Harriet Dashnow

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Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types(More)
1 Bioinformatics, Murdoch Childrens Research Institute, Parkville, Victoria, Australia, 2 Life Science Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria, Australia, 3 The University of Melbourne, Parkville, Victoria, Australia, 4 The Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany,(More)
The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne(More)
The mutation R403stop was found in an individual with mut(0) methylmalonic aciduria (MMA) which resulted from a single base change of C→T in exon 6 of the methylmalonyl-CoA mutase gene (producing a TGA stop codon). In order to accurately model the human MMA disorder we introduced this mutation onto the human methylmalonyl-CoA mutase locus of a bacterial(More)
1 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria, Australia, 2 Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, 3 School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia, 4 School of BioSciences,(More)
'Big data' analytics can be defined by the requirement for flexible, high throughput computational analysis methods applied to large, heterogeneous datasets. We propose an architectural approach to 'big data' challenges in which the movement of data is minimized, and analysis methods are implemented on the data as portable services. We term this approach(More)
Background Microsatellites are short (2-6bp) DNA sequences repeated in tandem, which make up approximately 3% of the human genome [1]. These loci are prone to frequent mutations and high polymorphism with the estimated mutation rates of 10 10 events per locus per generation, orders of magnitude higher than other parts of the genome [2]. Dozens of(More)
The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne(More)
Rapid identification of clinically significant variants is key to the successful application of next generation sequencing technologies in clinical practice. The Melbourne Genomics Health Alliance (MGHA) variant prioritization framework employs a gene prioritization index based on clinician-generated a priori gene lists, and a variant prioritization index(More)
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