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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(More)
Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As(More)
The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other(More)
There is an ever-expanding range of technologies that generate very large numbers of biomarkers for research and clinical applications. Choosing the most informative biomarkers from a high-dimensional data set, combined with identifying the most reliable and accurate classification algorithms to use with that biomarker set, can be a daunting task. Existing(More)
The rapidly diminishing cost of genome sequencing is driving renewed interest in large scale genome sequencing programs such as <i>Genome 10K</i> (G10K). Despite renewed interest the assembly of large genomes from short reads is still an extremely resource intensive process. This work presents a scalable algorithms to create scaffolds, or ordered and(More)
Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger(More)
Power's central role in international relations theory is unsurpassed, yet considerable debate persists over the quality of its most commonly used indicator, the Correlates of War project's Composite Indicator of National Capabilities (CINC). At issue is whether CINC's main feature, its ability to measure a nation's power relative to other nations' power(More)
INTRODUCTION Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects.(More)
RNA-Seq is a cost-efficient high-coverage powerful technology for transcrip-tome analysis. We propose a novel algorithm for transcriptome quantification from RNA-seq data (SimReg) which uses regression to find transcript frequencies for which the simulated read counts match the observed read counts. SimReg first aligns the reads to existing transcript(More)