonatal Respiratory Health Research
University of British Columbia
2020-2024
The University of Sydney
2022
Nepean Hospital
2022
Canadian Institutes of Health Research
2022
Simon Fraser University
2011-2018
Dalhousie University
2013
The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches producing a high-quality aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other strains. To aid analysis potentially thousands complete draft assemblies, this database platform was upgraded to integrate curated annotations isolate metadata enhanced tools larger scale visualization. Manually gene are supplemented...
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial archaeal genomes. GIs are clusters genes probable horizontal origin, high interest since they disproportionately encode involved medically environmentally important adaptations, including antimicrobial resistance virulence. We now report major new release IslandViewer, last 2013. 3 incorporates completely genome visualization tool,...
The human pathogen Listeria monocytogenes is a large concern in the food industry where its continuous detection products has caused string of recalls North America and Europe. Most recognized for ability to grow foods during refrigerated storage, L. can also tolerate several other food-related stresses with some strains possessing higher levels tolerances than others. objective this study was use combination phenotypic analyses whole genome sequencing elucidate potential relationships...
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial archaeal genomes. GIs are clusters genes probable horizontal origin high interest because they disproportionately encode virulence factors other adaptations medical, environmental industrial interest. Many tools exist GIs, but three most accurate methods available integrated form via IslandViewer: IslandPath-DIMOB,...
Systems biology is an approach to interrogate complex biological systems through large-scale quantification of numerous biomolecules. The immune system involves >1,500 genes/proteins in many interconnected pathways and processes, a systems-level critical broadening our understanding the response vaccination. Changes molecular can be detected using high-throughput omics datasets (e.g. transcriptomics, proteomics, metabolomics) by methods such as pathway enrichment, network analysis, machine...
Significance The host environment in which infection occurs plays a crucial role the interaction between Pseudomonas aeruginosa and antibiotic treatments. To make up for lack of new antibiotics, alternative approaches, such as combination therapy discovery novel activity known antibiotics environment, are vital treatment pathogens P. aeruginosa. This research demonstrates how vitro conditions that closely mimic human more accurately reflect antimicrobial antibiotics. We have shown...
Understanding the RNA processing of an organism's transcriptome is essential but challenging step in understanding its biology. Here we investigate with unprecedented detail Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped cleavage dephosphorylation sites that result 5′-monophosphate terminated (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start (TSS) were also differential (dRNA-Seq) both datasets...
Pseudomonas aeruginosa, like other pathogens, adapts to the limiting nutritional environment of host by altering patterns gene expression and utilizing alternative pathways required for survival. Understanding genes essential survival in gives insight into that this organism requires during infection has potential identify better ways treat infections. Here, we used a saturated transposon insertion mutant pool P. aeruginosa strain PAO1 sequencing (Tn-Seq), conditionally important under...
Abstract Recent advances in high-throughput experiments and systems biology approaches have resulted hundreds of publications identifying “immune signatures”. Unfortunately, these are often described within text, figures, or tables a format not amenable to computational processing, thus severely hampering our ability fully exploit this information. Here we present data model represent immune signatures, along with the Human Immunology Project Consortium (HIPC) Dashboard (...
Background Sepsis is a dysfunctional host response to infection. The syndrome leads millions of deaths annually (19.7% all in 2017) and the cause most from severe Covid infections. High throughput sequencing or ‘omics’ experiments molecular clinical sepsis research have been widely utilized identify new diagnostics therapies. Transcriptomics, quantifying gene expression, has dominated these studies, due efficiency measuring expression tissues technical accuracy technologies like RNA-Seq....
Understanding of newborn immune ontogeny in the first week life will enable age-appropriate strategies for safeguarding vulnerable newborns against infectious diseases. Here we conducted an observational study exploring immunological profile infants longitudinally throughout their life. Our Expanded Program on Immunization - Human Immunology Project Consortium (EPIC-HIPC) studies epigenetic regulation systemic immunity using small volumes peripheral blood samples collected from West African...
ABSTRACT Background Understanding the RNA processing of an organism's transcriptome is essential but challenging step in understanding its biology. Here we investigate with unprecedented detail Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped cleavage dephosphorylation sites that result 5'-monophosphate terminated using new high-throughput methodology called monophosphate RNA-Seq (pRNA-Seq). Transcriptional start (TSS)...
Abstract Recent advances in high-throughput experiments and systems biology approaches have resulted hundreds of publications identifying “immune signatures”. Unfortunately, these are often described within text, figures, or tables a format not amenable to computational processing, thus severely hampering our ability fully exploit this information. Here we present data model represent immune signatures, along with the Human Immunology Project Consortium (HIPC) Dashboard (...
The Pseudomonas aeruginosa Interaction Database, PaIntDB, is an intuitive web-based tool for network-based systems biology analyses using protein-protein interactions (PPI) in this medically important pathogen. It enables the integration and visualization of omics including RNA-Seq Tn-Seq. High-throughput datasets can be mapped onto PPI networks, which explored visually filtered to uncover novel putative molecular pathways related conditions study. PaIntDB contains most comprehensive...
<p>Antibiotic treatment regularly fails to cure patients suffering from infections caused by adaptively resistant microbial communities, referred as biofilms. Even though at least two thirds of all clinical are associated with biofilms, there no biofilm-specific therapies on the market or in trials. <em>Pseudomonas aeruginosa</em> is a remarkably antibiotic resistant, nosocomial pathogen and biofilm-former that causes morbidity mortality especially...
Biofilms are the most common cause of bacterial infections in humans and notoriously hard to treat due their ability withstand antibiotics host immune defenses. To overcome current lack effective antibiofilm therapies guide future design, identification novel biofilm-specific gene targets is crucial. In this regard, transcriptional regulators have been proposed as promising for antimicrobial drug design. Therefore, a Transposon insertion sequencing approach was employed systematically...