Congratulations to this year’s crop of BiomedDC 4A15 thesis students for 8 month research projects well done! From left to right:

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

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coverMcArthur AG & Tsang KK.

Ann N Y Acad Sci. 2017 Jan;1388(1):78-91.

The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings. To do so, efforts must be focused toward exploiting the advancements of genome sequencing and information technology. Currently, AMR bioinformatics software and databases reflect different scopes and functions, each with its own strengths and weaknesses. A review of the available tools reveals common approaches and reference data but also reveals gaps in our curated data, models, algorithms, and data-sharing tools that must be addressed to conquer the limitations and areas of unmet need within the AMR research field before DNA sequencing can be fully exploited for AMR surveillance and improved clinical outcomes.

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I spent July travelling to two great meetings in the British Isles. First was the Galaxy Community Conference in Norwich, UK which provided a crash course on the Galaxy Platform for data analysis – data intensive biology for everyone! We will definitely be using Galaxy for projects in 2015-2016. Second was the 2015 Annual Conference on Intelligent Systems for Molecular Biology / European Conference on Computational Biology joint meeting in Dublin, Ireland. This meeting covers a very broad spectrum of computational biology and our work on the CARD was well received. I also got a change to attend the Bio-Ontologies SIG for the first time, which provided a lot of perspective for our ontology development efforts. And yes, I had a few pints with colleagues…

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  • McArthur, A.G. 2015. Flash Update – The Antibiotic Resistance Ontology. Presentation at Bio-Ontologies 2015, Dublin, Ireland.
  • McArthur, A.G., Waglechner, N., Nizam, F., Pereira, S.K., Jia, B., Sardar, D., Westman, E.L., Pawlowski, A.C., Johnson, T., Lo, R., Courtot, M., Brinkman, F.S., Williams, L.E., Frye, J.G., & Wright, G.D. 2015. The Comprehensive Antibiotic Resistance Database. Poster Presentation at the 23rd Annual International Conference on Intelligent Systems for Molecular Biology, Dublin, Ireland.
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