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  • Articles  (54)
  • Latest Papers from Table of Contents or Articles in Press  (54)
  • Articles: DFG German National Licenses
  • American Geophysical Union  (23)
  • Oxford University Press  (20)
  • Geological Society of America  (10)
  • Arctic Institute of North America
  • Blackwell Publishing Ltd
  • International Union of Crystallography (IUCr)
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  • Mathematics  (5)
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  • Articles  (54)
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  • Latest Papers from Table of Contents or Articles in Press  (54)
  • Articles: DFG German National Licenses
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  • 1
    Publication Date: 2016-07-16
    Description: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 2
    Publication Date: 2013-09-26
    Description: We consider the expressive power of the first-order structure 〈, C 〉 where is either of two of different domains of extended regions in Euclidean space, and C(x,y) is the topological relation ‘Region x is in contact with region y .’ We prove two main theorems: Let $$\mathcal{P}$$ [Q] be the domain of bounded, non-empty, rational polyhedra in two- or three-dimensional Euclidean space. A relation over $$\mathcal{P}$$ [Q] is definable in the structure 〈 $$\mathcal{P}$$ [Q], C 〉 if and only if is arithmetic and invariant under rational PL-homeomorphisms of the space to itself. We also extend this result to a number of other domains, including the domain of all polyhedra and the domain of semi-algebraic regions. Let $$\mathcal{R}$$ be the space of bounded, non-empty, closed regular regions in n -dimensional Euclidean space. Any analytical relation over lower dimensional (i.e. empty interior) compact point sets that is invariant under homeomorphism is implicitly definable in the structure 〈 $$\mathcal{R}$$ , C 〉.
    Print ISSN: 0955-792X
    Electronic ISSN: 1465-363X
    Topics: Computer Science , Mathematics
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  • 3
    Publication Date: 2016-08-25
    Description: SKS arrivals from ocean bottom seismometer (OBS) data from an offshore southern California deployment are analysed for shear wave splitting. The project involved 34 OBSs deployed for 12 months in a region extending up to 500 km west of the coastline into the oceanic Pacific plate. The measurement process consisted of removing the effects of anisotropy using a range of values for splitting fast directions and delay times to minimize energy along the transverse seismometer axis. Computed splitting parameters are unexpectedly similar to onland parameters, exhibiting WSW–ENE fast polarization directions and delays between 0.8 and 1.8 s, even for oceanic plate sites. This is the first SKS splitting study to extend across the entire boundary between the North America and Pacific plates, into the oceanic part of the Pacific plate. The splitting results show that the fast direction of anisotropy on the Pacific plate does not align with absolute plate motion (APM), and they extend the trend of anisotropy in southern California an additional 500 km west, well onto the oceanic Pacific plate. We model the finite strain and anisotropy within the asthenosphere associated with density–buoyancy driven mantle flow and the effects of APM. In the absence of plate motion effects, such buoyancy driven mantle flow would be NE-directed beneath the Pacific plate observations. The best-fit patterns of mantle flow are inferred from the tomography-based models that show primary influences from foundering higher-density zones associated with the history of subduction beneath North America. The new offshore SKS measurements, when combined with measurements onshore within the plate boundary zone, indicate that dramatic lateral variations in density-driven upper-mantle flow are required from offshore California into the plate boundary zone in California and western Basin and Range.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
    Publication Date: 2013-01-18
    Description: A boundary-element method for Stokes flow is implemented to determine the drag force exerted on spherical, spheroidal, and cylindrical particles in periodic axisymmetric flow through a cylindrical tube. The pressure drop due to the motion of the particles in an otherwise quiescent fluid or due to the presence of the particles in Poiseuille flow is calculated in terms of the particle surface traction using an integral formulation. The computed drag and pressure coefficients are used to evaluate the hematocrit ratio of freely suspended particles, defined as the ratio of the mean velocity of the one-dimensional suspension to the particle velocity, and the apparent suspension viscosity. Numerical results are presented for an extended range of particle sizes and separations, and critical comparisons are made with available numerical and asymptotic solutions. In the case of freely suspended spherical particles, accurate correlations are presented for the hematocrit ratio and apparent intrinsic viscosity. The numerical results for cylindrical particles are consistent with analytical expressions based on the assumption of locally unidirectional flow. The results are discussed with reference to the numerical simulation of the flow of a suspension through a small capillary tube where the particle separation varies slowly along the tube axis.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
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  • 5
    Publication Date: 2016-01-23
    Description: The action dimension of a discrete group $\Gamma $ is the smallest dimension of a contractible manifold that admits a proper action of $\Gamma $ . Associated to any flag complex $L$ there is a right-angled Artin group, $A_L$ . We compute the action dimension of $A_L$ for many $L$ . Our calculations come close to confirming the conjecture that if an $\ell ^2$ -Betti number of $A_L$ in degree $l$ is nonzero, then the action dimension of $A_L$ is $\geqslant 2l$ .
