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  • Oxford University Press  (2)
  • Copernicus Publications (EGU)  (1)
  • 1
    Publication Date: 2013-01-17
    Description: Motivation: Systems Genetics approaches, in particular those relying on genetical genomics data, put forward a new paradigm of large-scale genome and network analysis. These methods use naturally occurring multi-factorial perturbations (e.g. polymorphisms) in properly controlled and screened genetic crosses to elucidate causal relationships in biological networks. However, although genetical genomics data contain rich information, a clear dissection of causes and effects as required for reconstructing gene regulatory networks is not easily possible. Results: We present a framework for reconstructing gene regulatory networks from genetical genomics data where genotype and phenotype correlation measures are used to derive an initial graph which is subsequently reduced by pruning strategies to minimize false positive predictions. Applied to realistic simulated genetic data from a recent DREAM challenge, we demonstrate that our approach is simple yet effective and outperforms more complex methods (including the best performer) with respect to (i) reconstruction quality (especially for small sample sizes) and (ii) applicability to large data sets due to relatively low computational costs. We also present reconstruction results from real genetical genomics data of yeast. Availability: A MATLAB implementation (script) of the reconstruction framework is available at www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html Contact: klamt@mpi-magdeburg.mpg.de
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2012-11-21
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
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    Copernicus Publications (EGU)
    In:  Annales of Geophysicae, 33 . pp. 55-61.
    Publication Date: 2017-04-13
    Description: Slant-integrated water vapor (SIWV) data derived from GPS STDs (slant total delays), which provide the spatial information on tropospheric water vapor, have a high potential for assimilation to weather models or for nowcasting or reconstruction of the 3-D humidity field with tomographic techniques. Therefore, the accuracy of GPS STD is important, and independent observations are needed to estimate the quality of GPS STD. In 2012 the GFZ (German Research Centre for Geosciences) started to operate a microwave radiometer in the vicinity of the Potsdam GPS station. The water vapor content along the line of sight between a ground station and a GPS satellite can be derived from GPS data and directly measured by a water vapor radiometer (WVR) at the same time. In this study we present the validation results of SIWV observed by a ground-based GPS receiver and a WVR. The validation covers 184 days of data with dry and wet humidity conditions. SIWV data from GPS and WVR generally show good agreement with a mean bias of −0.4 kg m−2 and an rms (root mean square) of 3.15 kg m−2. The differences in SIWV show an elevation dependent on an rms of 7.13 kg m−2 below 15° but of 1.76 kg m−2 above 15°. Nevertheless, this elevation dependence is not observed regarding relative deviations. The relation between the differences and possible influencing factors (elevation angles, pressure, temperature and relative humidity) are analyzed in this study. Besides the elevation, dependencies between the atmospheric humidity conditions, temperature and the differences in SIWV are found.
    Type: Article , PeerReviewed
    Format: text
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