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Seemann T.,Monash University | Seemann T.,Life science Computation Center
Bioinformatics | Year: 2014

The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. © 2014 The Author 2014.

Nunez-Iglesias J.,FlyEM Project | Nunez-Iglesias J.,Life science Computation Center | Kennedy R.,FlyEM Project | Kennedy R.,University of Pennsylvania | And 3 more authors.
Frontiers in Neuroinformatics | Year: 2014

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. © 2014 Nunez-Iglesias, Kennedy, Plaza, Chakraborty and Katz.

Yeoh L.M.,University of Melbourne | Goodman C.D.,University of Melbourne | Hall N.E.,La Trobe University | Hall N.E.,Life science Computation Center | And 3 more authors.
Nucleic Acids Research | Year: 2015

Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoured in this phylum. We investigated the mechanism of alternative splicing in Toxoplasma gondii, and have identified and localized TgSR3, a homologue of ASF/SF2 (alternative-splicing factor/splicing factor 2, a serine-arginine-rich, or SR protein) to a subnuclear compartment. In addition, we conditionally overexpressed this protein, which was deleterious to growth. qRT-PCR was used to confirm perturbation of splicing in a known alternatively-spliced gene. We performed high-throughput RNA-seq to determine the extent of splicing modulated by this protein. Current RNA-seq algorithms are poorly suited to compact parasite genomes, and hence we complemented existing tools by writing a new program, GeneGuillotine, that addresses this deficiency by segregating overlapping reads into distinct genes. In order to identify the extent of alternative splicing, we released another program, JunctionJuror, that detects changes in intron junctions. Using this program, we identified about 2000 genes that were constitutively alternatively spliced in T. gondii. Overexpressing the splice regulator TgSR3 perturbed alternative splicing in over 1000 genes. © 2015 The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Spitz G.,Monash University | Spitz G.,Monash Epworth Rehabilitation Research Center | Maller J.J.,Monash University | Maller J.J.,Monash Alfred Psychiatry Research Center | And 6 more authors.
Journal of Neurotrauma | Year: 2013

The development and utilization of newer neuroimaging modalities provides the capability to more accurately detect the extent of pathology after TBI. The current study examined the ability of susceptibility-weighted imaging (SWI) to detect lesions after TBI as well as the relationship to subsequent clinical outcome. The performance of SWI was compared to that of fluid-attenuated inversion recovery (FLAIR). This study comprised 79 individuals with mild-To-severe TBI, 38 of whom completed neuropsychological tests of attention, working memory, processing speed, memory, and executive functions. SWI was found to quantify a greater lesion volume over the entire brain, specifically in frontal, central, limbic, subcortical gray, and parietal brain regions, than did FLAIR. Moreover, SWI was able to identify TBI-related lesions in almost one third of patients for whom FLAIR was unable to detect any lesions. Greater overall SWI volume, as well as frontal SWI volume, was found to relate to the severity of TBI. Conversely, no association was found between FLAIR lesion volume and injury severity. In addition, there was some evidence that higher lesion volume, for both SWI and FLAIR, were associated with poorer memory as well as processing speed impairment. This study suggests that SWI may provide additional sensitivity in the detection of lesions after TBI. Consequently, this imaging sequence may provide a more accurate representation of the severity of individuals' injuries and their subsequent neuropsychological outcomes. © Copyright 2013, Mary Ann Liebert, Inc. 2013.

Wong N.C.,Murdoch Childrens Research Institute | Wong N.C.,Ludwig Institute for Cancer Research | Ng J.,Murdoch Childrens Research Institute | Hall N.E.,La Trobe University | And 7 more authors.
Genomics | Year: 2013

Illumina Infinium Human Methylation (HM) BeadChips are widely used for measuring genome-scale DNA methylation, particularly in relation to epigenome-wide association studies (EWAS) studies. The methylation profile of human samples can be assessed accurately and reproducibly using the HM27 BeadChip (27,578 CpG sites) or its successor, the HM450 BeadChip (482,421 CpG sites). To date no mouse equivalent has been developed, greatly hindering the application of this methodology to the wide range of valuable murine models of disease and development currently in existence. We found 1308 and 13,715 probes from HM27 and HM450 BeadChip respectively, uniquely matched the bisulfite converted reference mouse genome (mm9). We demonstrate reproducible measurements of DNA methylation at these probes in a range of mouse tissue samples and in a murine cell line model of acute myeloid leukaemia. In the absence of a mouse counterpart, the Infinium Human Methylation BeadChip arrays have utility for methylation profiling in non-human species. © 2013 Elsevier Inc.

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