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1.  The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers 
Bioinformatics  2014;31(1):140-142.
Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide.
Availability and implementation: http://mygoblet.org/training-portal
Contact: manuel.corpas@tgac.ac.uk
doi:10.1093/bioinformatics/btu601
PMCID: PMC4271145  PMID: 25189782
2.  Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia 
Briefings in Bioinformatics  2013;14(5):563-574.
The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
doi:10.1093/bib/bbt022
PMCID: PMC3771231  PMID: 23543352
training; next-generation sequencing; NGS; cloud; workshop
3.  Toward interoperable bioscience data 
Nature genetics  2012;44(2):121-126.
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared ‘Investigation-Study-Assay’ framework to support that vision.
doi:10.1038/ng.1054
PMCID: PMC3428019  PMID: 22281772
4.  Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development 
Renfree, Marilyn B | Papenfuss, Anthony T | Deakin, Janine E | Lindsay, James | Heider, Thomas | Belov, Katherine | Rens, Willem | Waters, Paul D | Pharo, Elizabeth A | Shaw, Geoff | Wong, Emily SW | Lefèvre, Christophe M | Nicholas, Kevin R | Kuroki, Yoko | Wakefield, Matthew J | Zenger, Kyall R | Wang, Chenwei | Ferguson-Smith, Malcolm | Nicholas, Frank W | Hickford, Danielle | Yu, Hongshi | Short, Kirsty R | Siddle, Hannah V | Frankenberg, Stephen R | Chew, Keng Yih | Menzies, Brandon R | Stringer, Jessica M | Suzuki, Shunsuke | Hore, Timothy A | Delbridge, Margaret L | Mohammadi, Amir | Schneider, Nanette Y | Hu, Yanqiu | O'Hara, William | Al Nadaf, Shafagh | Wu, Chen | Feng, Zhi-Ping | Cocks, Benjamin G | Wang, Jianghui | Flicek, Paul | Searle, Stephen MJ | Fairley, Susan | Beal, Kathryn | Herrero, Javier | Carone, Dawn M | Suzuki, Yutaka | Sugano, Sumio | Toyoda, Atsushi | Sakaki, Yoshiyuki | Kondo, Shinji | Nishida, Yuichiro | Tatsumoto, Shoji | Mandiou, Ion | Hsu, Arthur | McColl, Kaighin A | Lansdell, Benjamin | Weinstock, George | Kuczek, Elizabeth | McGrath, Annette | Wilson, Peter | Men, Artem | Hazar-Rethinam, Mehlika | Hall, Allison | Davis, John | Wood, David | Williams, Sarah | Sundaravadanam, Yogi | Muzny, Donna M | Jhangiani, Shalini N | Lewis, Lora R | Morgan, Margaret B | Okwuonu, Geoffrey O | Ruiz, San Juana | Santibanez, Jireh | Nazareth, Lynne | Cree, Andrew | Fowler, Gerald | Kovar, Christie L | Dinh, Huyen H | Joshi, Vandita | Jing, Chyn | Lara, Fremiet | Thornton, Rebecca | Chen, Lei | Deng, Jixin | Liu, Yue | Shen, Joshua Y | Song, Xing-Zhi | Edson, Janette | Troon, Carmen | Thomas, Daniel | Stephens, Amber | Yapa, Lankesha | Levchenko, Tanya | Gibbs, Richard A | Cooper, Desmond W | Speed, Terence P | Fujiyama, Asao | M Graves, Jennifer A | O'Neill, Rachel J | Pask, Andrew J | Forrest, Susan M | Worley, Kim C
Genome Biology  2011;12(8):R81.
Background
We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.
Results
The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.
Conclusions
Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
doi:10.1186/gb-2011-12-8-r81
PMCID: PMC3277949  PMID: 21854559
5.  Identification, analysis, and linkage mapping of expressed sequence tags from the Australian sheep blowfly 
BMC Genomics  2011;12:406.
Background
The Australian sheep blowfly Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) is a destructive pest of the sheep, a model organism for insecticide resistance research, and a valuable tool for medical and forensic professionals. However, genomic information on L. cuprina is still sparse.
Results
We report here the construction of an embryonic and 2 larval cDNA libraries for L. cuprina. A total of 29,816 expressed sequence tags (ESTs) were obtained and assembled into 7,464 unique clusters. The sequence collection captures a great diversity of genes, including those related to insecticide resistance (e.g., 12 cytochrome P450s, 2 glutathione S transferases, and 6 esterases). Compared to Drosophila melanogaster, codon preference is different in 13 of the 18 amino acids encoded by redundant codons, reflecting the lower overall GC content in L. cuprina. In addition, we demonstrated that the ESTs could be converted into informative gene markers by capitalizing on the known gene structures in the model organism D. melanogaster. We successfully assigned 41 genes to their respective chromosomes in L. cuprina. The relative locations of these loci revealed high but incomplete chromosomal synteny between L. cuprina and D. melanogaster.