    Print ISSN: 0024-6093
    Electronic ISSN: 1469-2120
    Topics: Mathematics
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  • 6
    Publication Date: 2016-03-14
    Description: For more than two decades, the number of data and model parameters in seismic tomography problems has exceeded the available computational resources required for application of direct computational methods, leaving iterative solvers the only option. One disadvantage of the iterative techniques is that the inverse of the matrix that defines the system is not explicitly formed, and as a consequence, the model resolution and covariance matrices cannot be computed. Despite the significant effort in finding computationally affordable approximations of these matrices, challenges remain, and methods such as the checkerboard resolution tests continue to be used. Based upon recent developments in sparse algorithms and high-performance computing resources, we show that direct methods are becoming feasible for large seismic tomography problems. We demonstrate the application of QR factorization in solving the regional P -wave structure and computing the full resolution matrix with 267 520 model parameters.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
    Publication Date: 2013-07-05
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
    Publication Date: 2013-05-17
    Description: We prove that the class of rational polyhedra and the class of topologically regular regions definable in an o-minimal structure over the reals are each elementarily equivalent to the class of polyhedra for topological languages.
    Print ISSN: 0955-792X
    Electronic ISSN: 1465-363X
    Topics: Computer Science , Mathematics
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  • 9
    Publication Date: 2013-11-22
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 10
    Publication Date: 2016-12-20
    Description: Motivation: Analyzing genome wide association data in the context of biological pathways helps us understand how genetic variation influences phenotype and increases power to find associations. However, the utility of pathway-based analysis tools is hampered by undercuration and reliance on a distribution of signal across all of the genes in a pathway. Methods that combine genome wide association results with genetic networks to infer the key phenotype-modulating subnetworks combat these issues, but have primarily been limited to network definitions with yes/no labels for gene-gene interactions. A recent method (EW_dmGWAS) incorporates a biological network with weighted edge probability by requiring a secondary phenotype-specific expression dataset. In this article, we combine an algorithm for weighted-edge module searching and a probabilistic interaction network in order to develop a method, STAMS, for recovering modules of genes with strong associations to the phenotype and probable biologic coherence. Our method builds on EW_dmGWAS but does not require a secondary expression dataset and performs better in six test cases. Results: We show that our algorithm improves over EW_dmGWAS and standard gene-based analysis by measuring precision and recall of each method on separately identified associations. In the Wellcome Trust Rheumatoid Arthritis study, STAMS-identified modules were more enriched for separately identified associations than EW_dmGWAS (STAMS P -value 3.0 x 10 –4 ; EW_dmGWAS- P -value = 0.8). We demonstrate that the area under the Precision-Recall curve is 5.9 times higher with STAMS than EW_dmGWAS run on the Wellcome Trust Type 1 Diabetes data. Availability and Implementation: STAMS is implemented as an R package and is freely available at https://simtk.org/projects/stams . Contact: rbaltman@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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