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  • Belief, L84 - Personal, Professional, and Business Services, O33 - Technological Change: Choices and Consequences  (1)
  • Repair  (1)
  • Oxford University Press  (2)
  • 1
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    PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-11
    Description: Correctly estimating isoform-specific gene expression is important for understanding complicated biological mechanisms and for mapping disease susceptibility genes. However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not appropriately corrected, can affect isoform expression estimation and downstream analysis. In this article, we present PennSeq, a statistical method that allows each isoform to have its own non-uniform read distribution. Instead of making parametric assumptions, we give adequate weight to the underlying data by the use of a non-parametric approach. Our rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. We evaluate the performance of PennSeq using both simulated data with known ground truth, and using two real Illumina RNA-Seq data sets including one with quantitative real time polymerase chain reaction measurements. Our results indicate superior performance of PennSeq over existing methods, particularly for isoforms demonstrating severe non-uniformity. PennSeq is freely available for download at http://sourceforge.net/projects/pennseq .
    Keywords: Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Global temporary networks of clusters: structures and dynamics of trade fairs in Asian economies (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-10
    Description: Acting as temporary clusters, trade fairs can turn into trans-local learning spaces in global industrial communities. However, up to now, how temporary gatherings are related to regional/national economies has not yet been systematically investigated. This article approaches the question with an international comparative study of trade fairs in Asian economies. Generally, consistent with a dynamic interpretation of temporary clusters, trade fairs exhibit a more diverse configuration of participants, being a setting more compatible for knowledge creation, in more developed Asian economies. However, structures of trade fairs are also influenced by organizational features of embedded economies. Further, seven flagship electronics fairs suggest an architecture of global temporary networks of clusters for high-end learning processes in the global knowledge economy.
    Keywords: D83 - Search ; Learning ; Information and Knowledge ; Communication ; Belief, L84 - Personal, Professional, and Business Services, O33 - Technological Change: Choices and Consequences ; Diffusion Processes, O53 - Asia including Middle East, R11 - Regional Economic Activity: Growth, Development, and Changes
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
    Published by Oxford University Press
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