Conclusions
Our results represent the first major transcriptomic undertaking in L. cuprina. These new genetic resources could be useful for the blowfly and insect research community.
doi:10.1186/1471-2164-12-406
PMCID: PMC3176259  PMID: 21827708
6.  A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds 
PLoS ONE  2009;4(3):e4668.
The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.
doi:10.1371/journal.pone.0004668
PMCID: PMC2652362  PMID: 19270757
7.  Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis 
PLoS ONE  2008;3(2):e1607.
Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We determined the genome sequence of L. biflexa, making it the first saprophytic Leptospira to be sequenced. The L. biflexa genome has 3,590 protein-coding genes distributed across three circular replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also carries essential genes, and a third 74-kb replicon. Comparative sequence analysis provides evidence that L. biflexa is an excellent model for the study of Leptospira evolution; we conclude that 2052 genes (61%) represent a progenitor genome that existed before divergence of pathogenic and saprophytic Leptospira species. Comparisons of the L. biflexa genome with two pathogenic Leptospira species reveal several major findings. Nearly one-third of the L. biflexa genes are absent in pathogenic Leptospira. We suggest that once incorporated into the L. biflexa genome, laterally transferred DNA undergoes minimal rearrangement due to physical restrictions imposed by high gene density and limited presence of transposable elements. In contrast, the genomes of pathogenic Leptospira species undergo frequent rearrangements, often involving recombination between insertion sequences. Identification of genes common to the two pathogenic species, L. borgpetersenii and L. interrogans, but absent in L. biflexa, is consistent with a role for these genes in pathogenesis. Differences in environmental sensing capacities of L. biflexa, L. borgpetersenii, and L. interrogans suggest a model which postulates that loss of signal transduction functions in L. borgpetersenii has impaired its survival outside a mammalian host, whereas L. interrogans has retained environmental sensory functions that facilitate disease transmission through water.
doi:10.1371/journal.pone.0001607
PMCID: PMC2229662  PMID: 18270594
8.  Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development 
Renfree, Marilyn B | Papenfuss, Anthony T | Deakin, Janine E | Lindsay, James | Heider, Thomas | Belov, Katherine | Rens, Willem | Waters, Paul D | Pharo, Elizabeth A | Shaw, Geoff | Wong, Emily SW | Lefèvre, Christophe M | Nicholas, Kevin R | Kuroki, Yoko | Wakefield, Matthew J | Zenger, Kyall R | Wang, Chenwei | Ferguson-Smith, Malcolm | Nicholas, Frank W | Hickford, Danielle | Yu, Hongshi | Short, Kirsty R | Siddle, Hannah V | Frankenberg, Stephen R | Chew, Keng Y | Menzies, Brandon R | Stringer, Jessica M | Suzuki, Shunsuke | Hore, Timothy A | Delbridge, Margaret L | Patel, Hardip | Mohammadi, Amir | Schneider, Nanette Y | Hu, Yanqiu | O'Hara, William | Al Nadaf, Shafagh | Wu, Chen | Feng, Zhi-Ping | Cocks, Benjamin G | Wang, Jianghui | Flicek, Paul | Searle, Stephen MJ | Fairley, Susan | Beal, Kathryn | Herrero, Javier | Carone, Dawn M | Suzuki, Yutaka | Sugano, Sumio | Toyoda, Atsushi | Sakaki, Yoshiyuki | Kondo, Shinji | Nishida, Yuichiro | Tatsumoto, Shoji | Mandiou, Ion | Hsu, Arthur | McColl, Kaighin A | Lansdell, Benjamin | Weinstock, George | Kuczek, Elizabeth | McGrath, Annette | Wilson, Peter | Men, Artem | Hazar-Rethinam, Mehlika | Hall, Allison | Davis, John | Wood, David | Williams, Sarah | Sundaravadanam, Yogi | Muzny, Donna M | Jhangiani, Shalini N | Lewis, Lora R | Morgan, Margaret B | Okwuonu, Geoffrey O | Ruiz, San J | Santibanez, Jireh | Nazareth, Lynne | Cree, Andrew | Fowler, Gerald | Kovar, Christie L | Dinh, Huyen H | Joshi, Vandita | Jing, Chyn | Lara, Fremiet | Thornton, Rebecca | Chen, Lei | Deng, Jixin | Liu, Yue | Shen, Joshua Y | Song, Xing-Zhi | Edson, Janette | Troon, Carmen | Thomas, Daniel | Stephens, Amber | Yapa, Lankesha | Levchenko, Tanya | Gibbs, Richard A | Cooper, Desmond W | Speed, Terence P | Fujiyama, Asao | M Graves, Jennifer A | O'Neill, Rachel J | Pask, Andrew J | Forrest, Susan M | Worley, Kim C
Genome Biology  2011;12(12):414.
doi:10.1186/gb-2011-12-12-414
PMCID: PMC3334613

Results 1-8 (8)