Today we say farewell to Arjun Sharma & Suman Virdee. Arjun joined the lab as a second year volunteer, staying to perform a Biochem 3R06 research project. He has been very active in our Comprehensive Antibiotic Resistance Database project, co-developing our CARD*Shark text mining tools for computer-guided curation of literature in PubMed, pipelines for our clinical isolate genome sequencing work, and developing novel algorithms for predicting glycopeptide resistance from genome assemblies. He was the recipient of an IIDR Summer Student Fellowship and leaves the Biochemistry program to enter medical school at the University of Toronto. Suman joined the lab in the 4th year of the Biomedical Discovery & Commercialization program, performing her thesis research on RNA-Seq bioinformatics workflows in a collaboration between our lab and the laboratory of Dr. Kristen Hope (McMaster Stem Cell and Cancer Research Institute), extending her research into the summer by winning a CIHR Summer Undergraduate Research Award. Suman finished her degree and this September starts in the McMaster Master of Science in Global Health program. Bon chance Suman & Arjun!
Suman Virdee – Developing a Galaxy based Pipeline for RNA-Seq Analysis in Stem Cell Biology
Kirill Pankov – The Cytochrome P450 (CYP) Superfamily in the Cnidarian Phylum
Jonsson Liu – Clinical virulence detection and Clostridium difficile clonality
Annie Cheng – Predicting Plasmid-Mediated Antimicrobial Resistance from Whole Genome Sequencing
Godwin Chan – Using the Galaxy Platform to Increase Accessibility for Structure Determination via Cryo-Electron Microscopy
Congratulations to 4th Year Biomedical Discovery & Commercialization student and McArthur lab member Suman Virdee for her CIHR Undergraduate Summer Studentship Award for her summer project “Development and implementation of computational tools to dissect cancer stem cell circuitry”, a joint project between our laboratory and that of Dr. Kristin Hope!
Congratulations to Kara Tsang and Zachary Lin on completion of their Biomedical Discovery and Commercialization (BDC) 4A15 thesis research! Both Kara & Zachary presented their research results at the 2016 BDC Engage Symposium.
Zachary Lin: Adapting Galaxy bioinformatics to outbreak- associated Clostridium difficile
Kara Tsang: The translation of biocuration to metagenomic analysis for combatting multi-drug resistant Pseudomonas aeruginosa
The completion of the human genome project in 2001 sparked the beginning of a sequencing revolution with applications that are only now being realized by researchers. The decreasing cost of DNA sequencing has ignited a continuous generation of genomic data with a limited number of researchers able to manipulate the output. Consequentially the demand to examine this genetic information has forced bioinformaticians to improve the analytical tools involved in sequence analysis. Galaxy is a user-friendly analytical platform where researchers without a computational background can navigate their way through an investigation and use various analytical tools and workflows to assist them with their genomic research (1). Galaxy enables the addition of novel software into the environment by individual users to fill in the gaps of tools that haven’t been created by the Galaxy team. This project will focus on a particular analytical gap concerning tools related to antibiotic resistance, phylogenetics, and bacterial virulence. Currently, the proposed software to be adapted to the galaxy setting includes a resistance gene identifier (RGI) associated with the comprehensive antibiotic resistance database (CARD) (2), a single nucleotide polymorphism identifier (BANSP) , and novel virulence factor identification software associated with the virulence factor database (VFDB) (3). The combination of Galaxy’s existing ToolShed and these unique additions will create a comprehensive analytical environment that can be applied to realistic situations. One such situation that this project will concentrate on refers specifically to the outbreaks of Clostridium difficile (C. diff) in the health care system.
The loss of effective antimicrobials is reducing the ability to protect the global population from infectious diseases, leading to profound impacts on the healthcare system, international trade, agriculture, and environment. The field of antibiotic drug discovery and the monitoring of the dynamic and new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. The curation and directed development of the Comprehensive Antibiotic Database (CARD) will advance the understanding of the genetics, genomics, and threat severity of antibiotic resistance, while simultaneously improving its ability to accurately predict and screen for antibiotic resistance genes within raw genomes. Strategically advancing the Antibiotic Resistance Ontology (ARO), the unique organizing principle of the CARD, allows the value of big data in disparate realms of research to be used and understood by the multidisciplinary efforts working to combat the emergence and prevalence of the ESKAPE pathogens, a critical driving force of the global health crisis.